- G - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- GAP - Static variable in interface org.forester.sequence.Sequence
-
- GAP_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- GAP_STR - Static variable in interface org.forester.sequence.Sequence
-
- GapArray - Class in org.biojava.nbio.structure.align.helper
-
- GapArray() - Constructor for class org.biojava.nbio.structure.align.helper.GapArray
-
- gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- gapPenalty - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- GapPenalty - Interface in org.biojava.nbio.alignment.template
-
Defines a data structure for the gap penalties used during a sequence alignment routine.
- GapPenalty.Type - Enum in org.biojava.nbio.alignment.template
-
Defines the possible types of gap penalties.
- GCStats - Class in org.biojava.nbio.genome.parsers.gff
-
- GCStats() - Constructor for class org.biojava.nbio.genome.parsers.gff.GCStats
-
- GENBANK_FORMAT - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
The name of this format
- GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
-
- GenbankProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
-
- GenbankProxySequenceReader(String, String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- GenbankReader<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the
primary class used to read Genbank files
- GenbankReader(InputStream, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
-
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
- GenbankReader(File, SequenceHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReader
-
If you are going to use the FileProxyProteinSequenceCreator then you
need to use this constructor because we need details about
the location of the file.
- GenbankReaderHelper - Class in org.biojava.nbio.core.sequence.io
-
- GenbankReaderHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankReaderHelper
-
- GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenbankSequenceParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- genbankSplitPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser
-
Decodes a split pattern.
- GenbankWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
-
Use default line length of 60
- GenbankWriter(OutputStream, Collection<S>, GenbankHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriter
-
Set custom lineLength
- GenbankWriterHelper - Class in org.biojava.nbio.core.sequence.io
-
The class that should be used to write out genbank file of a sequence
collection
- GenbankWriterHelper() - Constructor for class org.biojava.nbio.core.sequence.io.GenbankWriterHelper
-
- GENE_NAME - Static variable in class org.forester.io.parsers.nhx.NHXtags
-
- GENE_NAME_SYNONYM - Static variable in class org.forester.io.parsers.nhx.NHXtags
-
- gene_tree_preprocess - Class in org.forester.application
-
- gene_tree_preprocess() - Constructor for class org.forester.application.gene_tree_preprocess
-
- GeneChromosomePosition - Class in org.biojava.nbio.genome.parsers.genename
-
- GeneChromosomePosition() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- GeneChromosomePositionParser - Class in org.biojava.nbio.genome.parsers.genename
-
A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
- GeneChromosomePositionParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
-
- GeneFeatureHelper - Class in org.biojava.nbio.genome
-
- GeneFeatureHelper() - Constructor for class org.biojava.nbio.genome.GeneFeatureHelper
-
- GeneIDGFF2Reader - Class in org.biojava.nbio.genome.parsers.gff
-
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
- GeneIDGFF2Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
-
- GeneIDXMLReader - Class in org.biojava.nbio.genome.parsers.geneid
-
- GeneIDXMLReader(String) - Constructor for class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
-
- GeneMarkGTFReader - Class in org.biojava.nbio.genome.parsers.gff
-
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
- GeneMarkGTFReader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
-
- GeneName - Class in org.biojava.nbio.genome.parsers.genename
-
A simple bean that contains gene name information as available from www.genenames.org
- GeneName() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneName
-
- GeneNamesParser - Class in org.biojava.nbio.genome.parsers.genename
-
Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
- GeneNamesParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
-
- GeneralMsaParser - Class in org.forester.io.parsers
-
- GeneralMsaParser() - Constructor for class org.forester.io.parsers.GeneralMsaParser
-
- GeneralTable<IDENTIFIER_TYPE,VALUE_TYPE> - Class in org.forester.util
-
- GeneralTable() - Constructor for class org.forester.util.GeneralTable
-
- generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns what the value of a compound is in the backing bit storage i.e.
- generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
Returns a Map which encodes the contents of CompoundSet.
- generateCompoundsToIndex() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
-
Returns a Map which encodes TCAG into positions 0,1,2,3.
- generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
- generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker
-
Returns a List which reverse encodes the Compound, Integer map
- generateIndexToCompounds() - Method in class org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
-
Returns a List which encodes TCAG into positions 0,1,2,3.
- GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
We store the original header if the sequence is parsed from a fasta file and will use that exact
sequence if we write out the sequences to a fasta file.
- GenericFastaHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
-
- GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
The default fasta header parser where some headers are well defined based on the source
database which allows us to set the source of the protein sequence and the identifier
that can be used in future implementations to load features from external sources
If the user has a custom header with local data then they can create their own implementation
of a FastaHeaderParserInterface
- GenericFastaHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser
-
- GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenericGenbankHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
-
- GenericGenbankHeaderFormat(String) - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
-
- GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenericGenbankHeaderParser() - Constructor for class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
-
- GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.io
-
- GenericInsdcHeaderFormat() - Constructor for class org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat
-
- GeneSequence - Class in org.biojava.nbio.core.sequence
-
- GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.GeneSequence
-
A class that keeps track of the details of a GeneSequence which is difficult to properly model.
- GenomeWideCombinableDomains - Interface in org.forester.surfacing
-
- GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder - Enum in org.forester.surfacing
-
- get(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Returns the window specified at the given index in offsets i.e.
- get(Object) - Method in class org.biojava.nbio.core.util.SoftHashMap
-
- get(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap
-
- get(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap
-
- get(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
-
- get(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Gets the interface corresponding to given id.
- get(K) - Method in class org.biojava.nbio.structure.domain.SerializableCache
-
- get(Object) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- get(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a single element.
- get(int, int) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix
-
access a value at i,j
- get(int) - Method in class org.biojava.nbio.structure.math.SparseVector
-
get a value
- get(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable
-
Return the value paired with given key; null if key is not in table.
- get(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
-
- get(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
-
- get(DomainId) - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- get(DomainId) - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
- get1LetterCode(String) - Static method in class org.biojava.nbio.structure.StructureTools
-
Convert a three letter code into single character.
- GET_ASSEMBLY - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- GET_ASSEMBLY_GENS - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- GET_STRUCT_OPER - Static variable in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getA() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getAA3Hash() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getAAComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the composition of the 20 standard amino acid in the sequence.
- getAAComposition(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
- getAAComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getAACompositionChar(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
- getAACompositionString(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of the 20 standard amino acid in the sequence.
- getAAIndexProvider() - Static method in class org.biojava.nbio.alignment.aaindex.AAindexFactory
-
- getAboutMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getAbsolutePercentialRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getAbsolutePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentileClashscore property.
- getAbsolutePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getAbsolutePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentilePercentRamaOutliers property.
- getAbsolutePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentilePercentRotaOutliers property.
- getAbsolutePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the absolutePercentilePercentRSRZOutliers property.
- getAbsorbance(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the absorbance (optical density) of sequence.
- getAbsorbance(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to returns the absorbance (optical density) of sequence.
- getAbsorbance(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getAbsorpt_coefficient_mu() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_T_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_T_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_process_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getAbstractRenderer(int, int) - Method in class org.forester.development.MsaRenderer
-
- getAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getAccept1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getAccept2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getAcceptedAtomNames() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
by default the parser will read in all atoms (unless using the CAonly switch).
- getAccession() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getAccession() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Unsupoorted
- getAccession() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getAccession() - Method in interface org.biojava.nbio.core.sequence.template.Accessioned
-
Returns the AccessionID this location is currently bound with
- getAccession() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getAccession() - Method in class org.forester.phylogeny.data.Sequence
-
- getAccession() - Method in class org.forester.protein.BasicProtein
-
- getAccession() - Method in interface org.forester.protein.Protein
-
- getAccession() - Method in class org.forester.ws.seqdb.EbiDbEntry
-
- getAccession() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry
-
- getAccession() - Method in class org.forester.ws.seqdb.UniProtEntry
-
- getAccession() - Method in class org.forester.ws.uniprot.EbiDbEntry
-
- getAccession() - Method in interface org.forester.ws.uniprot.SequenceDatabaseEntry
-
- getAccession() - Method in class org.forester.ws.uniprot.UniProtEntry
-
- getAccessionNr() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getAccessionNumber() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getAccessions() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Pull uniprot accessions associated with this sequence
- getAccessions() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein accessions mapped from the Fasta file.
- getAccessions() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
-
- getAcentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the acentricOutliers property.
- getAdapter() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- getAddress() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- getAdjustedMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
-
- getAfpAftIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpBefIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChain() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- getAFPChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getAfpChain() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- getAFPChainFromServer(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getAFPChainFromServer(String, String, String, String, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getAfpChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainTwiBin() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainTwiList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpChainTwiNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getAfpDisCut0() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getAfpIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAfpSet() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the set of AFPs for this alignment.
- getAlgebraicFromMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getAlgorithm() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlgorithmName() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Get the name of the Algorithm
- getAligMap() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- getAligMat() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getAligMat(int, int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getAligMat() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getAlign(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
Extract the alignment output
- getAlign(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getAlign_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getAlignedAtoms1(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getAlignedAtoms2(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getAlignedCalphaAtoms() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getAlignedSequence(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getAlignedSequence(S) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getAlignedSequence(int) - Method in interface org.biojava.nbio.alignment.template.Profile
-
- getAlignedSequence(S) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Searches for the given
Sequence within this alignment profile.
- getAlignedSequence(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Uses bioIndex starting at 1 instead of 0
- getAlignedSequence(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
- getAlignedSequences() - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getAlignedSequences(int...) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getAlignedSequences(S...) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getAlignedSequences() - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns a
List containing the individual
AlignedSequences of this alignment.
- getAlignedSequences(int...) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns a
List containing some of the individual
AlignedSequences of this alignment.
- getAlignedSequences(S...) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns a
List containing some of the individual
AlignedSequences of this alignment.
- getAlignedSequences() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the list of sequences
- getAlignedSequences() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
Returns a
List containing the individual
Sequences of this alignment.
- getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Get an artifical Structure containing both chains.
- getAlignedStructure(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
create an artifical Structure object that contains the two
structures superimposed onto each other.
- getAlignedUserCollection(String) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
-
Takes a protein sequence string with capital and lowercase letters and sets its
user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).
- getAlignment() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- getAlignment1() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getAlignment2() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getAlignmentAtoms(Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Returns the atoms that are being used for the alignment.
- getAlignmentFractionThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getAlignmentIndexAt(int) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getAlignmentIndexAt(int) - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
Returns the column index within an alignment corresponding to the given index in the original
Sequence.
- getAlignmentLengthFraction() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- getAlignmentMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getAlignmentNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getAlignmentOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Gets the value of specified parameter or null if it is not set.
- getAlignmentOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
-
Method that returns the value associated with the key given in parameter.
- getAlignmentOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Gets parameters, which are currently set
- getAlignmentOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
-
Method to get all keys to the information stored in this object.
- getAlignmentOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getAlignmentPairsFromServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
talk to centralized server and fetch all alignments to run.
- getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Extracts the actual Blast report for given request id according to options provided in outputProperties
argument.
- getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
-
Getting the actual alignment results from this instantiated service for a given ID with specific
formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
- getAlignments() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getAlignments() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
return the alternative alignments that can be found for the two structures
- getAlignmentString() - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
-
- getAlignmentTextMenu(JFrame, ActionListener, AFPChain) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
Create the menu for the "Text Only" representation of alignments
- getAlignPairs() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
The file that contains a list of PDB pairs to be aligned
- getAlignPos(int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
-
record the aligned pairs in alignList[][0], alignList[][1];
return the number of aligned pairs
- getAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlignScoreUpdate() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAligSeq(Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
returns the AligSeq (0 or 1) for a point
returns -1 if not over an alig seq.
- getAliLenth() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getAll() - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives
-
Returns the current list of all PDB IDs.
- getAllAlgorithmNames() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
- getAllAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
- getAllAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Convert all atoms of the structure (first model) into an Atom array
- getAllAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all atoms of the chain (first model), including
Hydrogens (if present) and all HETATOMs.
- getAllBinaryDomainCombinations() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
Does not return binary combinations which contain one or two domains
to be ignored -- if ignoring is allowed.
- getAllColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of column names including those that may be hidden
- getAllCombinableDomainsIds() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- getAllCombinableDomainsIds() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
- getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getAllCompounds() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getAllCompounds() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getAllCompounds() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getAllCompounds() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
- getAllCytobands(URL) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
-
- getAllCytobands(InputStream) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
-
- getAllDescendants(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- getAllDescendants() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getAllDomainIds() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- getAllDomainIds() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
This should return all domains ids present in the genome.
- getAllDomainIds(List<GenomeWideCombinableDomains>) - Static method in class org.forester.surfacing.SurfacingUtil
-
- getAllDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getAllDomains() - Method in interface org.forester.surfacing.CombinableDomains
-
This must return all domains in this set of combinable domains (i.e.
- getAllDomains() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
Does not return domains which are to be
ignored -- if ignoring is allowed.
- getAllExternalDescendants() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns a List containing references to all external children of this
PhylogenyNode.
- getAllExternalDescendantsNames() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns a List containing references to all names of the external
children of this PhylogenyNode.
- getAllExternalNodeNames() - Method in class org.forester.phylogeny.Phylogeny
-
- getAllFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
- getAllNonHAtomArray(Structure, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all non-Hydrogen atoms in the given Structure,
optionally including HET atoms or not.
- getAllNonHAtomArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns and array of all non-Hydrogen atoms in the given Chain,
optionally including HET atoms or not
Waters are not included.
- getAllowsChildren() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getAllOxidationStates() - Method in enum org.biojava.nbio.structure.Element
-
Returns a list of all oxidation states the element is found in.
- getAllPairsAlignments(List<S>, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a sequence alignment for all
Sequence pairs in the given
List.
- getAllPairsScorers(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which sets up a sequence pair scorer for all
Sequence pairs in the given
List.
- getAllPairsScores(List<S>, Alignments.PairwiseSequenceScorerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a sequence pair score for all
Sequence pairs in the given
List.
- getAllPairsScores() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns a sequence pair score for all
Sequence pairs in the given
List.
- getAllPDBIDs() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
Returns a list of all PDB IDs that are available in this installation
- getAllPossibleRanks() - Static method in class org.forester.archaeopteryx.AptxUtil
-
- getAllRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get all rows including those that may be hidden
- getAllSpaceGroups() - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
-
- getAllSuperGoIds(GoId, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
-
- getAllSuperGoTerms(GoId, List<GoTerm>) - Static method in class org.forester.go.GoUtils
-
- getAllSuperGoTerms(GoId, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
-
- getAllSuperGoTerms(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
-
- getAlnbeg1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnbeg2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnseq1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnseq2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlnsymb() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getAlpha() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getAlpha() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getAlt_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getAltAligNumber() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the sequential number of this alternative alignment
- getAltcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the altcode property.
- getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getAlternativeAligs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getAltIds() - Method in class org.forester.go.BasicGoTerm
-
- getAltIds() - Method in interface org.forester.go.GoTerm
-
- getAltitude() - Method in class org.forester.phylogeny.data.Point
-
- getAltiudeUnit() - Method in class org.forester.phylogeny.data.Point
-
- getAltLoc() - Method in interface org.biojava.nbio.structure.Atom
-
Get alternate Location.
- getAltLoc() - Method in class org.biojava.nbio.structure.AtomImpl
-
get alternate Location.
- getAltLoc1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getAltLoc2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getAltLocGroup(Character) - Method in interface org.biojava.nbio.structure.Group
-
Gets the alternate location group to this group that has the alt-loc character code passed.
- getAltLocGroup(Character) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getAltLocs() - Method in interface org.biojava.nbio.structure.Group
-
Get the list of alternate locations.
- getAltLocs() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getAltShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the alternative international short name (as sometimes used in PDB),
e.g.
- getAmbiguity(NucleotideCompound...) - Method in class org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet
-
Calculates the best symbol for a collection of compounds.
- getAminoacid() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getAminoAcid() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getAminoAcid(String) - Static method in class org.biojava.nbio.structure.StandardAminoAcid
-
get a standard amino acid.
- getAminoAcidCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getAminoAcidCompoundSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getAminoAcidCompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getAminoAcids(Chain) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
Get all amino acids in a chain.
- getAminoAcidSubstitutionMatrix(String) - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns a substitution matrix for
amino acids given by the name
name.
- getAminoOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getAminoThreeLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getAminoType() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Returns the name of the AA, in single letter code.
- getAminoType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Returns the name of the AA, in single letter code.
- getAnchors() - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
Returns the list of anchors.
- getAngle() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
The rotation angle
- getAngle(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Calculate the rotation angle for a structure
- getAngle(Matrix) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Calculate the rotation angle for a given matrix
- getAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
Returns the pitch angle of the helix
- getAngle_alpha() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_alpha_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_beta() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_beta_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_gamma() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngle_gamma_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getAngleDiff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the angleOutlier property.
- getAngleThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getAniso_B() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getAnnotation() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getAnnotation() - Method in interface org.biojava.nbio.ontology.utils.Annotatable
-
Should return the associated annotation object.
- getAnnotation(int) - Method in class org.forester.phylogeny.data.Sequence
-
- getAnnotations() - Method in class org.forester.phylogeny.data.Sequence
-
- getAnnotationType() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getApliphaticIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the apliphatic index of sequence.
- getApliphaticIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the apliphatic index of sequence.
- getApliphaticIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getAppliesTo() - Method in class org.forester.phylogeny.data.Property
-
- getApprovedName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getApprovedSymbol() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getArchitectureId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getArray() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Access the internal two-dimensional array.
- getArrayCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Copy the internal two-dimensional array.
- getAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the ASA of the residue in the complexed state
- getAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the ASA of the residue in the uncomplexed state
- getAsList() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns this Sequence store as a List
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getAsList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getAsList() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the Sequence as a List of compounds
- getAsList() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getAssembly_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- getAssignments() - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
-
- getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAsym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAsym_id_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- getAsymUnit(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
-
load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object
- getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- getAsymUnit() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
get the asym unit for this PDB ID
- getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
-
- getAsymUnit(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
-
- getAtcc() - Method in class org.biojava.nbio.structure.Compound
-
- getAtom(String) - Method in interface org.biojava.nbio.structure.Group
-
Get an atom given its PDB name.
- getAtom(int) - Method in interface org.biojava.nbio.structure.Group
-
Get at atom by position.
- getAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Get an atom given its PDB name.
- getAtom(int) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Get at atom by position.
- getAtom() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the atom property.
- getAtom() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the atom property.
- getAtom0() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the atom0 property.
- getAtom0() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the atom0 property.
- getAtom1() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- getAtom1() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the atom1 property.
- getAtom1() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the atom1 property.
- getAtom2() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- getAtom2() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the atom2 property.
- getAtom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getAtom_id_1() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getAtom_id_2() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getAtomA() - Method in class org.biojava.nbio.structure.Bond
-
Gets atom 'A' of this bond.
- getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
- getAtomArray(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an array of the requested Atoms from the Structure object.
- getAtomArray(Chain, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an array of the requested Atoms from the Chain object.
- getAtomArrayAllModels(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an array of the requested Atoms from the Structure object.
- getAtomAsaCs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- getAtomAsaUs() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- getAtomB() - Method in class org.biojava.nbio.structure.Bond
-
Gets atom 'B' of this bond.
- getAtomCAArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns an Atom array of the C-alpha atoms.
- getAtomCAArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Return an Atom array of the C-alpha atoms.
- getAtomCache() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getAtomCache() - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
-
- getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
-
- getAtomCache() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
-
- getAtomCaThreshold() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
the maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
- getAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getAtomCoordinateBounds(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
- getAtomDistance(Atom, Atom) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getAtomForAligPos(AFPChain, int, int, Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
return the atom at alignment position aligPos.
- getAtomGroup(int) - Method in interface org.biojava.nbio.structure.Chain
-
Return the Group at given position,
from within Groups with observed density in the chain, i.e.
- getAtomGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the Group at given position,
from within Groups with observed density in the chain, i.e.
- getAtomGroups() - Method in interface org.biojava.nbio.structure.Chain
-
Return all Groups with observed density in the chain, i.e.
- getAtomGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain
-
- getAtomGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl
-
- getAtomGroups() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return all Groups with observed density in the chain, i.e.
- getAtomicMass() - Method in enum org.biojava.nbio.structure.Element
-
Returns the atomic mass for this Element.
- getAtomicNumber() - Method in enum org.biojava.nbio.structure.Element
-
Returns the atomic number of this Element.
- getAtomLength() - Method in interface org.biojava.nbio.structure.Chain
-
Return the number of Groups with observed density in the chain, i.e.
- getAtomLength() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the number of Groups with observed density in the chain, i.e.
- getAtomLigands() - Method in interface org.biojava.nbio.structure.Chain
-
Get all groups that are not polymer groups and that are not solvent groups.
- getAtomLigands() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get all groups that are not polymer groups and that are not solvent groups.
- getAtomLinkages() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getAtomName() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
-
- getAtomName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getAtomNames(Group) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the CA atoms for the provided name.
- getAtoms() - Method in interface org.biojava.nbio.structure.Group
-
Get list of atoms.
- getAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Get list of atoms.
- getAtoms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getAtoms() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the atoms property.
- getAtoms() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the atoms property.
- getAtomsCAInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard
aminoacids appearing as HETATM groups), i.e.
- getAtomSequence() - Method in interface org.biojava.nbio.structure.Chain
-
Return the sequence of amino acids as it has been provided in the ATOM records.
- getAtomSequence() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the sequence of amino acids as it has been provided in the ATOM records.
- getAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getAtomsInContact(Chain, String[], double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of intra-chain contacts for the given chain for given atom names, i.e.
- getAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e.
- getAtomsInContact(Chain, Chain, String[], double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of inter-chain contacts between the two given chains for the given atom names.
- getAtomsInContact(Chain, Chain, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Returns the set of inter-chain contacts between the two given chains for all non-H atoms.
- getAttemptedValidationSteps() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the attemptedValidationSteps property.
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
- getAttribute() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Return the attribute of the grouping
- getAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get value of specified attribute key.
- getAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
-
Get the attribute value for this key.
- getAttribute(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getAttributeOld(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
- getAttributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
- getAttributes() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
-
- getAttributes() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getAtttributeValue(XmlElement, String) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
-
- getAtttributeValue(XmlElement, String) - Static method in class org.forester.io.parsers.tol.TolXmlHandler
-
- getAuBoundingBox(int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
-
Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU)
The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
- getAuth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAuth_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAuth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAuth_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAuthority() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getAuthorList() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the list of Authors of the JournalArticle
- getAuthors() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getAuthors() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the names of the authors as listed in the AUTHORS section of a PDB file.
- getAutoFetch() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getAutoSuggestProvider() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
-
- getAvailablePhylogeniesWebserviceClient(int) - Method in class org.forester.archaeopteryx.webservices.WebservicesManager
-
- getAvailablePhylogeniesWebserviceClients() - Method in class org.forester.archaeopteryx.webservices.WebservicesManager
-
- getAvarageNormalizedScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
-
- getAvarageRawScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
-
- getAverageTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getAverageTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getAvgHydropathy(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the average hydropathy value of sequence.
- getAvgHydropathy(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the average hydropathy value of sequence.
- getAvgHydropathy(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getAvgoccu() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the avgoccu property.
- getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
Returns the AxisAngle of the helix transformation
- getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
-
- getAxisAngle(int, AxisAngle4f) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getAxisAngle4d() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns the rotation axis and angle in a single javax.vecmath.AxisAngle4d object
- getAxisFoldType(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold
and for improper rotations: -1, -2, -3, -4 and -6
- getAxisTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getAxisTypes() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getB() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getB() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getB_iso_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getB_iso_mean() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getB_iso_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getB_iso_or_equiv() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getB_iso_or_equiv_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getBackboneAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Return an Atom array of the main chain atoms: CA, C, N, O
Any group that contains those atoms will be included, be it a standard aminoacid or not
- getBackingSequence() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Access the sequence which backs this window
- getBadRmsd() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getBaseFontFamilyName() - Method in class org.forester.archaeopteryx.Configuration
-
- getBaseUrl() - Static method in class org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer
-
- getBegin() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
- getBeta() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getBeta() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getBinaryCharacters() - Method in class org.forester.phylogeny.data.NodeData
-
- getBinaryDomainCombinationsSpecificToGenome0() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
- getBinaryDomainCombinationsSpecificToGenome1() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
- getBinaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
-
Returns a list of operators for this assembly.
- getBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the map of biological assemblies.
- getBioBegin() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getBioEnd() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getBioEnd() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
-
1-indexed, inclusive.
- getBiol_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getBiolAssembly(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Loads the biological assembly for a given PDB ID and bioAssemblyId.
- getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
Returns the first biologicalAssembly that is available for a protein structure.
- getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO
-
By default the getStructure method loads asym units.
- getBiologicalMoleculeBounds(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
- getBiologicalMoleculeCentroid(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
Returns the centroid of the biological molecule.
- getBiologicalMoleculeMaximumExtend(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
Returns the maximum extend of the biological molecule in the x, y, or z direction.
- getBiologicalUnit(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Loads the default biological unit (*.pdb1.gz) file.
- getBiologicalUnit() - Method in class org.biojava.nbio.structure.Compound
-
- getBioSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
used to retrieve sequences from the structure
- getBioSequences(boolean, String) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).
- getBioSequences(boolean) - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
Because some database files have incorrectly small letters (e.g.
- getBioStart() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getBioStart() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
-
1-indexed, inclusive.
- getBioUnitDataProvider() - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
-
- getBioUnitTransformationList(PdbxStructAssembly, List<PdbxStructAssemblyGen>, List<PdbxStructOperList>) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
-
Returns a list of transformation matrices for the generation of a macromolecular
assembly for the specified assembly Id.
- getBioUnitTransformationList(String, int) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
-
get the data for a particular assembly, counting starts at 1...
- getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
-
- getBioUnitTransformationList(String, int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
-
- getBJSequence() - Method in interface org.biojava.nbio.structure.Chain
-
Convert the SEQRES groups of a Chain to a Biojava Sequence object.
- getBJSequence() - Method in class org.biojava.nbio.structure.ChainImpl
-
Convert the SEQRES groups of a Chain to a Biojava Sequence object.
- getBlastAdvancedOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastDatabase() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastExpect() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastFromPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastGapCosts() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the actual string for the GAPCOSTS parameter which is used to build the URL
- getBlastGapCreation() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
- getBlastGapExtension() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
- getBlastMatrix() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value of the specified substitution matrix
- getBlastProgram() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastToPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- getBlastWordSize() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Returns the value of the WORD_SIZE parameter used for this blast run
- getBlock2Afp() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockGap() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
Deprecated.
use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
- getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
get the block number for an aligned position
- getBlockNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The number of blocks in the alignment
- getBlockNumClu() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockNumIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockNumSpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockResList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
tracks the residues of the initial blocks (before optimization)
- getBlockResSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockRotationMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockShiftVector() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlockSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getBlosum100() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 100 matrix by Henikoff & Henikoff
- getBlosum30() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 30 matrix by Henikoff & Henikoff
- getBlosum35() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 35 matrix by Henikoff & Henikoff
- getBlosum40() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 40 matrix by Henikoff & Henikoff
- getBlosum45() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 45 matrix by Henikoff & Henikoff
- getBlosum50() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 50 matrix by Henikoff & Henikoff
- getBlosum55() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 55 matrix by Henikoff & Henikoff
- getBlosum60() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 60 matrix by Henikoff & Henikoff
- getBlosum62() - Static method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getBlosum62() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 62 matrix by Henikoff & Henikoff
- getBLOSUM62() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getBLOSUM62(char, char) - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getBlosum65() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 65 matrix by Henikoff & Henikoff
- getBlosum70() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 70 matrix by Henikoff & Henikoff
- getBlosum75() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 75 matrix by Henikoff & Henikoff
- getBlosum80() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 80 matrix by Henikoff & Henikoff
- getBlosum85() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 85 matrix by Henikoff & Henikoff
- getBlosum90() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Blosum 90 matrix by Henikoff & Henikoff
- getBondOrder() - Method in class org.biojava.nbio.structure.Bond
-
Gets the bond order of this bond.
- getBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the bondOutlier property.
- getBonds() - Method in interface org.biojava.nbio.structure.Atom
-
Get all
Bonds this atom is part of.
- getBonds() - Method in class org.biojava.nbio.structure.AtomImpl
-
- getBonds() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getBootstraps() - Method in class org.forester.sdi.RIO
-
Returns the numbers of trees analyzed.
- getBootstrapSamples() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getBorderColor() - Method in class org.forester.phylogeny.data.NodeVisualization
-
- getBottom() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getBranchColor() - Method in class org.forester.phylogeny.data.BranchData
-
- getBranchColorValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method
- getBranchData() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getBranchesInPreorder(Phylogeny) - Static method in class org.forester.sdi.SDIR
-
- getBranchWidth() - Method in class org.forester.phylogeny.data.BranchData
-
- getBranchWidthValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method
- getBravLattice() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getBsa() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the BSA value for this group, i.e.
- getBsaToAsaRatio() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the bsa/asa(uncomplexed) ratio, i.e.
- getBtype() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getBufferedReader() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Returns the reader representation of this classpath resource
- getBuildMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getBulkSolventB() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the bulkSolventB property.
- getBulkSolventK() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the bulkSolventK property.
- getByCategory(ModificationCategory) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByCategory(CathCategory) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return list of CATH descriptions for node representatives at a CATH category (e.g.
- getByCategory(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getByCategory(ScopCategory) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get all records of a particular classification.
- getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getByChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- getByComponent(Component, Component...) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
Get ProteinModifications that involves one or more components.
- getById(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByKeyword(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory
-
- getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
-
- getByLargestContacts() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getByLargestContactsNotLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getByLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getByName(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
-
Returns the ExpTechnique given an experimental technique name as used in the PDB,
e.g.
- getByName(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getByOccurrenceType(ModificationOccurrenceType) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByPdbccId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByPsimodId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getByResidId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry
-
- getBytesRead() - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
-
Keep track of bytesread via ReadLine to account for CR-LF in the stream.
- getByUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- getC() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get C atom.
- getC() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get C atom.
- getC() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getC() - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- getC() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getC2Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getC3Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getC4Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getCA() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get CA atom.
- getCA() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get CA atom.
- getCA() - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- getCa1() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getCa1() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- getCa1Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getCa2() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- getCa2Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getCache() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getCache() - Static method in class org.biojava.nbio.structure.align.util.CacheFactory
-
- getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getCacheFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getCacheFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getCacheLocation() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCacheLocation() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getCachePath() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns the path that contains the caching file for utility data, such as domain definitions.
- getCalculationTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getCalculationTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getCalphaAtoms() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getCalphaCoordinates() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getCalphaTraces() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getCalphaTraces() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
-
- getCAOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter
-
Convert a List of chain objects to another List of chains, containing C-alpha atoms only.
- getCAOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter
-
Convert a Chain to a new Chain containing C-alpha atoms only.
- getCartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_x_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_y_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCartn_z_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getCategory() - Method in class org.biojava.nbio.ontology.Synonym
-
- getCategory() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getCategory() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getCategory() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getCategory() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getCATH() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getCathDatabase() - Static method in class org.biojava.nbio.structure.cath.CathFactory
-
Returns the default (singleton) CathDatabase.
- getCathDatabase(String) - Static method in class org.biojava.nbio.structure.cath.CathFactory
-
Returns a CATH database of the specified version.
- getCathDownloadUrl() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCathNode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return the CathNode for a node ID.
- getCathNode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCathVersion() - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return the CATH release version.
- getCathVersion() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getCB() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get CB atom.
- getCB() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get CB atom.
- getCCP4Version() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the ccp4Version property.
- getCdsEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the CDS sequences that have been added to the TranscriptSequences
- getCdsStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getCECalculator() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getCell() - Method in class org.biojava.nbio.structure.Compound
-
- getCell(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get cell value
- getCell_setting() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getCellColor() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getCellColor() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getCellDouble(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getCellIndices(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Get the index of a unit cell to which the query point belongs.
- getCellLine() - Method in class org.biojava.nbio.structure.Compound
-
- getCellTranslation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getCellularLocation() - Method in class org.biojava.nbio.structure.Compound
-
- getCenter(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
-
get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
- getCenter1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCenter2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getCenterVector(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the Vector that needs to be applied to shift a set of atoms
to the Centroid.
- getCenterVector(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the Vector that needs to be applied to shift a set of atoms
to the Centroid, if the centroid is already known
- getCentricOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the centricOutliers property.
- getCentroid(Atom[]) - Static method in class org.biojava.nbio.structure.Calc
-
Returns the center of mass of the set of atoms.
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getChain() - Method in interface org.biojava.nbio.structure.Group
-
Returns the parent Chain of the Group.
- getChain() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- getChain() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Returns the parent Chain of the Group.
- getChain(int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a chain by its position within the Structure .
- getChain(int, int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve a chain by its position within the Structure and model number.
- getChain(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getChain(int, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getChain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the chain property.
- getChain1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getChain1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getChain2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getChainBoundingBox(int, int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
-
Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU)
and chain index
- getChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure
-
Request a chain by its PDB code
by default takes only the first model
- getChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure
-
Request a chain by its PDB code
by default takes only the first model
- getChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getChainId() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getChainId() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
- getChainId() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getChainID() - Method in interface org.biojava.nbio.structure.Chain
-
Get the name of this chain (Chain id in PDB file ).
- getChainID() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the name of this chain (Chain id in PDB file ).
- getChainId() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- getChainId() - Method in class org.biojava.nbio.structure.DBRef
-
The chain ID of the corresponding chain.
- getChainId() - Method in interface org.biojava.nbio.structure.Group
-
Utility method for returning the chainId of the Group or null if no
Chain has been set.
- getChainId() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Utility method for returning the chainId of the Group or null if no
Chain has been set.
- getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getChainId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Returns the chain identifier this transformation should be applied to.
- getChainId() - Method in class org.biojava.nbio.structure.ResidueNumber
-
- getChainId() - Method in class org.biojava.nbio.structure.ResidueRange
-
- getChainId() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getChainId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getChainID1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getChainID1() - Method in class org.biojava.nbio.structure.SSBond
-
- getChainId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getChainID2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getChainID2() - Method in class org.biojava.nbio.structure.SSBond
-
- getChainIds() - Method in class org.biojava.nbio.structure.Compound
-
Return the list of member chain IDs that are described by this Compound
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
-
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getChainRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getChains() - Method in class org.biojava.nbio.structure.Compound
-
Get the list of chains that are part of this Compound
- getChains() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getChains() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
- getChains() - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all chains - if it is a NMR structure will return the chains of the first model.
- getChains(int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all chains of a model.
- getChains(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
retrieve all chains of a model.
- getChains() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getCharacter(int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getCharacter(int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getCharacterIndex(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getCharacterIndex(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getCharge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getCharStateLabels() - Method in class org.forester.io.parsers.nexus.NexusCharactersParser
-
- getChemComp() - Method in interface org.biojava.nbio.structure.Group
-
Get the chemical component that closer describes this group.
- getChemComp() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.AllChemCompProvider
-
Returns a new instance of a chemical component definition.
- getChemComp(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getChemComp(String) - Method in interface org.biojava.nbio.structure.io.mmcif.ChemCompProvider
-
Returns a new instance of a chemical component definition.
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
Loads the definitions for this
ChemComp from a local file and instantiates a new object.
- getChemComp(String) - Method in class org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider
-
- getChemCompProvider() - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getChild1() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChild1() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the first child node of this node.
- getChild2() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChild2() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the second child node of this node.
- getChildAt(int) - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChildCount() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getChildElement(int) - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getChildNode(int) - Method in class org.forester.phylogeny.PhylogenyNode
-
This return child node n of this node.
- getChildNode(int) - Method in interface org.forester.phylogeny.PhylogenyNodeI
-
- getChildNode1() - Method in class org.forester.phylogeny.PhylogenyNode
-
Convenience method.
- getChildNode2() - Method in class org.forester.phylogeny.PhylogenyNode
-
Convenience method.
- getChildNodeIndex() - Method in class org.forester.phylogeny.PhylogenyNode
-
This gets the child node index of this node.
- getChildNodeIndex(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
-
This gets the child node index of this node, given that parent is its
parent
- getChildren() - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Get the children features
- getChildrenFeatures() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getChildrenFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the features contained by this feature
- getChiSquare() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getChrLoc() - Method in class org.biojava.nbio.phosphosite.Site
-
- getChromosome() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getChromosomeMappings() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
-
- getChromosomeMappings(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
-
- getChromosomeNumber() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
- getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
- getCid() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the cid property.
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getCirumscribedRadius() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of a circumscribed sphere (length of diagonal of
rectangular prism/2, that goes through at least four vertices
- getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getClaFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getClan() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the clash property.
- getClashmag() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the clashmag property.
- getClashmag() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the clashmag property.
- getClashscore() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the clashscore property.
- getClassId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getClassId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getClassification() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getClassificationId(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getClassificationId(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
Return a portion of the classificationID corresponding to the specified
category (class, fold, superfamily, family).
- getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getClaURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getCloseMenuItem(JFrame) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
get the number of the cluster this alignment belongs to
- getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCluster() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getCluster1() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- getCluster2() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- getClusters(double) - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer
-
Get the clusters by cutting the dendrogram at given cutoff
- getClusters() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Calculate the interface clusters for this StructureInterfaceList
using a contact overlap score to measure the similarity of interfaces.
- getClusterValue() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getCode() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getCode() - Method in class org.forester.ws.seqdb.UniProtTaxonomy
-
- getCode() - Method in class org.forester.ws.uniprot.UniProtTaxonomy
-
- getCodingSequence() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
A CDS sequence if negative stranded needs to be reverse complement
to represent the actual coding sequence.
- getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
Returns the compound set of codons
- getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
-
- getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
Returns a list of codons where the source and target compounds
are the same as those given by the parameters.
- getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava.nbio.core.sequence.transcription.Table
-
- getCodons(String) - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getCoeff() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getCoefficient(String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getCoefficientsList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getCoefficientText(boolean, String, String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getCohortName() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getCol() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- getColor() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- getColor() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
- getColor(double) - Method in interface org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
-
- getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform
-
Return the color corresponding to submapper.getColor(transform(value)).
- getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- getColor(double) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- getColor(int) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
-
- getColor() - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Get the current color in the color chooser.
- getColorBrewer() - Method in class org.jcolorbrewer.ui.ColorPanelSelectionModel
-
- getColorPalette(int) - Method in enum org.jcolorbrewer.ColorBrewer
-
- getColorPalette() - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Get the current color in the color chooser.
- getCols() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getCols() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getCols() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getColumn(AminoAcidCompound) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getColumn(C) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getColumn(C) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
- getColumnAt(int) - Method in class org.forester.msa.BasicMsa
-
- getColumnAt(int) - Method in interface org.forester.msa.Msa
-
- getColumnDimension() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get column dimension.
- getColumnIdentifiers() - Method in class org.forester.util.GeneralTable
-
- getColumnIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getColumnLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getColumnPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Make a one-dimensional column packed copy of the internal array.
- getColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of column names.
- getColumns() - Method in class org.forester.development.MsaRenderer
-
- getColumnsAsMap(int, int) - Method in class org.forester.util.BasicTable
-
- getColumnsAsMapDouble(int, int) - Method in class org.forester.util.BasicTable
-
- getCombinableDomainIds(Species) - Method in interface org.forester.surfacing.DomainSimilarity
-
- getCombinableDomainIds(Species) - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getCombinableDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getCombinableDomains() - Method in interface org.forester.surfacing.CombinableDomains
-
- getCombinableDomainsIds() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getCombinableDomainsIds() - Method in interface org.forester.surfacing.CombinableDomains
-
Returns the combinable domain identifiers sorted in alphabetical manner: -
keys are the combinable domain identifiers - values are the counts of
proteins exhibiting a particular combination
- getCombiningDomainIdsAsStringBuilder() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getCombiningDomainIdsAsStringBuilder() - Method in interface org.forester.surfacing.CombinableDomains
-
- getCombiningDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getComFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getCommandLineArgsAsString() - Method in class org.forester.util.CommandLineArguments
-
- getComment() - Static method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getComment() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getComment() - Method in class org.forester.go.BasicGoTerm
-
- getComment() - Method in interface org.forester.go.GoTerm
-
- getComments(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getComments(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getComments(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get comments about a SCOP domain by its sunid
- getComments(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getCommentsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getCommentsXML(List<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getCommon_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getCommonName() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getCommonName() - Method in class org.forester.ws.seqdb.UniProtTaxonomy
-
- getCommonName() - Method in class org.forester.ws.uniprot.UniProtTaxonomy
-
- getCommonValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the common valence for this Element.
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getComp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getComparator(int) - Method in class org.biojava.nbio.structure.align.gui.MyTableRowSorter
-
- getComplement() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- getComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Returns a Sequence which will complement every base
- getComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the complement view of the RNA sequence
- getComplement() - Method in interface org.biojava.nbio.core.sequence.template.ComplementCompound
-
- getComplexSignature() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getComplexStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getComponent(int) - Method in class org.biojava.nbio.structure.symmetry.utils.ComponentFinder
-
- getComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getComponentCount() - Method in class org.biojava.nbio.structure.symmetry.utils.ComponentFinder
-
- getComponents() - Method in interface org.biojava.nbio.protmod.ModificationCondition
-
- getComponents() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl
-
}
- getComponents() - Method in class org.biojava.nbio.structure.symmetry.utils.ComponentFinder
-
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
Returns the composition of the specific grouping for the given attribute.
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getComposition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
An adaptor method which returns the composition of the specific grouping for the given attribute.
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getComposition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getComposition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getComposition(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Does a linear scan over the given Sequence and records the number of
times each base appears.
- getCompositionId() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getCompound() - Method in interface org.biojava.nbio.structure.Chain
-
Return the Compound for this chain.
- getCompound() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the Compound for this chain.
- getCompoundAt(int) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getCompoundAt(int, int) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundAt(S, int) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundAt(int, int) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns the
Compound at row of given sequence and column of alignment index.
- getCompoundAt(S, int) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns the
Compound at row of given sequence and column of alignment index.
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns the compound at the specified biological index
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the compound at the specified biological index
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Always returns the compound given at construction
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getCompoundAt(int) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the Compound at the given biological index
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
-
- getCompoundAt(int) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getCompoundById(int) - Method in interface org.biojava.nbio.structure.Structure
-
Request a particular compound by its molId (entity_id in mmCIF dictionary)
- getCompoundById(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
- getCompoundCountsAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundCountsAt(int, List<C>) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundCountsAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile
-
- getCompoundCountsAt(int, List<C>) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns the number of each
Compound in the given column only for compounds in the given list.
- getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getCompoundForString(String) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getCompoundForString(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getCompoundForString(String) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
Return null if not recognised.
- getCompoundInQueryAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getCompoundInQueryAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the
Compound in query sequence at given column index in alignment.
- getCompoundInTargetAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getCompoundInTargetAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the
Compound in target sequence at given column index in alignment.
- getCompounds(int) - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
For a given position into the windowed view this will return those
compounds we can see in the window.
- getCompounds() - Method in interface org.biojava.nbio.structure.Structure
-
Get all the Compounds for this Structure.
- getCompounds() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getCompoundsAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundsAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile
-
- getCompoundsAt(int) - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get a list of compounds at a sequence position
- getCompoundsAt(int) - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getCompoundSet() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getCompoundSet() - Method in interface org.biojava.nbio.alignment.template.Profile
-
- getCompoundSet() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns the
CompoundSet on which the matrix is defined.
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompound
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the Compounds defined in the first sequence
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns the compound set backing this store
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the compound set backing this store
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns the compound set given at construction
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
- getCompoundSet() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Gets the compound set used to back this Sequence
- getCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getCompoundsOfQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getCompoundsOfTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getCompoundsToIndexLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns a map which converts from compound to an integer representation
- getCompoundType() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getCompoundWeightsAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundWeightsAt(int, List<C>) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getCompoundWeightsAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile
-
- getCompoundWeightsAt(int, List<C>) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns the fraction of each
Compound in the given column only for compounds in the given list.
- getComputationTime() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getComputationTime() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getComputationTime() - Method in interface org.biojava.nbio.alignment.template.Aligner
-
Returns the computation time needed for an alignment computed in nanoseconds.
- getComURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getCondition() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getCondition() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getConfidence() - Method in class org.forester.phylogeny.data.Annotation
-
- getConfidence(int) - Method in class org.forester.phylogeny.data.BranchData
-
- getConfidence() - Method in class org.forester.phylogeny.data.Event
-
- getConfidence() - Method in class org.forester.phylogeny.data.ProteinDomain
-
- getConfidence() - Method in class org.forester.phylogeny.data.SequenceRelation
-
- getConfidence() - Method in class org.forester.phylogeny.Phylogeny
-
- getConfidences() - Method in class org.forester.phylogeny.data.BranchData
-
- getConfidenceValue(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method
- getConfidenceValuesAsArray(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method
- getConfig() - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
-
- getConfiguration() - Method in class org.forester.archaeopteryx.MainFrame
-
- getConn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getConn_type_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getConnectedFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getConnectedNode(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch
-
- getConnectedTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getConnections() - Method in interface org.biojava.nbio.structure.Structure
-
Return the connections value.
- getConnections() - Method in class org.biojava.nbio.structure.StructureImpl
-
Return the connections value.
- getConsAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
- getConsituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- getConstituents() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- getContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
-
Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms
- getContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
-
Returns the corresponding GroupContact or null if no contact exists between the 2 given groups
- getContactOverlapScore(StructureInterface, boolean) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Calculates the contact overlap score between this StructureInterface and
the given one.
- getContacts() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getContacts() - Method in class org.biojava.nbio.structure.contact.Grid
-
Returns all contacts, i.e.
- getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getContactsToOtherCell(GridCell, Atom[], Atom[], double) - Method in class org.biojava.nbio.structure.contact.GridCell
-
Calculates all distances of atoms between this cell and the given cell returning those that are
within the given cutoff as a list of AtomContacts
- getContactsWithinCell(Atom[], Atom[], double) - Method in class org.biojava.nbio.structure.contact.GridCell
-
Calculates all distances of atoms within this cell returning those that are within the given cutoff
as a list of AtomContacts
- getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
-
Returns the list of contacts from this set that are within the given distance.
- getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.GroupContact
-
Returns the list of atom contacts in this GroupContact that are within the given distance.
- getContig() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
-
- getContinuousVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getControlPanel() - Method in class org.forester.archaeopteryx.MainPanel
-
- getCoordManager() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- getCoordpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getCoords() - Method in interface org.biojava.nbio.structure.Atom
-
Get the coordinates.
- getCoords() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get the coordinates.
- getCopiedAndPastedNodes() - Method in class org.forester.archaeopteryx.MainPanel
-
- getCopy() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- getCopyWorkSheet(WorkSheet) - Static method in class org.biojava.nbio.survival.data.WorkSheet
-
Create a copy of a worksheet.
- getCopyWorkSheetSelectedRows(WorkSheet, ArrayList<String>) - Static method in class org.biojava.nbio.survival.data.WorkSheet
-
Create a copy of a worksheet.
- getCoreElectronCount() - Method in enum org.biojava.nbio.structure.Element
-
Returns the number of core electrons for this Element.
- getCoreOntology() - Static method in class org.biojava.nbio.ontology.OntoTools
-
Get the Ontology that defines our core "central dogma".
- getCoreResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the interface core, defined as those residues at
the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff
- getCorrelation_coeff_Fo_to_Fc() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getCorrelation_coeff_Fo_to_Fc_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getCost() - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- getCost() - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- getCost() - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- getCost() - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getCount() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
-
- getCount() - Method in class org.forester.sdi.SDIR
-
Returns the number of differently rooted trees which minimize the
(rooting) "criterion" - as determined by method "infer".
- getCovalentRadius() - Method in enum org.biojava.nbio.structure.Element
-
Returns the covalent radius of this Element.
- getCoverage1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the coverage of protein 1 with the alignment
- getCoverage2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the coverage of protein 2 with the alignment
- getCovered() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getCoxInfo(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getCoxInfoHashMap() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getCPPoint() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getCreate_co() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getCreator() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- getCrystalCell() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Return the crystal cell
- getCrystalIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns a pair of identifiers for each of the 2 member molecules that
identify them uniquely in the crystal:
<molecule id (asym unit id)>+<operator id>+<crystal translation>
- getCrystallographicInfo() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getCrystallographicInfo() - Method in interface org.biojava.nbio.structure.Structure
-
Get crystallographic information for this structure
- getCrystallographicInfo() - Method in class org.biojava.nbio.structure.StructureImpl
-
Gets crystallographic information for this structure
- getCrystals_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getCurrent(String) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Gets the current version of a PDB ID.
- getCurrentChain() - Method in class org.biojava.nbio.structure.AtomIterator
-
Get the chain that contains the current atom.
- getCurrentChain() - Method in class org.biojava.nbio.structure.GroupIterator
-
Get the current Chain.
- getCurrentDateTime() - Static method in class org.forester.util.ForesterUtil
-
- getCurrentModel() - Method in class org.biojava.nbio.structure.AtomIterator
-
Get the model number of the model containing the current atom.
- getCurrentModel() - Method in class org.biojava.nbio.structure.GroupIterator
-
Get the model number of the current model.
- getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.PDBStatus
-
Returns a list of current PDB IDs
- getCurrentPhylogeny(String) - Method in class org.forester.archaeopteryx.ArchaeopteryxE
-
This method returns the current phylogeny as a string in the chosen format
- getCurrentPhylogenyGraphicsAsBase64EncodedString(String) - Method in class org.forester.archaeopteryx.ArchaeopteryxE
-
This method returns a view of the current phylogeny in a chosen
graphics format, base64-encoded in a string so that in can be used
from javascript.
- getCurrentSequencePosition() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- getCurrentTreePanel() - Method in class org.forester.archaeopteryx.MainPanel
-
- getCurrentUserDesktopPath() - Static method in class org.forester.util.WindowsUtils
-
- getCustomChain1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getCustomFile1() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getCut_sites() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- getCutoff() - Method in class org.biojava.nbio.structure.contact.Grid
-
- getCuts(int, AlignerHelper.Subproblem, int[], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
- getCutsPerSection() - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher
-
Returns the number of cuts added to each section during each pass.
- getD() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the block diagonal eigenvalue matrix
- getData() - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
-
- getData() - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
-
- getData() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
-
- getData() - Method in interface org.forester.phylogeny.Edge
-
- getData() - Method in class org.forester.phylogeny.PhylogenyBranch
-
- getData() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getData() - Method in interface org.forester.util.DescriptiveStatistics
-
- getDataAnisotropy() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dataAnisotropy property.
- getDataAsDoubleArray() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getDataAsDoubleArray() - Method in interface org.forester.util.DescriptiveStatistics
-
- getDatabase() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- getDatabase() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
- getDatabase() - Method in class org.biojava.nbio.structure.DBRef
-
The database of the db-ref.
- getDatabaseReferences() - Method in interface org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface
-
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
The Uniprot mappings to other database identifiers for this sequence
- getDatabaseReferences() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getDataCompleteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dataCompleteness property.
- getDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of row names
- getDataSource() - Method in class org.biojava.nbio.core.sequence.AccessionID
-
- getDataSource() - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
-
- getDataSource() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
-
- getDataType() - Method in class org.forester.phylogeny.data.Property
-
- getDataValue() - Method in class org.forester.development.ResidueRenderer
-
- getDataVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getDate() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDate() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getDate() - Method in class org.forester.phylogeny.data.NodeData
-
- getDate_original() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getDb_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getDb_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getDb_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getDb_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getDbAccession() - Method in class org.biojava.nbio.structure.DBRef
-
Sequence database accession code.
- getDbComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getDbIdCode() - Method in class org.biojava.nbio.structure.DBRef
-
Sequence database identification code.
- getDbReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getDBRefs() - Method in interface org.biojava.nbio.structure.Structure
-
Get the list of database references
- getDBRefs() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getDBResultMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getDBSearch() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getDBSearchParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDbSearchResult(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getDbSeqBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Initial sequence number of the
database seqment.
- getDbSeqEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Ending sequence position of the database segment.
- getDbxrefList(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getDCCR() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dccr property.
- getDCCRefinementProgram() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dccRefinementProgram property.
- getDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the dccRfree property.
- getDcl() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getDefault() - Static method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
Default instance to use when Transcribing from DNA -> RNA ->
Protein.
- getDefaultBootstrapSamples() - Method in class org.forester.archaeopteryx.Configuration
-
- getDefaultConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
-
- getDefaultDnaMatrix() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getDefaultFactory() - Static method in class org.biojava.nbio.ontology.OntoTools
-
- getDefaultFrame() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
- getDefaultNodeFill() - Method in class org.forester.archaeopteryx.Configuration
-
- getDefaultNodeShape() - Method in class org.forester.archaeopteryx.Configuration
-
- getDefaultNodeShapeSize() - Method in class org.forester.archaeopteryx.Configuration
-
- getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script to set the default orientation for a structure
- getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script to set the default orientation for a structure
- getDefaultOrientation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getDefaultParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDefaultParameters() - Static method in class org.forester.msa.Mafft
-
- getDefaultPeptideMatrix() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getDefaultText() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
-
- getDefinition() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getDefinition() - Method in class org.forester.go.BasicGoTerm
-
- getDefinition() - Method in interface org.forester.go.GoTerm
-
- getDegreeFreedom() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getDelta() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getDendrogram() - Method in class org.biojava.nbio.core.util.SingleLinkageClusterer
-
Get the full dendrogram (size n-1) result of the hierarchical clustering
- getDensityCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDepDate() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getDesc() - Method in class org.forester.phylogeny.data.Annotation
-
- getDesc() - Method in class org.forester.phylogeny.data.Date
-
- getDesc() - Method in class org.forester.phylogeny.data.Distribution
-
- getDescendants() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getDesciption() - Method in class org.forester.pccx.BranchCountingBasedScoringMethod
-
- getDesciption() - Method in class org.forester.pccx.BranchLengthBasedScoringMethod
-
- getDesciption() - Method in class org.forester.pccx.LogBranchLengthBasedScoringMethod
-
- getDesciption() - Method in interface org.forester.pccx.ScoringMethodForExternalNode
-
This returns a short description of this scoring method
- getDescription() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getDescription() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getDescription() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns the description of this matrix.
- getDescription() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the description that can be used to describe the feature
- getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getDescription() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getDescription() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getDescription() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return a human-readable description of this ontology, or the empty
string if none is available
- getDescription() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getDescription() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getDescription() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getDescription() - Method in interface org.biojava.nbio.ontology.Term
-
Return a human-readable description of this term, or the empty string if
none is available.
- getDescription() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getDescription() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getDescription() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getDescription() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getDescription() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
return a description of this compound
- getDescription() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getDescription() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq
-
Return the description of this FASTQ formatted sequence.
- getDescription() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder
-
Return the description for this FASTQ formatted sequence builder.
- getDescription() - Method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant
-
Return the description of this FASTQ sequence format variant.
- getDescription() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getDescription() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getDescription() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getDescription() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getDescription() - Method in class org.biojava.nbio.structure.Site
-
gets the REMARK 800 description of the site
- getDescription() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
-
- getDescription() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- getDescription() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getDescription() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
A short description of the webservice (~20 characters).
- getDescription() - Method in class org.forester.phylogeny.data.Reference
-
- getDescription() - Method in class org.forester.phylogeny.data.Uri
-
- getDescription() - Method in class org.forester.phylogeny.Phylogeny
-
- getDescription() - Method in class org.forester.protein.BasicProtein
-
- getDescription() - Method in interface org.forester.protein.Protein
-
- getDescription() - Method in class org.forester.surfacing.MappingResults
-
- getDescription() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getDescription() - Method in interface org.forester.util.DescriptiveStatistics
-
- getDescription2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get a textual description for the protein 2 of the alignment.
- getDescriptionByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return CATH description for CATH domain ID.
- getDescriptionByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDescriptionByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return CATH description for node representative by node ID.
- getDescriptionByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDescriptionNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getDescriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getDescriptors() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getDesFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getDesURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getDetails() - Method in class org.biojava.nbio.structure.Compound
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getDetails() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getDf() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
-
- getDiagonalAtK(Atom[], int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
-
- getDiagonalDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDiagonalDistance2() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getDictionary() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- getDifferenceInCounts() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
-
- getDifferenceInCounts() - Method in class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity
-
Returns (counts for domain 1) minus (counts for domain 2).
- getDifferenceInCounts() - Method in interface org.forester.surfacing.PairwiseDomainSimilarity
-
This should return the -- not normalized, not absolute -- difference in
counts (for example domain counts) for the two domains.
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getDimension() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getDir(String, boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Gets the directory in which the file for a given MMCIF file would live,
creating it if necessary.
- getDirection() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getDiscreteColumnValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get back a list of unique values in the column
- getDiscreteRowValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get back a list of unique values in the row
- getDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
-
- getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
Get the distance cutoff used during AFP chain connectivity checks
- getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getDisFilter() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getDisorder(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the disordered regions of the sequence.
- getDisorder(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the disordered regions of the sequence for many sequences in the input.
- getDisorder(String) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the disordered regions of the protein sequence.
- getDisorderScores(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the probability value for each residue in the protein sequence,
telling the probability that the residue belongs to disordered region.
- getDisorderScores(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the probability value for each residue in the protein sequence,
telling the probability that the residue belongs to disordered region.
- getDisorderScores(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn
-
Calculates the probability of disorder scores for each residue in the sequence for
many sequences in the input.
- getDisplayName() - Method in class org.jcolorbrewer.ui.DivergingColorPalettePanel
-
- getDisplayName() - Method in class org.jcolorbrewer.ui.QualitativeColorPalettePanel
-
- getDisplayName() - Method in class org.jcolorbrewer.ui.SequentialColorPalettePanel
-
- getDisSmooth() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getDist() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getDist() - Method in class org.biojava.nbio.structure.validation.Clash
-
Gets the value of the dist property.
- getDist() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the dist property.
- getDist1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getDist1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getDist2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getDist2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getDisTable1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getDisTable2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getDistance() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getDistance(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getDistance() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a distance between 0.0 and 1.0.
- getDistance(double) - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a distance between 0.0 and scale.
- getDistance() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- getDistance(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
calculate distance between two atoms.
- getDistance() - Method in class org.biojava.nbio.structure.contact.AtomContact
-
- getDistance() - Method in class org.biojava.nbio.structure.secstruc.DistEn
-
- getDistance() - Method in class org.forester.phylogeny.data.SequenceRelation
-
- getDistance(String) - Method in class org.forester.sdi.RIO
-
Returns the distance to a sequences/taxa after a distance list file has
been read in with readDistanceList(File).
- getDistance(String, String) - Method in class org.forester.sdi.RIO
-
- getDistanceFast(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Will calculate the *square* of distances between two atoms.
- getDistanceIncrement() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getDistanceMatrix() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the distance matrix used to construct this guide tree.
- getDistanceMatrix() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer
-
Returns the distance matrix used in clustering.
- getDistanceMatrix() - Method in class org.biojava.nbio.phylo.TreeConstructor
-
- getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
-
matrix of all distances between two sets of 3d coords"
- getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
A matrix with ca1length rows and ca2length columns.
- getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
The distance matrix this alignment is based on
- GetDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp
-
- GetDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
-
- getDistanceMatrix(Atom[]) - Method in class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
-
A set of Calpha atoms that are representing the protein
- getDistanceToLCA(String) - Method in class org.forester.sdi.DistanceCalculator
-
Calculates the distance of the PhylogenyNode with seq name seq_name to
the LCA of ext_nodes, which has been set either with constructor
DistanceCalculator(Phylogeny,Vector) or method
setTreeAndExtNodes(Phylogeny,Vector).
- getDistanceToNode(PhylogenyNode, PhylogenyNode) - Method in class org.forester.sdi.DistanceCalculator
-
Calculates the distance of PhylogenyNode outer to PhylogenyNode inner.
- getDistanceToNode(String, PhylogenyNode) - Method in class org.forester.sdi.DistanceCalculator
-
Calculates the distance of the PhylogenyNode with seq name seq_name to
PhylogenyNode inner.
- getDistanceToParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getDistanceToParent() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the difference in height of this node and it's parent node.
- getDistanceToParent() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns the length of the branch leading to the _parent of this
PhylogenyNode (double).
- getDistanceToParent() - Method in interface org.forester.phylogeny.PhylogenyNodeI
-
- getDistanceToRoot(PhylogenyNode) - Method in class org.forester.sdi.DistanceCalculator
-
Calculates the distance of PhylogenyNode n to the root of Phylogeny t
which has been set either with a constructor, setTree(Phylogeny), or
setTreeAndExtNodes(Phylogeny,Vector).
- getDistanceToRoot(String) - Method in class org.forester.sdi.DistanceCalculator
-
Calculates the distance of the PhylogenyNode with seq name seq_name to
the root of Phylogeny t, which has been set either with a constructor,
setTree(Phylogeny), or setTreeAndExtNodes(Phylogeny,Vector).
- getDistanceUnit() - Method in class org.forester.phylogeny.Phylogeny
-
- getDistMat() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
return the difference of distance matrix between the two structures
- getDistribution(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
- getDistribution() - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always returns the first Distribution.
- getDistribution(int) - Method in class org.forester.phylogeny.data.NodeData
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getDistributionPosition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING, IProfeatProperties.DISTRIBUTION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.GROUPING) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDistributionPosition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDistributionPosition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getDistributions() - Method in class org.forester.phylogeny.data.NodeData
-
- getDivergingColorPalettes(boolean) - Static method in enum org.jcolorbrewer.ColorBrewer
-
- getDNA() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getDNACodingSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the stitched together CDS sequences then maps to the cDNA
- getDNACodingSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
-
- getDnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
-
- getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
-
- getDNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.DNACompoundSet
-
- getDNAOneLetter(String) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getDnaRnaTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getDnaToRna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getDNATwoLetter(Character) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getDNAType() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
- getDoi() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of DOI field.
- getDoi() - Method in class org.forester.phylogeny.data.Reference
-
- getDomain(String, AtomCache) - Method in interface org.biojava.nbio.structure.domain.PDPProvider
-
- getDomain(String, AtomCache) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
- getDomain(int) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getDomain(int) - Method in class org.forester.phylogeny.data.DomainArchitecture
-
- getDomainArchitecture() - Method in class org.forester.phylogeny.data.Sequence
-
- getDomainByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return CATH domain for CATH domain ID.
- getDomainByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getDomainByScopID(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
- getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getDomainCombinationType() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- getDomainCombinationType() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
- getDomainCounter() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDomainCounts(List<Protein>) - Static method in class org.forester.surfacing.SurfacingUtil
-
- getDomainDescriptionFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainDistanceScoresMeans() - Method in class org.forester.surfacing.PairwiseGenomeComparator
-
- getDomainId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDomainId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getDomainId() - Method in class org.forester.protein.BasicDomain
-
- getDomainId() - Method in interface org.forester.protein.Domain
-
- getDomainId() - Method in class org.forester.surfacing.DomainLengths
-
- getDomainId() - Method in interface org.forester.surfacing.DomainSimilarity
-
- getDomainId() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getDomainId() - Method in class org.forester.surfacing.SimpleDomain
-
- getDomainLengths(DomainId) - Method in class org.forester.surfacing.DomainLengthsTable
-
- getDomainLengthsList() - Method in class org.forester.surfacing.DomainLengthsTable
-
- getDomainListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainName() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getDomainNames(String) - Method in interface org.biojava.nbio.structure.domain.DomainProvider
-
- getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider
-
Gets a list of domain representatives for a given PDB ID.
- getDomainNames(String) - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
-
- getDomainProvider() - Static method in class org.biojava.nbio.structure.domain.DomainProviderFactory
-
- getDomainRangesFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomainRangesXML(SortedSet<String>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomains() - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
-
- getDomains() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getDomains() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getDomains() - Method in class org.forester.phylogeny.data.DomainArchitecture
-
- getDomainsByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return all CATH domains for a particular CATH node.
- getDomainsByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainsEncountered() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsEncountered() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return all CATH domains for a PDB ID.
- getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getDomainsForPDB(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get a list of ScopDomains that have been assigned to a PDB ID
- getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getDomainsFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomainsIgnoredDueToDuf() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToDuf() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsIgnoredDueToEval() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToEval() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsIgnoredDueToIndividualScoreCutoff() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToIndividualScoreCutoff() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsIgnoredDueToNegativeDomainFilter() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToNegativeDomainFilter() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsIgnoredDueToNegativeDomainFilterCountsMap() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToNegativeDomainFilterCountsMap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsIgnoredDueToOverlap() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToOverlap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsIgnoredDueToVirusLikeIdCountsMap() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToVirusLikeIdCountsMap() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsIgnoredDueToVirusLikeIds() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsIgnoredDueToVirusLikeIds() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsSpecificToGenome0() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
- getDomainsSpecificToGenome1() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
- getDomainsStored() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsStored() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainsStoredSet() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getDomainsStoredSet() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getDomainStructureBaseColor() - Method in class org.forester.archaeopteryx.Configuration
-
- getDomainStructureFontColor() - Method in class org.forester.archaeopteryx.Configuration
-
- getDomainsXML(SortedSet<Domain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getDomallFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getDonor1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getDonor2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getDoublePivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return pivot permutation vector as a one-dimensional double array
- getDssp3state(String) - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
translate from other dssp secondary structure alphabets to 3-state
- getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- getDuplicationsSum() - Method in class org.forester.sdi.SDI
-
Returns the number of duplications.
- getDVar() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getEcNums() - Method in class org.biojava.nbio.structure.Compound
-
- getEdgeCount() - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- getEdgeCount() - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- getEdges() - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- getEdges() - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- getEditorList() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the list of editors of the JournalArticle
- getEDSR() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the edsr property.
- getEDSResolution() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the edsResolution property.
- getEDSResolutionLow() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the edsResolutionLow property.
- getElement() - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
-
- getElement(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
-
- getElement() - Method in interface org.biojava.nbio.structure.Atom
-
Get element of the atom, e.g.
- getElement() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get element of the atom, e.g.
- getElement1() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
-
- getElement2() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
-
- getElementFromHillIndex(int) - Static method in enum org.biojava.nbio.structure.Element
-
Returns the Element that corresponds to the specified Hill Order.
- getElementList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getElementType() - Method in enum org.biojava.nbio.structure.Element
-
Returns the Element Type for this Element.
- getElipsisRadii() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- getEmail() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Get the email for QBlast.
- getEmbTrees() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getEmptyChemComp() - Method in class org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider
-
- getEmptySequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Returns an empty sequence with the given compound set of the editing
sequence
- getEnd() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getEnd() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
Returns the
Point within an alignment of the last element of the original
Sequence.
- getEnd() - Method in interface org.biojava.nbio.alignment.template.ProfileView
-
Returns the column index of the viewed
Profile corresponding to the final element in this view
- getEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
- getEnd(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
-
Must use this rather than the no-args getEnd as this can return
-1 and the length of a sub is dependent on the length of the
Sequence; we cannot assume 1:1 mapping between characters in a
String and the number of compounds we will have to insert.
- getEnd() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getEnd() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
End of the location
- getEnd() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
- getEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getEnd() - Method in class org.biojava.nbio.structure.ResidueRange
-
- getEndLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
- getEnergy() - Method in class org.biojava.nbio.structure.secstruc.DistEn
-
- getEnergy() - Method in class org.biojava.nbio.structure.secstruc.HBond
-
- getEngineered() - Method in class org.biojava.nbio.structure.Compound
-
- getEnrichment(ProteinSequence, AminoAcidCompound) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the composition of specified amino acid in the sequence.
- getEnrichment(String, PeptideProperties.SingleLetterAACode) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of specified amino acid in the sequence.
- getEnrichment(String, char) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of specified amino acid in the sequence.
- getEnrichment(String, String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the composition of specified amino acid in the sequence.
- getEnrichment(ProteinSequence, AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getEnsemblGeneId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getEnt() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ent property.
- getEntities() - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getEntity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getEntityId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- getEntry() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Gets the value of the entry property.
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- getEntry_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getEnumValuesAsString(Class<T>) - Static method in class org.biojava.nbio.structure.align.util.CliTools
-
Constructs a comma-separated list of values for an enum.
- getEnzClass() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getEqr() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the number of euqivalent residues in this alignment
- getEQRAlignmentPos(AFPChain) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
- getEquivalent() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getEquivalentCompounds(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getEquivalentCompounds(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
- getError() - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- getErrorCount() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- getErrorCount() - Method in class org.forester.io.parsers.tol.TolParser
-
- getErrorDescription() - Method in class org.forester.msa.Mafft
-
- getErrorDescription() - Method in class org.forester.msa.MafftOLD
-
- getErrorDescription() - Method in interface org.forester.msa.MsaInferrer
-
- getErrorMessages() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- getErrorMessages() - Method in class org.forester.io.parsers.tol.TolParser
-
- getErrorStream() - Method in class org.forester.util.ExternalProgram
-
- getEvalCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getEvCode() - Method in class org.biojava.nbio.structure.Site
-
gets the REMARK 800 EVIDENCE CODE for the site.
- getEvent() - Method in class org.forester.phylogeny.data.NodeData
-
- getEventType() - Method in class org.forester.phylogeny.data.Event
-
- getEvidence() - Method in class org.forester.phylogeny.data.Annotation
-
- getExampleUnitCell() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getExitCode() - Method in class org.forester.msa.Mafft
-
- getExitCode() - Method in class org.forester.msa.MafftOLD
-
- getExitCode() - Method in interface org.forester.msa.MsaInferrer
-
- getExitMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getExonCount() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getExonEnds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getExonSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the exons as an ArrayList
- getExonStarts() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getExpectedExecutionTime() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
- getExperimentalTechniques() - Method in class org.biojava.nbio.structure.PDBHeader
-
Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid
experimental techniques when the Set will contain 2 or more values
- getExportPDBMenuItem(StructureAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getExpression_system_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getExpressionSystem() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemAtccNumber() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemCell() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemCellLine() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemCellularLocation() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemGene() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemOrgan() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemOrganelle() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemOtherDetails() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemPlasmid() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemStrain() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemTaxId() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemTissue() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemVariant() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemVector() - Method in class org.biojava.nbio.structure.Compound
-
- getExpressionSystemVectorType() - Method in class org.biojava.nbio.structure.Compound
-
- getExtensionPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
Returns the negative of the extension penalty passed to the constructor.
- getExtensionPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
Returns penalty given when an already open gap elongates by a single element
- getExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Returns a list of extensions supported by this class
- getExternalDescendantsTaxonomy(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Returns taxonomy t if all external descendants have
the same taxonomy t, null otherwise.
- getExternalNodes() - Method in class org.forester.phylogeny.Phylogeny
-
Warning.
- getExtinctionCoefficient(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the extinction coefficient of sequence.
- getExtinctionCoefficient(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the extinction coefficient of sequence.
- getExtinctionCoefficient(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getExtNodesOfAnalyzedGeneTrees() - Method in class org.forester.sdi.RIO
-
Returns the numbers of number of ext nodes in gene trees analyzed (after
stripping).
- getFailedLines() - Method in class org.biojava.nbio.structure.scop.Astral
-
Gets a map describing lines read in the file that weren't understood.
- getFalseDiscoveryRate() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getFamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getFarmJob() - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
-
- getFarthestNode1() - Method in class org.forester.phylogeny.PhylogenyMethods
-
- getFarthestNode2() - Method in class org.forester.phylogeny.PhylogenyMethods
-
- getFatCatAligner() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
-
- getFeatureRetriever() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFeatures() - Method in interface org.biojava.nbio.core.sequence.features.FeatureRetriever
-
- getFeatures(String) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getFeatures() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getFeatures() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getFeatures(String, int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Return features at a sequence position by type
- getFeatures(int) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Return features at a sequence position
- getFeatures() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFeaturesByType(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFeaturesKeyWord() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Get the behavior for fetching files from the server
- getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getFetchBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Get the behavior for fetching files from the server
- getFile() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- getFile(int) - Method in class org.forester.util.CommandLineArguments
-
- getFile1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getFile2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getFileAnnotation() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
- getFileExtension(File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
-
- getFileFormat() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getFileFormatSelect() - Static method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getFilename(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Converts a PDB ID into a filename with the proper extension
- getFilename(String) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getFilename(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
- getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.PDBFileParser
-
- getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
- getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.StructureProvider
-
Get the parameters that should be used for file parsing
- getFileParsingParams() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getFilePath1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getFilePrefix(File) - Static method in class org.biojava.nbio.structure.io.util.FileDownloadUtils
-
- getFileSeparator() - Static method in class org.forester.util.ForesterUtil
-
- getFillColor() - Method in class org.forester.phylogeny.data.NodeVisualization
-
- getFillType() - Method in class org.forester.phylogeny.data.NodeVisualization
-
- getFirst(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getFirst() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getFirst() - Method in class org.biojava.nbio.structure.contact.Pair
-
- getFirstAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getFirstChildNode() - Method in class org.forester.phylogeny.PhylogenyNode
-
Convenience method.
- getFirstExternalNode() - Method in class org.forester.phylogeny.Phylogeny
-
Returns the first external PhylogenyNode.
- getFirstGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets the GroupAsa for the corresponding residue number of first chain
- getFirstGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.
- getFirstLine(Object) - Static method in class org.forester.util.ForesterUtil
-
- getFirstNode() - Method in interface org.forester.phylogeny.Edge
-
- getFirstNode() - Method in class org.forester.phylogeny.PhylogenyBranch
-
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Should return the 5-prime end of the given Sequence according to
the edit.
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
-
- getFivePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
-
- getFlippableSidechain() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the flippableSidechain property.
- getFocusAfpList() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusAfpn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusRes1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusRes2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFocusResn() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getFoFcCorrelation() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the foFcCorrelation property.
- getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getFoldId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getFoldType() - Method in enum org.biojava.nbio.structure.xtal.TransformType
-
- getFont() - Method in class org.forester.archaeopteryx.FontChooser
-
- getFontName() - Method in class org.forester.archaeopteryx.FontChooser
-
- getFontSize() - Method in class org.forester.archaeopteryx.FontChooser
-
- getFontStyle() - Method in class org.forester.archaeopteryx.FontChooser
-
- getForesterLibraryInformation() - Static method in class org.forester.util.ForesterUtil
-
- getFormat() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getFormat() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getFormatedSequence(int) - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
Format sequence per width letter in one string.
- getFormattedFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- getFormula() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getFormula() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getFormula() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getFormula() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getFormula_weight() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getForwardFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
Returns all frames in the forward orientation
- getFragCompat() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getFragLen() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getFragLenSq() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getFragment(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
-
get a continue subset of Atoms based by the starting position and the length
- getFragment() - Method in class org.biojava.nbio.structure.Compound
-
- getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
-
get a subset of Atoms based by their positions
- getFragmentId() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getFragmentMiniDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignTools
-
get a continue subset of Atoms based by the starting position and the length
does not clone the original atoms.
- getFragmentPairs() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
get the results of step 1 - the FragmentPairs used for seeding the alignment
- getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getFragmentPairs() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getFragmentsByPdbId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
- getFragmentsByPdbId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getFragScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getFrame() - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
-
- getFrom() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- getFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getFrom() - Method in class org.forester.phylogeny.data.ProteinDomain
-
- getFrom() - Method in class org.forester.protein.BasicDomain
-
- getFrom() - Method in interface org.forester.protein.Domain
-
- getFrom() - Method in class org.forester.surfacing.SimpleDomain
-
- getFromCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- getFromFtp() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
-
- getFromHeteroAtomId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromHeteroAtomIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbId(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbId(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(InputStream) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(List<String>) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(String) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFromPdbIds(String...) - Static method in class org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
-
- getFullAtomSequence(List<Group>, Map<Integer, Integer>) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
-
Returns the full sequence of the Atom records of a parent
with X instead of HETATMSs.
- getFullMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns a matrix that describes both rotation and translation.
- getFurthestDescendant(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- getGainedCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getGainedCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getGainedCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getGainedCount() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getGainLossCountsMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getGainLossMatrix() - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- getGainLossMatrix() - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- getGainLossMatrix() - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- getGainLossMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getGamma() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getGamma() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getGapCreate() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getGapExtCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapExtCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapExtend() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getGapExtension() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getGapExtRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapExtRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- getGapOpen() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getGapOpenCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapOpenCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapOpenRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getGapOpenRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getGapPenalty() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns the gap penalties.
- getGaps() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
return the number of gaps in this alignment
- getGatheringThreshs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
Not always 2.
It may undergo further change.
- getGC() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
- getGCCount() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Get the GC count in the DNA Sequence
- getGCGChecksum(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Calculates GCG checksum for entire list of sequences
- getGCGChecksum(S) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Calculates GCG checksum for a given sequence
- getGCGHeader(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Assembles a GCG file header
- getGCGType(CompoundSet<C>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Determines GCG type
- getGCStats(Collection<DNASequence>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
-
- getGCStatsString(Collection<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
-
- getGenbankDirectoryCache() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
Local directory cache of Genbank that can be downloaded
- getGene(String) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Get the gene based on accession.
- getGene() - Method in class org.biojava.nbio.structure.Compound
-
- getGene_src_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_dev_stage() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGene_src_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getGenebankId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getGeneName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Get the gene name associated with this sequence.
- getGeneName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getGeneNames() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
-
- getGeneNames(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
-
Get a list of GeneNames from an input stream.
- getGenes() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getGeneSequences() - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
- getGeneSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
- getGeneSet() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
- getGeneSymb() - Method in class org.biojava.nbio.phosphosite.Site
-
- getGeneTree() - Method in class org.forester.sdi.SDI
-
Returns the gene tree.
- getGenus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getGeodeticDatum() - Method in class org.forester.phylogeny.data.Point
-
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
Returns a transformation matrix transform polyhedra for Cn structures.
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
Returns a transformation matrix transform polyhedra for Cn structures.
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
Returns the geometric center of polyhedron.
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
Returns the geometric center of polyhedron.
- getGlobalSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns list of global quaternary structure symmetry results
- getGoId() - Method in class org.forester.go.BasicGoRelationship
-
- getGoId() - Method in class org.forester.go.BasicGoTerm
-
- getGoId() - Method in class org.forester.go.etc.OntologizerResult
-
- getGoId() - Method in interface org.forester.go.GoRelationship
-
- getGoId() - Method in interface org.forester.go.GoTerm
-
- getGoId(int) - Method in class org.forester.protein.BasicDomain
-
- getGoId(int) - Method in interface org.forester.protein.Domain
-
- getGoId(int) - Method in class org.forester.protein.DomainId
-
- getGoId(int) - Method in class org.forester.surfacing.SimpleDomain
-
- getGoIds() - Method in class org.forester.protein.DomainId
-
- getGoNameSpace() - Method in class org.forester.go.BasicGoTerm
-
- getGoNameSpace() - Method in interface org.forester.go.GoTerm
-
- getGoNamespaceLimit() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getGonnet250() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns PAM 250 matrix by Gonnet, Cohen & Benner
- getGoRelationships() - Method in class org.forester.go.BasicGoTerm
-
- getGoRelationships() - Method in interface org.forester.go.GoTerm
-
- getGoSubsets() - Method in class org.forester.go.BasicGoTerm
-
- getGoSubsets() - Method in interface org.forester.go.GoTerm
-
- getGoTermCount() - Method in class org.forester.go.OBOparser
-
- getGoXRefs() - Method in class org.forester.go.BasicGoTerm
-
- getGoXRefs() - Method in interface org.forester.go.GoTerm
-
- getGradientMapper(int, double, double) - Static method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
Constructs a gradientMapper to draw one of the pre-defined gradients
For example,
GradientMapper.getGradientMapper(GradientMapper.RAINBOW_GRADIENT, 0, 10)
- getGroup() - Method in class org.biojava.nbio.phosphosite.Site
-
- getGroup() - Method in class org.biojava.nbio.protmod.structure.StructureAtom
-
- getGroup() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- getGroup() - Method in interface org.biojava.nbio.structure.Atom
-
Return the parent Group of the Atom.
- getGroup() - Method in class org.biojava.nbio.structure.AtomImpl
-
Return the parent Group of the Atom.
- getGroup_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getGroupAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator
-
Calculates ASA for all atoms and return them as a GroupAsa
array (one element per residue in structure) containing ASAs per residue
and per atom.
- getGroupByPDB(ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain
-
Get a group by its PDB residue numbering.
- getGroupByPDB(ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl
-
Get a group by its PDB residue numbering.
- getGroupByPDBResidueNumber(Structure, ResidueNumber) - Static method in class org.biojava.nbio.structure.StructureTools
-
Get a group represented by a ResidueNumber.
- getGroupCategories(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getGroupCategories(String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
- getGroupContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getGroupDistancesWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
- getGroupFromChemCompDictionary(String) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
-
- getGrouping() - Method in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Returns the groupings of the attribute
- getGroups() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getGroups(boolean) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getGroups() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getGroups(boolean) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getGroups() - Method in class org.biojava.nbio.structure.secstruc.SecStruc
-
- getGroups() - Method in class org.biojava.nbio.structure.Site
-
- getGroups() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
Get the name of the groups that are being plotted in the figure
- getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain
-
Get all groups that are located between two PDB residue numbers.
- getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in interface org.biojava.nbio.structure.Chain
-
Get all groups that are located between two PDB residue numbers.
- getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in class org.biojava.nbio.structure.ChainImpl
-
Deprecated.
- getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl
-
Get all groups that are located between two PDB residue numbers.
- getGroupsWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getGroupsWithinShell(Structure, Group, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getGroupTable() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getH() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
-
Return the Householder vectors
- getH() - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- getHazardRatio() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHazardRatioHiCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHazardRatioLoCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHeader() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat
-
- getHeader(S) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat
-
- getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface
-
- getHeader(S) - Method in interface org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface
-
- getHeader() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getHeaderParser() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getHeaderVars() - Method in class org.biojava.nbio.structure.Compound
-
- getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of a sphere, that is tangent to each
of the octahedron's edges
- getHeight() - Method in class org.forester.phylogeny.Phylogeny
-
This calculates the height for rooted, tree-shaped phylogenies.
- getHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getHelixRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getHelixRmsdToRiseRatio() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getHelpMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getHetero() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getHetGroups() - Method in interface org.biojava.nbio.structure.Structure
-
- getHetGroups() - Method in class org.biojava.nbio.structure.StructureImpl
-
Caution: we should probably remove this to avoid confusion.
- getHgncId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getHieFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getHieURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
- getHigherOrderRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getHillOrder() - Method in enum org.biojava.nbio.structure.Element
-
Returns the Hill Order of this Element.
- getHitsQueryDef(double) - Method in class org.biojava.nbio.genome.query.BlastXMLQuery
-
- getHmmAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmName() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHmmTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getHomologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getHost_org_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_genus() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_species() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHost_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getHRText() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getHSVColorSpace() - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
- getHyd() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getHydmax() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getHydmin() - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getIcode() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the icode property.
- getiCode1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getiCode2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getIconHeight() - Method in class org.jcolorbrewer.ui.PaletteIcon
-
- getIconWidth() - Method in class org.jcolorbrewer.ui.PaletteIcon
-
- getID() - Method in class org.biojava.nbio.core.sequence.AccessionID
-
- getId() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
- getId() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
- getID() - Method in class org.biojava.nbio.core.sequence.TaxonomyID
-
- getId() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
Gets the value of id
- getId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getId() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getId() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getId() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get the Hibernate database ID.
- getId() - Method in interface org.biojava.nbio.structure.Chain
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.nbio.structure.ChainImpl
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.nbio.structure.Compound
-
get the ID used by Hibernate
- getId() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getId() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- getId() - Method in class org.biojava.nbio.structure.DBRef
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getId() - Method in class org.biojava.nbio.structure.HetatomImpl
-
the Hibernate database ID
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getId() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getId() - Method in class org.biojava.nbio.structure.PDBHeader
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
The identifier for this Biological Assembly, from 1 to n
- getId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Returns the identifier for this biological assembly transformation.
- getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getId() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
-
- getId() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
-
- getId() - Method in interface org.biojava.nbio.structure.Structure
-
Get the ID used by Hibernate
- getId() - Method in class org.biojava.nbio.structure.StructureImpl
-
get the ID used by Hibernate
- getId() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getId() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the standard numeric identifier for the space group.
- getId() - Method in enum org.biojava.nbio.structure.xtal.TransformType
-
- getId() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getId() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
Request id (RID) as received from QBlast server
- getId() - Method in class org.forester.archaeopteryx.tools.ProcessRunning
-
- getId() - Method in class org.forester.evoinference.matrix.character.DiscreteState
-
- getId() - Method in class org.forester.go.GoId
-
- getId() - Method in class org.forester.phylogeny.data.ProteinDomain
-
- getId() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns the ID (int) of this PhylogenyNode.
- getId() - Method in interface org.forester.phylogeny.PhylogenyNodeI
-
- getId() - Method in class org.forester.protein.DomainId
-
- getId() - Method in class org.forester.protein.ProteinId
-
- getId() - Method in class org.forester.ws.seqdb.UniProtTaxonomy
-
- getId() - Method in class org.forester.ws.uniprot.UniProtTaxonomy
-
- getId0() - Method in interface org.forester.protein.BinaryDomainCombination
-
- getId0() - Method in class org.forester.surfacing.BasicBinaryDomainCombination
-
- getId1() - Method in interface org.forester.protein.BinaryDomainCombination
-
- getId1() - Method in class org.forester.surfacing.BasicBinaryDomainCombination
-
- getIdbnsBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Insertion code of initial residue of the segment, if PDB is the
reference.
- getIdbnsEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Insertion code of the ending
residue of the segment, if PDB is
the reference.
- getIdCode() - Method in class org.biojava.nbio.structure.DBRef
-
get the idCode for this entry
- getIdCode() - Method in class org.biojava.nbio.structure.PDBHeader
-
The PDB code for this protein structure.
- getIdenticalSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getIdentification() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getIdentifiedModifiedCompound() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getIdentifier() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getIdentifier() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getIdentifier() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getIdentifier() - Method in interface org.biojava.nbio.structure.StructureIdentifier
-
The unique identifier, using the following formal specification:
- getIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getIdentifier() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
-
- getIdentifier(int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getIdentifier(int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getIdentifier(int) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- getIdentifier(int) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix
-
- getIdentifier(int) - Method in class org.forester.msa.BasicMsa
-
- getIdentifier(int) - Method in interface org.forester.msa.Msa
-
- getIdentifier() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getIdentifier() - Method in class org.forester.phylogeny.Phylogeny
-
- getIdentifier() - Method in class org.forester.sequence.BasicSequence
-
- getIdentifier() - Method in interface org.forester.sequence.Sequence
-
- getIdentifierIndex(String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getIdentifierIndex(String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getIdentity() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
- getIdentity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The percent of residues that are sequence-identical in the alignment.
- getIDFormat(List<S>) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates format String for accession IDs
- getIdRef() - Method in class org.forester.phylogeny.data.Property
-
- getIdx1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
the positions of the structure equivalent positions in atom set 1
- getIdx1() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
get the identical position in the alignment
- getIdx2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
the positions of the structure equivalent atoms in atom set 2
- getIdx2() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
get the identical position in the alignment
- getIdxlist() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
-
- getIgnoredSequenceIds() - Method in class org.forester.msa.MsaMethods
-
- getImagEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the imaginary parts of the eigenvalues
- getImageMap() - Method in class org.forester.archaeopteryx.TreePanel
-
- getImat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getInChI() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getInChIKey() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getIndex(TreeNode) - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getIndex() - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- getIndex() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getIndex() - Method in class org.biojava.nbio.survival.data.HeaderInfo
-
- getIndex(String) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- getIndex(String) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix
-
- getIndexColumnName() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getIndexInQueryAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getIndexInQueryAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the query index corresponding to a given alignment column.
- getIndexInQueryForTargetAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getIndexInQueryForTargetAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the query index corresponding to a given target index.
- getIndexInTargetAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getIndexInTargetAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the target index corresponding to a given alignment column.
- getIndexInTargetForQueryAt(int) - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getIndexInTargetForQueryAt(int) - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the target index corresponding to a given query index.
- getIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getIndexOf(C) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Searches for the given
Compound within this alignment profile.
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the first occurrence of the given compound in this store; performs
a linear search
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns 1 if the given compound is equal to the one given during
construction; otherwise will return -1.
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Scans through the Sequence looking for the first occurrence of the given
compound
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getIndexOfComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getIndexOfComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getIndexToCompoundsLookup() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Returns a list of compounds the index position of which is used
to translate from the byte representation into a compound.
- getIndicator() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns the _indicator value of this PhylogenyNode.
- getIndicesAt(int) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getIndicesAt(int) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns the indices in the original
Sequences corresponding to the given column.
- getIndividualCutoffAppliesTo() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getInertiaTensor() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- getInferredOrthologs(String) - Method in class org.forester.sdi.RIO
-
Returns a HashMap containing the inferred orthologs of the external gene
tree node with the sequence name seq_name.
- getInferredSuperOrthologs(String) - Method in class org.forester.sdi.RIO
-
Returns a HashMap containing the inferred "super orthologs" of the
external gene tree node with the sequence name seq_name.
- getInferredUltraParalogs(String) - Method in class org.forester.sdi.RIO
-
Returns a HashMap containing the inferred "ultra paralogs" of the
external gene tree node with the sequence name seq_name.
- getInitialK() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getInitials() - Method in class org.biojava.nbio.structure.Author
-
- getInputStream() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Returns the InputStream instance of this classpath resource
- getInputStream(String) - Static method in class org.biojava.nbio.core.util.FlatFileCache
-
- getInputStream(String) - Method in class org.biojava.nbio.core.util.InputStreamProvider
-
get an InputStream for this file
- getInputStream(URL) - Method in class org.biojava.nbio.core.util.InputStreamProvider
-
- getInputStream(File) - Method in class org.biojava.nbio.core.util.InputStreamProvider
-
get an InputStream for the file
- getInputStream(URL, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools
-
connect to DAS server and return result as an InputStream.
- getInputStream(URL) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools
-
connect to DAS server and return result as an InputStream.
- getInputStream(URL, boolean, int) - Static method in class org.biojava.nbio.structure.align.util.HTTPConnectionTools
-
open a URL and return an InputStream to it
if acceptGzipEncoding == true, use GZIPEncoding to
compress communication
- getInputStream(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Load or download the specified structure and return it as an InputStream
for direct parsing.
- getInputStream() - Method in class org.forester.util.ExternalProgram
-
- getInputStreamToAAindexFile() - Method in class org.biojava.nbio.alignment.aaindex.DefaultAAIndexProvider
-
- getInsCode() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getInsCode() - Method in class org.biojava.nbio.structure.ResidueNumber
-
- getInsCode1() - Method in class org.biojava.nbio.structure.SSBond
-
- getInsCode2() - Method in class org.biojava.nbio.structure.SSBond
-
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Returns the radius of an inscribed sphere, that is tangent to each
of the icosahedron's faces
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the radius of an inscribed sphere, that is tangent to each
of the octahedron's faces
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the radius of an inscribed sphere, that is tangent to each
of the icosahedron's faces
- getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the radius of an inscribed sphere, that is tangent to each
of the tetrahedrons's faces
- getInsertBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Initial insertion code of the PDB sequence segment.
- getInsertEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Ending insertion code of the PDB sequence segment.
- getInstabilityIndex(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the instability index of sequence.
- getInstabilityIndex(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the instability index of sequence.
- getInstabilityIndex(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getInstalledDomainDescription() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstalledDomainList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstalledDomall() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstalledNodeList() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getInstance() - Static method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
- getInstance() - Static method in class org.biojava.nbio.core.util.FlatFileCache
-
- getInstance() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getInstance(int) - Static method in class org.biojava.nbio.structure.gui.util.color.HSVColorSpace
-
- getInstance() - Static method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
-
- getInstance(QuatSymmetryResults) - Static method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)
- getInstance(AxisAligner, String) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)
- getInstance() - Static method in class org.forester.archaeopteryx.tools.InferenceManager
-
- getInstance() - Static method in class org.forester.archaeopteryx.webservices.WebservicesManager
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.AccessionParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.AnnotationParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.BinaryCharactersParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.BranchWidthParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ColorParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ConfidenceParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.DateParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.DistributionParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.DomainArchitectureParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.EventParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.IdentifierParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.PointParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.PolygonParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.PropertyParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ProteinDomainParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.ReferenceParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.SequenceParser
-
- getInstance(Phylogeny) - Static method in class org.forester.io.parsers.phyloxml.data.SequenceRelationParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.TaxonomyParser
-
- getInstance() - Static method in class org.forester.io.parsers.phyloxml.data.UriParser
-
- getInstance(CoverageCalculationMethod, CoverageCalculationOptions) - Static method in class org.forester.pccx.CoverageCalculator
-
- getInstance() - Static method in class org.forester.phylogeny.factories.ParserBasedPhylogenyFactory
-
- getInstance() - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- getInstanceNoVisibilityChange() - Static method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getInstructions() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getInstructions() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
Instructions (and examples) on how to use the webservice.
- getInt_Tables_number() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getIntegerOntology() - Static method in class org.biojava.nbio.ontology.OntoTools
-
Get the Ontology that defines integers.
- getInteractingRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getInterfacingResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the interface, i.e.
- getIntermediate(Color, Color, int, int) - Static method in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
- getIntermediateFilesBase() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getInternalChainID() - Method in interface org.biojava.nbio.structure.Chain
-
If available, returns the internal chain ID that is used in mmCif files, otherwise null
- getInternalChainID() - Method in class org.biojava.nbio.structure.ChainImpl
-
- getInternalStatesMatrix() - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- getInternalStatesMatrix() - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- getInternalStatesMatrix() - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- getInternalStatesMatrix() - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getInternalStatesMatrixPriorToTraceback() - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
Returns a view of the internal states prior to trace-back.
- getInternalStatesMatrixPriorToTraceback() - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
Returns a view of the internal states prior to trace-back.
- getInterpolator() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- getIntersection(DistanceBox<T>) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
- getIntronSequences() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the introns as an ArrayList
- getInverse() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the inverse view of the sequence.
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getInverse() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getInverse() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Does the right thing to get the inverse of the current
Sequence.
- getInverse() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getIoTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getIoTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getIoverSigma() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the ioverSigma property.
- getIsoelectricPoint(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the isoelectric point of sequence.
- getIsoelectricPoint(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
- getIsoelectricPoint(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the isoelectric point of sequence.
- getIsoelectricPoint(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
- getIsoelectricPoint(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getIsoelectricPoint(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getIsotope(String) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
-
- getIsotopeList() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getIsotopes() - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- getIterations() - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- getJclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getJmolColor(Color4f) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolColorScript(Map<Color4f, List<String>>) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolLigandScript() - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolPanel() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getJmolPoint(Tuple3d) - Static method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- getJmolScript(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns a Jmol script which will display the axis of rotation.
- getJmolScript4Block(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getJmolString(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getJoinRMSCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader
-
Get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalArticle() - Method in interface org.biojava.nbio.structure.Structure
-
Get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl
-
get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalName() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getJSpecViewProperty(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- getKappa() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getKey() - Method in class org.biojava.nbio.ontology.utils.KeyedWeakReference
-
- getKey() - Method in interface org.forester.go.Mapping
-
- getKey() - Method in class org.forester.go.PfamToGoMapping
-
- getKeyDomain() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getKeyDomain() - Method in interface org.forester.surfacing.CombinableDomains
-
Returns the domain whose combinable domains are in stored in this
combinable domains.
- getKeyDomainConfidenceDescriptiveStatistics() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getKeyDomainConfidenceDescriptiveStatistics() - Method in interface org.forester.surfacing.CombinableDomains
-
Gets descriptive statistics for the confidence (i.e.
- getKeyDomainCount() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getKeyDomainCount() - Method in interface org.forester.surfacing.CombinableDomains
-
Returns how many times the key domain is present in a given species
genome.
- getKeyDomainProteinsCount() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getKeyDomainProteinsCount() - Method in interface org.forester.surfacing.CombinableDomains
-
Returns how many proteins with the key domain are present in a given
species genome.
- getKeywords() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getKeyWords() - Method in interface org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface
-
- getKeyWords() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- getKeyWords() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Pull UniProt key words which is a mixed bag of words associated with this sequence
- getKeywords() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getKeywords() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getKMFigureInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getL() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition
-
Return triangular factor.
- getL() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return lower triangular factor
- getLabel_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_entity_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabel_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getLabelOfAtomOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getLabelOfAtomOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getLargeDisplayIcon() - Method in class org.jcolorbrewer.ui.DivergingColorPalettePanel
-
- getLargeDisplayIcon() - Method in class org.jcolorbrewer.ui.QualitativeColorPalettePanel
-
- getLargeDisplayIcon() - Method in class org.jcolorbrewer.ui.SequentialColorPalettePanel
-
- getLargestComponent() - Method in class org.biojava.nbio.structure.symmetry.utils.ComponentFinder
-
- getLargestSubunit() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getLast(String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getLast() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getLastChildNode() - Method in class org.forester.phylogeny.PhylogenyNode
-
Convenience method.
- getLastIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getLastIndexOf(C) - Method in interface org.biojava.nbio.alignment.template.Profile
-
Searches for the given
Compound within this alignment profile.
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the last occurrence of the given compound in this store; performs
a linear search
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns the length of the Sequence if the given compound was equal to
the one given during construction.
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getLastIndexOf(C) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Scans through the Sequence looking for the last occurrence of the given
compound
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getLastIndexOf(C) - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getLastIndexOf(NucleotideCompound) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getLatitude() - Method in class org.forester.phylogeny.data.Point
-
- getLayerLines() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getLeft() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getLegend(String) - Static method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getLegendPosition(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2
- getLength() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getLength() - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getLength() - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns the number of columns in the alignment profile.
- getLength() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.ExonSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.IntronSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
The sequence length
- getLength() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getLength() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Returns the length of the outer bounds of this location
- getLength() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the length of the MSA where it is assumed that
all sequence position
- getLength() - Method in class org.biojava.nbio.core.sequence.StartCodonSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.StopCodonSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the length of the sequence
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getLength() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Returns the length given during construction
- getLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getLength() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
Returns the number of columns in the alignment profile.
- getLength() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the length of the Sequence
- getLength() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getLength() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getLength() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Returns the size of the windowed sequence which is the length by the
window size.
- getLength() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- getLength() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getLength(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of residues of the specified chain in a given range, inclusive.
- getLength(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of atoms between two ResidueNumbers, inclusive.
- getLength() - Method in class org.biojava.nbio.structure.Bond
-
Gets the distance between the two atoms of this bond.
- getLength() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getLength() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getLength() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getLength() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getLength() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength
-
- getLength() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of a circumscribed sphere, that goes
through all vertices
- getLength() - Method in class org.forester.msa.BasicMsa
-
- getLength() - Method in interface org.forester.msa.Msa
-
- getLength() - Method in class org.forester.phylogeny.data.ProteinDomain
-
- getLength() - Method in class org.forester.protein.BasicDomain
-
- getLength() - Method in class org.forester.protein.BasicProtein
-
- getLength() - Method in interface org.forester.protein.Domain
-
- getLength() - Method in interface org.forester.protein.Protein
-
- getLength() - Method in class org.forester.sequence.BasicSequence
-
- getLength() - Method in interface org.forester.sequence.Sequence
-
- getLength() - Method in class org.forester.surfacing.SimpleDomain
-
- getLength1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getLength2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getLength_a() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_a_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_b() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_b_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_c() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLength_c_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getLengthDirectional(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of residues of the specified chain in a given range.
- getLengthDirectional(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Calculates the number of atoms between two ResidueNumbers, inclusive.
- getLengthStatistic(Species) - Method in class org.forester.surfacing.DomainLengths
-
- getLengthStatistic(DomainId, Species) - Method in class org.forester.surfacing.DomainLengthsTable
-
- getLengthStatisticsList() - Method in class org.forester.surfacing.DomainLengths
-
- getLfrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getLigands() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
-
- getLigRSRnbrMean() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRnbrMean property.
- getLigRSRnbrStdev() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRnbrStdev property.
- getLigRSRnumnbrs() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRnumnbrs property.
- getLigRSRZ() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the ligRSRZ property.
- getLikeSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getLineage() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getLineage() - Method in class org.forester.ws.seqdb.UniProtTaxonomy
-
- getLineage() - Method in class org.forester.ws.uniprot.UniProtTaxonomy
-
- getLineage(String) - Static method in class org.forester.ws.wabi.TxSearch
-
- getLineageToRankMap() - Static method in class org.forester.archaeopteryx.MainPanel
-
- getLinearPredictor() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
-
- getLineLength() - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
-
- getLineLength() - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getLineLoops() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getLineSeparator() - Static method in class org.forester.util.ForesterUtil
-
- getLink() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns a refernce to the linked PhylogenyNode of this PhylogenyNode.
- getLinkages() - Method in interface org.biojava.nbio.protmod.ModificationCondition
-
- getLinkages() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl
-
}
- getList() - Method in class org.biojava.nbio.core.sequence.io.util.ClasspathResource
-
Returns this resource as a list of Strings
- getList(BufferedReader) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Returns the contents of a buffered reader as a list of strings
- getList(InputStream) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
- getList(File) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
- getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
-
- getLoadMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getLocalDir() - Method in class org.biojava.nbio.phosphosite.Dataset
-
- getLocalFile(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Searches for previously downloaded files
- getLocalFileName(String) - Static method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
Returns the file name that contains the definition for this
ChemComp
- getLocalFiles() - Method in class org.biojava.nbio.phosphosite.Dataset
-
- getLocalSymmetries() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
-
Returns a list of lists of local quaternary structure symmetry results
- getLocalTimeLimit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getLocation() - Method in class org.forester.phylogeny.data.Sequence
-
- getLocationInAlignment() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getLocationInAlignment() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
- getLocations() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
- getLocations() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getLocations() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
The location(s) of this feature where the location should contain a reference to parent and sequence etc.
- getLocus() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getLogScale(double) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the log scale of this worksheet where a zero value will be set to .1
as Log(0) is undefined
- getLogScale(double, double) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the log scale of this worksheet
- getLongitude() - Method in class org.forester.phylogeny.data.Point
-
- getLongName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getLongName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getLongName() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getLongName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getLostCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getLostCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getLostCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getLostCount() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getLower() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getLowerBound() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getLs_d_res_high() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_d_res_low() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_matrix_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_parameters() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_number_restraints() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_percent_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_percent_reflns_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_all() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free_error_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_redundancy_reflns_obs() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_wR_factor_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLs_wR_factor_R_work() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getLto() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getM() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getMacromolecularSize() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
- getMainPanel() - Method in class org.forester.archaeopteryx.MainFrame
-
- getMainPanel() - Method in class org.forester.archaeopteryx.MainFrameApplet
-
- getMainPanel() - Method in class org.forester.archaeopteryx.MainFrameApplication
-
- getMainPanel() - Method in class org.forester.archaeopteryx.TreePanel
-
- getMappedExternalSpeciesTreeNodes() - Method in class org.forester.sdi.GSDI
-
- getMappingCount() - Method in class org.forester.go.PfamToGoParser
-
- getMappingSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- getMapProperty() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
-
- getMass() - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- getMass() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- getMatches(File, double) - Static method in class org.biojava.nbio.genome.homology.BlastHomologyHits
-
- getMatchingAtomRes(Chain, List<Chain>) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
-
- getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
Caution: this matrix is overwriten with very different data at several
points in the alignment algorithm.
- getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
Caution: this matrix is overwriten with very different data at several
points in the alignment algorithm.
- getMatrices() - Method in class org.biojava.nbio.alignment.aaindex.AAIndexFileParser
-
- getMatrix(String) - Method in interface org.biojava.nbio.alignment.aaindex.AAIndexProvider
-
- getMatrix(String) - Method in class org.biojava.nbio.alignment.aaindex.DefaultAAIndexProvider
-
- getMatrix() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getMatrix() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getMatrix() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns entire matrix.
- getMatrix() - Method in class org.biojava.nbio.phylo.ScoreMatrix
-
- getMatrix() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getMatrix() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getMatrix() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix(int, int, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int[], int[]) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int, int, int[]) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int[], int, int) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
-
- getMatrix11() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix12() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix13() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix21() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix22() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix23() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix31() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix32() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrix33() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getMatrixAsString() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getMatrixAsString() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getMatrixAsString() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns this matrix as a formatted String with
Compound labels along the axes.
- getMatrixFromAAINDEX(String) - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns any matrix from the AAINDEX database file
- getMatrixFromAlgebraic(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getMatrixPanel() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getMatTransform() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getMax() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getMax() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Scans through a list of locations to find the Location with the
highest end
- getMax(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Scans through a list of locations to find the Location with the
highest end
- getMax() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
-
- getMax() - Method in class org.forester.phylogeny.data.Date
-
- getMax() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getMax() - Method in interface org.forester.util.DescriptiveStatistics
-
- getMaxAtoms() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
the maximum numbers of atoms to load in a protein structure (prevents memory overflows)
- getMaxDimension() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Gets the maximum dimension of the unit cell.
- getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns the maximum extension (length) of structure
- getMaxExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
Returns the maximum extension (length) of structure
- getMaxGap() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMaxGapFrag() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
the Max gap size parameter G .
- getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
CE specific parameter: set the Max gap size parameter G (during AFP extension).
- getMaximalDifference() - Method in interface org.forester.surfacing.DomainSimilarity
-
For pairwise similarities, this should return the "difference"; for example the difference in counts
for copy number based features (the same as getMaximalDifferenceInCounts(), or the number
of actually different domain combinations.
- getMaximalDifference() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getMaximalDifferenceInCounts() - Method in interface org.forester.surfacing.DomainSimilarity
-
For pairwise similarities, this should return the difference in counts,
while for comparisons of more than two domains, this should return the maximal difference
in counts
- getMaximalDifferenceInCounts() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getMaximalSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
-
- getMaximalSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getMaximumColorCount() - Method in enum org.jcolorbrewer.ColorBrewer
-
- getMaximumConfidenceValue(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Returns the largest confidence value found on phy.
- getMaximumCovalentValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the maximum valence for this Element.
- getMaximumExtend(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
Returns the maximum extend of the structure in the x, y, or z direction.
- getMaximumLocalCombinations() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMaximumLocalResults() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMaximumLocalSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMaximumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- getMaximumValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the maximum valence for this Element.
- getMaxIter() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getMaxIterations() - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- getMaxNrIterationsForOptimization() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
- getMaxNrSuggestions() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
Get the maximun nr of suggestions
- getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- getMaxNrSuggestions() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
- getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
(jCE specific): maximum RMSD that shall be calculated for the alignment.
- getMaxPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMaxrefine() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getMaxRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getMaxScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getMaxScore() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns maximum possible score.
- getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getMaxSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getMaxSingleCompoundStringLength() - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
Returns the maximum size of a compound String this set holds
- getMaxTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
get the maximum number of Twists that are allowed...
- getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getMaxTra() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
get the maximum nr of Twists that are allowed...
- getMaxValue() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getMaxValue() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getMaxValue() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns the maximum value in this matrix.
- getMean() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the mean property.
- getMean() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getMean() - Method in class org.forester.sdi.DistanceCalculator
-
Returns the mean distance.
- getMeanBasedOutlierSpecies(double) - Method in class org.forester.surfacing.DomainLengths
-
- getMeanExtension() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
Returns the mean extension (length) of structure
- getMeanSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
-
- getMeanSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getMembers() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- getMembership() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getMenuName() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getMenuName() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
A name/description which can appear on a menu.
- getMergedClusters(double) - Method in class org.biojava.nbio.structure.symmetry.core.ClusterMerger
-
- getMessage() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
-
- getMetaDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMetaDataColumnsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMetaDataFilter() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getMetaDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMetaDataRowsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getMethod() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- getMethod() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getMethod() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns name of method used for symmetry perception.
- getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- getMethod_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Returns the radius of a sphere, that is tangent to each
of the icosahedron's edges
- getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the radius of a sphere, that is tangent to each
of the octahedron's edges
- getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the radius of a sphere, that is tangent to each
of the tetrahedron's edges
- getMin() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getMin() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.LocationHelper
-
Scans through a list of locations to find the Location with the
lowest start
- getMin(List<Location>) - Static method in class org.biojava.nbio.core.sequence.location.template.Location.Tools
-
Scans through a list of locations to find the Location with the
lowest start
- getMin() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
-
- getMin() - Method in class org.forester.phylogeny.data.Date
-
- getMin() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getMin() - Method in interface org.forester.util.DescriptiveStatistics
-
- getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- getMindiff() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the mindiff property.
- getMindiff() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the mindiff property.
- getMinDistance() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getMinimalDiffInSubTreeHeights() - Method in class org.forester.sdi.SDIR
-
Returns the (absolue value of the) minimal difference in tree heights of
the two subtrees at the root (of the (re)rooted gene tree) - as
determined by method "infer" - if minimize_height is set to true.
- getMinimalDuplications() - Method in class org.forester.sdi.SDIR
-
Returns the minimal number of duplications - as determined by method
"infer".
- getMinimalMappingCost() - Method in class org.forester.sdi.SDIR
-
Returns the minimal mapping cost L - as determined by method "infer" - if
minimize_mapping_cost is set to true.
- getMinimalSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
-
- getMinimalSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getMinimalTreeHeight() - Method in class org.forester.sdi.SDIR
-
Returns the minimal tree height - as determined by method "infer" - if
minimize_height is set to true.
- getMinimumDescendentsPerInternalNodes(Phylogeny) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- getMinimumHelixAngle() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMinimumHelixRise() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMinimumSequenceLength() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMinimumSequenceLengthFraction() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getMinimumSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- getMinimumValence() - Method in enum org.biojava.nbio.structure.Element
-
Returns the minimum valence for this Element.
- getMinLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getMinMax(double[]) - Method in class org.biojava.nbio.structure.contact.BoundingBox
-
Returns an array of size 2 with min and max values of given double array
- getMinRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMinScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getMinScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getMinScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getMinScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getMinScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getMinScore() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns minimum possible score.
- getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getMinSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getMinTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getMinValue() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getMinValue() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getMinValue() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns the minimum value in this matrix.
- getMirrors() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getMisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMisLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getMisScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getMMcifConsumer() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getMod_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getModDate() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getModel(int) - Method in class org.biojava.nbio.ronn.ModelLoader
-
- getModel(int) - Method in interface org.biojava.nbio.structure.Structure
-
Retrieve all Chains belonging to a model .
- getModel(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
retrieve all Chains belonging to a model .
- getModel() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the model property.
- getModel_Cartn_x() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getModel_Cartn_y() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getModel_Cartn_z() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getModelledSubgroup() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Gets the value of the modelledSubgroup property.
- getModelNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getModelNumber() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
-
- getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getModelVariables() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
-
- getModelVariables() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- getModification() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- getModification() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- getModType() - Method in class org.biojava.nbio.phosphosite.Site
-
- getMogAngleOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the mogAngleOutlier property.
- getMogBondOutlier() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the mogBondOutlier property.
- getMogulIgnore() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the mogulIgnore property.
- getMolecularSequence() - Method in class org.forester.phylogeny.data.Sequence
-
- getMolecularSequence() - Method in class org.forester.sequence.BasicSequence
-
- getMolecularSequence() - Method in interface org.forester.sequence.Sequence
-
- getMolecularWeight(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeight(ProteinSequence, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeight(ProteinSequence, File, File) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeight(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the molecular weight of sequence.
- getMolecularWeight(String, File, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the molecular weight of sequence.
- getMolecularWeight(String, File) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the molecular weight of sequence.
- getMolecularWeight(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecularWeight(ProteinSequence, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecularWeight(ProteinSequence, File, File) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecularWeight(Character) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getMolecularWeight() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getMolecularWeight() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the molecular weight of sequence.
- getMolecularWeightBasedOnXML(String, AminoAcidCompositionTable) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method that returns the molecular weight of sequence.
- getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getMolecule() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getMoleculeIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getMolecules() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getMolId() - Method in class org.biojava.nbio.structure.Compound
-
Return the molecule identifier, called entity_id in mmCIF dictionary.
- getMolName() - Method in class org.biojava.nbio.structure.Compound
-
- getMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getMon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getMon_nstd_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getMon_nstd_parent_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getMostPromiscuosDomain() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- getMostPromiscuosDomain() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
- getMsa() - Method in class org.forester.archaeopteryx.MainFrameApplication
-
- getMsaFile() - Method in class org.forester.archaeopteryx.MainFrameApplication
-
- getMsaPrg() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getMsaPrgParameters() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getMsaProcessingMaxAllowedGapRatio() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getMsaProcessingMinAllowedLength() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getMTranspose() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- getMultipleSequenceAlignment(List<S>, Object...) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a multiple sequence alignment for the given
List of
Sequences.
- getMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getMutation() - Method in class org.biojava.nbio.structure.Compound
-
- getN() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get N atom.
- getN() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get N atom.
- getN() - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- getN() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
-
- getN() - Method in class org.forester.sdi.DistanceCalculator
-
Returns the sum of all Nodes used to calculate the mean.
- getN() - Method in interface org.forester.surfacing.DomainSimilarity
-
This should return the number of pairwise distances used to calculate
this similarity score
- getN() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getN() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getN() - Method in interface org.forester.util.DescriptiveStatistics
-
- getNaive_imat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getNaiveVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- getName() - Method in class org.biojava.nbio.aaproperties.xml.Name2Count
-
- getName() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getName() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getName() - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getName() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the name of this node.
- getName() - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns the name (short description) of this matrix.
- getName() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
-
- getName() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable
-
- getName() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getName() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getName() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return the name of this ontology
- getName() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.Synonym
-
- getName() - Method in interface org.biojava.nbio.ontology.Term
-
Return the name of this term.
- getName() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getName() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getName() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
- getName() - Method in interface org.biojava.nbio.structure.Atom
-
Get atom name, e.g.
- getName() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get atom name, e.g.
- getName() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getName() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique
-
- getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getName() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBMacromolecule
-
- getName() - Method in class org.biojava.nbio.structure.rcsb.RCSBTaxonomy
-
- getName() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getName() - Method in interface org.biojava.nbio.structure.Structure
-
Get biological name of Structure.
- getName() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getName() - Method in class org.biojava.nbio.structure.validation.Program
-
Gets the value of the name property.
- getName() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
- getName() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getName() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getName() - Method in class org.forester.archaeopteryx.tools.ProcessRunning
-
- getName() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getName() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
The name of the webservice.
- getName() - Method in class org.forester.go.BasicGoTerm
-
- getName() - Method in interface org.forester.go.GoTerm
-
- getName() - Method in class org.forester.phylogeny.data.ProteinDomain
-
- getName() - Method in class org.forester.phylogeny.data.Sequence
-
- getName() - Method in class org.forester.phylogeny.Phylogeny
-
Returns the name of this Phylogeny.
- getName() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns the name of this node.
- getName() - Method in interface org.forester.phylogeny.PhylogenyNodeI
-
- getName() - Method in class org.forester.protein.BasicProtein
-
- getName() - Method in interface org.forester.protein.Protein
-
- getName(int) - Method in class org.forester.util.CommandLineArguments
-
- getName1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getName1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getName1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getName2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getName2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getName2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getNames() - Method in class org.biojava.nbio.structure.scop.Astral
-
- getNames() - Method in class org.forester.util.CommandLineArguments
-
- getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getNatomsEDS() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the natomsEDS property.
- getNaturalPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getNavMap() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
- getNcbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getNcens() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNChar() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
-
- getNclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- getNcsOperators() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Get the NCS operators.
- getNcuts() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getNdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getNdead() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNdom() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getNearestAtRisk(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
Selection of number of risk will depend on the precision and rounding of
time in the survival table.
- getNearestTime(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
Need to find the actual time for the nearest time represented as a
percentage Would be used to then look up the number at risk at that
particular time
- getNeighborIndices(int) - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- getNeighborIndices(int) - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- getNeighbors(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
- getNeighborsWithCache(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
-
- getNestedValue(NestedValue, String, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getNetCharge(ProteinSequence, boolean, double) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
Returns the net charge of sequence at pH 7.
- getNetCharge(ProteinSequence, boolean) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
- getNetCharge(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.IPeptideProperties
-
- getNetCharge(String, boolean, double) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
An adaptor method to return the net charge of sequence at pH 7.
- getNetCharge(String, boolean) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
- getNetCharge(String) - Static method in class org.biojava.nbio.aaproperties.PeptideProperties
-
- getNetCharge(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getNetCharge(ProteinSequence, boolean) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getNetCharge(ProteinSequence, boolean, double) - Method in class org.biojava.nbio.aaproperties.PeptidePropertiesImpl
-
- getNetGainsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getNeutronsNum() - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- getNevent() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNewDocument() - Static method in class org.biojava.nbio.core.util.XMLHelper
-
- getNewickString(boolean, boolean) - Method in class org.biojava.nbio.phylo.TreeConstructor
-
- getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
-
- getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
-
- getNextExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns a refernce to the next external PhylogenyNode of this
PhylogenyNode.
- getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getNode() - Method in class org.forester.phylogeny.iterators.PostOrderStackObject
-
- getNode(int) - Method in class org.forester.phylogeny.Phylogeny
-
Finds the PhylogenyNode of this Phylogeny which has a matching ID number.
- getNode(String) - Method in class org.forester.phylogeny.Phylogeny
-
Returns a PhylogenyNode of this Phylogeny which has a matching name.
- getNodeCount() - Method in class org.forester.phylogeny.Phylogeny
-
This is time-inefficient since it runs a iterator each time it is called.
- getNodeCount() - Static method in class org.forester.phylogeny.PhylogenyNode
-
Returns the total number of all Nodes created so far.
- getNodeData() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getNodeDistance(PhylogenyNode, PhylogenyNode) - Method in class org.biojava.nbio.phylo.CheckTreeAccuracy
-
- getNodeField() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getNodeField() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
The node data field in which to place node names from simple unannotated formats
(such as Newick).
- getNodeId() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getNodeIdentifier() - Method in class org.forester.phylogeny.data.NodeData
-
- getNodeListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getNodeName() - Method in class org.forester.phylogeny.data.NodeData
-
- getNodes(String) - Method in class org.forester.phylogeny.Phylogeny
-
Returns a List with references to all Nodes of this Phylogeny which have
a matching name.
- getNodesViaSequenceName(String) - Method in class org.forester.phylogeny.Phylogeny
-
- getNodesViaTaxonomyCode(String) - Method in class org.forester.phylogeny.Phylogeny
-
- getNodesWithMatchingSpecies(String) - Method in class org.forester.phylogeny.Phylogeny
-
Returns a Vector with references to all Nodes of this Phylogeny which
have a matching species name.
- getNodeViaSequenceName(String) - Method in class org.forester.phylogeny.Phylogeny
-
- getNodeViaTaxonomyCode(String) - Method in class org.forester.phylogeny.Phylogeny
-
- getNodeVisualizations() - Method in class org.forester.phylogeny.data.NodeData
-
- getNoiseCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
Not always 2.
It may undergo further change.
- getNonenantpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getNormAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.BranchCountingBasedScoringMethod
-
- getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.BranchLengthBasedScoringMethod
-
- getNormalizationFactor(Phylogeny) - Method in class org.forester.pccx.LogBranchLengthBasedScoringMethod
-
- getNormalizationFactor(Phylogeny) - Method in interface org.forester.pccx.ScoringMethodForExternalNode
-
This calculates a normalization factor, so that a normalized score of 1.0
means complete coverage.
- getNotesList() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getNotObserved() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getNParents() - Method in class org.forester.go.etc.OntologizerResult
-
- getNrAlignments() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getNrAtoms(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Count how many number of Atoms are contained within a Structure object.
- getNrBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader
-
Get the number of biological assemblies available in the PDB header
- getNrBiolAssemblies(String) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
-
Returns the number of available biological assemblies.
- getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- getNrBiolAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
-
- getNrBiolAssemblies() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
-
Returns the number of available biological assemblies.
- getNrBiolAssemblies(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
-
- getNrBiolAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getNrBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
- getNrCPU() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getNreported() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getNrEQR() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Get the number of structurally equivalent residues
- getNrGroups(Structure) - Static method in class org.biojava.nbio.structure.StructureTools
-
Count how many groups are contained within a structure object.
- getNrisk() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getNseg() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getnStart() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getNStart() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
Returns the number of starts if this rotation represents a helical rotation
- getNTax() - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
-
- getNuc4_2() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Nuc 4.2 matrix by Lowe
Only the first nucleotide sequence to align can contain ambiguous nucleotides
- getNuc4_4() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns Nuc 4.4 matrix by Lowe
Both of the nucleotide sequences to align can contain ambiguous nucleotides
- getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
-
- getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
-
- getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
-
- getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getNucleicAcidChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getNullValue() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getNum() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- getNumAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getNumber() - Method in class org.forester.protein.BasicDomain
-
- getNumber() - Method in interface org.forester.protein.Domain
-
- getNumber() - Method in class org.forester.surfacing.SimpleDomain
-
- getNumberCoefficients() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getNumberDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
-
- getNumberOfBranches() - Method in class org.forester.phylogeny.Phylogeny
-
- getNumberOfCharacters() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getNumberOfCharacters() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getNumberOfChildElements() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getNumberOfColumns() - Method in class org.forester.util.BasicTable
-
- getNumberOfCombinableDomains() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getNumberOfCombinableDomains() - Method in interface org.forester.surfacing.CombinableDomains
-
- getNumberOfConfidences() - Method in class org.forester.phylogeny.data.BranchData
-
- getNumberOfDescendants() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getNumberOfDifferentDomains() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
-
- getNumberOfDomains() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getNumberOfDomains() - Method in class org.forester.phylogeny.data.DomainArchitecture
-
- getNumberOfDuplications() - Method in class org.forester.phylogeny.data.Event
-
- getNumberOfExternalNodes() - Method in class org.forester.phylogeny.Phylogeny
-
Returns the sum of external Nodes of this Phylogeny (int).
- getNumberOfExternalNodes() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns the total number of external Nodes originating from this
PhylogenyNode (int).
- getNumberOfGapResidues() - Method in class org.forester.sequence.BasicSequence
-
- getNumberOfGapResidues() - Method in interface org.forester.sequence.Sequence
-
- getNumberOfGeneLosses() - Method in class org.forester.phylogeny.data.Event
-
- getNumberOfGoIds() - Method in class org.forester.protein.BasicDomain
-
- getNumberOfGoIds() - Method in interface org.forester.protein.Domain
-
- getNumberOfGoIds() - Method in class org.forester.protein.DomainId
-
- getNumberOfGoIds() - Method in class org.forester.surfacing.SimpleDomain
-
- getNumberOfIdentifiers() - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getNumberOfIdentifiers() - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getNumberOfInvalidChar(String, Set<Character>, boolean) - Static method in class org.biojava.nbio.aaproperties.Utils
-
Return the number of invalid characters in sequence.
- getNumberOfNames() - Method in class org.forester.util.CommandLineArguments
-
- getNumberOfNodesLackingName(Phylogeny, StringBuilder) - Static method in class org.forester.surfacing.SurfacingUtil
-
- getNumberOfParents() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getNumberOfProteinDomains() - Method in class org.forester.protein.BasicProtein
-
- getNumberOfProteinDomains() - Method in interface org.forester.protein.Protein
-
- getNumberOfProteinsExhibitingCombination(DomainId) - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getNumberOfProteinsExhibitingCombination(DomainId) - Method in interface org.forester.surfacing.CombinableDomains
-
- getNumberOfRows() - Method in class org.forester.util.BasicTable
-
- getNumberOfSameDomains() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
-
- getNumberOfSequences() - Method in class org.forester.msa.BasicMsa
-
- getNumberOfSequences() - Method in interface org.forester.msa.Msa
-
- getNumberOfSpeciations() - Method in class org.forester.phylogeny.data.Event
-
- getNumberVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getNumericalBondOrder() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
Converts this ChemCompBond's value_order attribute into an int using the
conversion:
- getNumericRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
-
- getNumFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the numFreeReflections property.
- getNumGaps() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getNumGaps() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
Returns number of gaps in the sequence.
- getNumHReduce() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the numHReduce property.
- getNumHReduce() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the numHReduce property.
- getNumIdenticals() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getNumIdenticals() - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the number of indices for which both the query and target sequences have an identical
Compound.
- getNumIindices() - Method in class org.biojava.nbio.structure.contact.GridCell
-
- getNumJindices() - Method in class org.biojava.nbio.structure.contact.GridCell
-
- getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
-
- getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
-
- getNumMillerIndices() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the numMillerIndices property.
- getNumobs() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the numobs property.
- getNumobs() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the numobs property.
- getNumOperators() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the number of symmetry operators corresponding to this SpaceGroup (counting
the identity operator)
- getNumRes() - Method in class org.biojava.nbio.structure.Compound
-
- getNumSequences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getNumSimilars() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getNumSimilars() - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
Returns the number of indices for which both the query and target sequences have a similar
Compound.
- getO() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get O atom.
- getO() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get O atom.
- getO() - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- getO3Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
Returns the O3' atom if present, otherwise null
- getO5Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
Returns the O5' atom if present, otherwise null
- getObject() - Method in interface org.biojava.nbio.ontology.Triple
-
Return the object term of this triple.
- getObject() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getOboFileEventListener() - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getObs() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the obs property.
- getObs() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the obs property.
- getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns how this instance deals with obsolete entries.
- getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getObsoleteBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Returns how this instance deals with obsolete entries.
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Location of obsolete files within the directory, as an array of paths.
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getObsval() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the obsval property.
- getObsval() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the obsval property.
- getOccupancy() - Method in interface org.biojava.nbio.structure.Atom
-
Get occupancy.
- getOccupancy() - Method in class org.biojava.nbio.structure.AtomImpl
-
- getOccupancy() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_esd() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_max() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOccupancy_min() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOccurrenceType() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getOccurrenceType() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getOffset() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getOligomeric_count() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getOligomeric_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- getOmega() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getOmimId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getOne() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- getOne() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getOne_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
-
- getOneLetterCode(ChemComp) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- getOnelineFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
- getOntology() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getOntology() - Method in interface org.biojava.nbio.ontology.OntologyTerm
-
Get the remote ontology referenced by this term
- getOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getOntology() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getOntology() - Method in interface org.biojava.nbio.ontology.Term
-
Return the ontology in which this term exists.
- getOntology() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getOntology() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getOpenPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getOpenPenalty() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
Returns the negative of the opening penalty passed to the constructor.
- getOpenPenalty() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
Returns penalty given when a deletion or insertion gap first opens
- getOper_expression() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- getOperator() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- getOps() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getOps() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return the associated OntologyOps.
- getOps() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getOptAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Tracks the Atom positions in the optimal alignment.
- getOptAlnAsList(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Retrieves the optimum alignment from an AFPChain and returns it as a
java collection.
- getOptions() - Method in class org.forester.archaeopteryx.ArchaeopteryxE
-
- getOptions() - Method in class org.forester.archaeopteryx.MainFrame
-
- getOptions() - Method in class org.forester.archaeopteryx.MainPanel
-
- getOptionValue(String) - Method in class org.forester.util.CommandLineArguments
-
- getOptionValueAsCleanString(String) - Method in class org.forester.util.CommandLineArguments
-
Removes quotes
- getOptionValueAsDouble(String) - Method in class org.forester.util.CommandLineArguments
-
- getOptionValueAsInt(String) - Method in class org.forester.util.CommandLineArguments
-
- getOptionValueAsLong(String) - Method in class org.forester.util.CommandLineArguments
-
- getOptLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The length of each block
- getOptLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getOptRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getOrbits() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getOrder(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getOrder() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getOrder(int) - Static method in class org.forester.sdi.RIO
-
Returns the order in which ortholog (o), "super ortholog" (s) and
distance (d) are returned and sorted (priority of sort always goes from
left to right), given sort.
- getOrderedPairs() - Method in class org.biojava.nbio.structure.quaternary.CartesianProduct
-
Generates the list of ordered pair between two sets.
- getOrderHelp() - Static method in class org.forester.sdi.RIO
-
- getOrgan() - Method in class org.biojava.nbio.structure.Compound
-
- getOrganelle() - Method in class org.biojava.nbio.structure.Compound
-
- getOrganism() - Method in class org.biojava.nbio.phosphosite.Site
-
- getOrganism_common_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getOrganism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getOrganismCommon() - Method in class org.biojava.nbio.structure.Compound
-
- getOrganismName() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Get the organism name assigned to this sequence
- getOrganismScientific() - Method in class org.biojava.nbio.structure.Compound
-
- getOrganismTaxId() - Method in class org.biojava.nbio.structure.Compound
-
- getOrientation() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that sets a specific orientation
- getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getOrientation(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns the number of orientations available for this structure
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getOrientationCount() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns the name of a specific orientation
- getOrientationName(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script that sets a specific orientation and zoom
to draw either axes or polyhedron
- getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script that sets a specific orientation and zoom
to draw either axes or polyhedron
- getOrientationWithZoom(int) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getOriginal() - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- getOriginalCenters() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getOriginalHeader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getOriginalMetaData(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getOriginalModificationId() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
Deprecated.
use getModification().getId()
- getOriginalSequence() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getOriginalSequence() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
Returns the original
Sequence before alignment.
- getOriginalSequences() - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getOriginalSequences() - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns a
List containing the original
Sequences used for alignment.
- getOriginalSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getOriginalSize() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
-
- getOriginalSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- getORmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Get the Original RMSD threshold from which the alignment optimization is started
- getOrthologousNodes(Phylogeny, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyMethods
-
Returns all orthologs of the external PhylogenyNode n of this Phylogeny.
- getOrthologousSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getOrthologs() - Method in class org.forester.sdi.RIOn
-
- getOther(Atom) - Method in class org.biojava.nbio.structure.Bond
-
A utility method to get the other atom in a bond, given one of its atoms.
- getOtherTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Deprecated.
- getOutFile() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getOutFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getOutFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getOutFileLocation() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getOutputOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- getOutputOption(BlastOutputParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Gets the value of specified parameter or null if it is not set
- getOutputOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
-
Method that returns the value associated with the key given in parameter.
- getOutputOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Gets output parameters, which are currently set
- getOutputOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
-
Method to get all keys to the information stored in this object.
- getOutputStream() - Method in class org.forester.util.ExternalProgram
-
- getOverall_FOM_free_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_FOM_work_R_set() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_B() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_ML() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getOverallModelFitPvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getOverlapCount() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getOverlapCount() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
Returns the maximum number of elements contributed to a column of an alignment by this
Sequence.
- getOverlapLength(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
Get the overlap between two HmmerResult objects
- getOwab() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the owab property.
- getOxidationState() - Method in enum org.biojava.nbio.structure.Element
-
Returns a typical oxidation state for this Element.
- getP() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
Returns the P atom if present, otherwise null
- getP() - Method in class org.forester.go.etc.OntologizerResult
-
- getP1() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getP2() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getPAdjusted() - Method in class org.forester.go.etc.OntologizerResult
-
- getPair() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getPair() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getPair() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceAligner
-
Returns sequence alignment pair.
- getPair() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileAligner
-
Returns alignment profile pair.
- getPair() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- getPair() - Method in class org.biojava.nbio.structure.contact.AtomContact
-
- getPair() - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- getPairInProfileScorer() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getPairInProfileScorer() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner
-
Returns class type of pairwise scoring subroutine.
- getPairs() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- getPairwiseAligner(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which constructs a pairwise sequence aligner.
- getPairwiseAlignment(S, S, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method which computes a sequence alignment for the given
Sequence pair.
- getPairwiseAlignment(SequenceAlignmentCluster) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getPairwiseScore(String, String) - Method in class org.biojava.nbio.phylo.ScoreMatrix
-
- getPairwiseScore(char, char) - Method in class org.biojava.nbio.phylo.ScoreMatrix
-
- getPaletteDescription() - Method in enum org.jcolorbrewer.ColorBrewer
-
- getPAM250() - Static method in class org.biojava.nbio.alignment.SubstitutionMatrixHelper
-
Returns PAM 250 matrix by Dayhoff
- getPAM250(String, String) - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getPAM250(char, char) - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
- getPanelPos(int, int) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
get the position of the sequence position on the Panel
- getPanelPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
-
- getPara(int, int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
-
- getParalogousNodes(PhylogenyNode, String[]) - Method in class org.forester.phylogeny.Phylogeny
-
Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
- getParalogs() - Method in class org.forester.sdi.RIOn
-
- getParameter() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getParameter() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
-
- getParameter() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- getParameters() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
-
- getParameters() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
- getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getParameters() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Return the paramers for this algorithm.
- getParameters() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
-
- getParams() - Method in class org.biojava.nbio.structure.align.FarmJob
-
- getParams() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
get the parameters.
- getParent() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getParent() - Method in interface org.biojava.nbio.structure.Chain
-
Returns the parent Structure of this chain.
- getParent() - Method in class org.biojava.nbio.structure.ChainImpl
-
Returns the parent Structure of this chain.
- getParent() - Method in class org.biojava.nbio.structure.DBRef
-
Get the structure object that this DBRef relates to.
- getParent(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
Get the parent of a component.
- getParent() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getParent() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns a refernce to the parent PhylogenyNode of this PhylogenyNode.
- getParentChromosomeSequence() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
The parent ChromosomeSequence which contains the actual DNA sequence data
- getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Get the parent Feature
- getParentFeature() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getParentFeature() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the parent feature
- getParentId() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getParentPlateRenderer() - Method in class org.forester.development.ResidueRenderer
-
- getParentSequence() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getParentSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- getPartner() - Method in class org.biojava.nbio.structure.secstruc.HBond
-
- getPath() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getPath() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPath() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getPath() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Get the path that is used to cache PDB files.
- getPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Returns the path value.
- getPathSize() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getPathSize() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getPathToClustalOmega() - Method in class org.forester.archaeopteryx.Configuration
-
- getPathToFastME() - Method in class org.forester.archaeopteryx.Configuration
-
- getPathToMafft() - Method in class org.forester.archaeopteryx.Configuration
-
- getPaulingElectronegativity() - Method in enum org.biojava.nbio.structure.Element
-
Returns the Pauling electronegativity for this Element.
- getPdb1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getPdb1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getPdb2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getPdb2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_mon_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdbAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
used temporarily during XML serialization to track the PDB positions of the alignmnet
- getPdbccId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPdbccId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPdbccIds() - Method in class org.biojava.nbio.protmod.Component
-
- getPdbccName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPdbccName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPdbChainIdClusters() - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getPdbChainIdClusters(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getPDBCharacter(boolean, char, char, boolean, char) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates formatted String for a single character of PDB output
- getPDBCode() - Method in interface org.biojava.nbio.structure.Structure
-
Get PDB code of structure.
- getPDBCode() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPDBCode1() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getPDBCode2() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getPDBConservation(boolean, char, char, boolean) - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates formatted String for displaying conservation in PDB output
- getPDBDirField() - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
-
- getPdbEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getPdbFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getPdbFilePath() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getPdbFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- getPDBHeader() - Method in interface org.biojava.nbio.structure.Structure
-
Return the header information for this PDB file
- getPDBHeader() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName
-
PDB IDs are always returned as upper case
- getPdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getPdbId() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
-
- getPdbId() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigands
-
- getPdbId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getPdbId() - Method in interface org.biojava.nbio.structure.StructureIdentifier
-
Returns the PDB identifier associated with this StructureIdentifier.
- getPdbId() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getPdbId() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
-
- getPdbIdAndChain() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
Returns a string of the form PDBID.CHAIN.
- getPdbInfo(Atom) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
-
get jmol style info:
jmol style: [MET]508:A.CA/1 #3918
insertion code: [ASP]1^A:A.CA/1 #2
- getPdbInfo(Atom, boolean) - Static method in class org.biojava.nbio.structure.align.gui.jmol.JmolTools
-
- getPDBLegend() - Static method in class org.biojava.nbio.core.sequence.io.util.IOUtils
-
Creates formatted String for displaying conservation legend in PDB output
- getPDBName() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getPDBName() - Method in interface org.biojava.nbio.structure.Group
-
Get the PDB 3-letter name for this group.
- getPDBName() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Returns the PDBName.
- getPDBNameOfPotentialAtomsOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getPDBNameOfPotentialAtomsOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage
-
- getPdbPairs(String, int, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getPDBResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getPdbResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getPDBresnum(int, AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
- getPdbResNum() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getPDBresnum1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPDBresnum2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPDBRevisionNumber() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the pdbRevisionNumber property.
- getPDBserial() - Method in interface org.biojava.nbio.structure.Atom
-
Get PDB atom number.
- getPDBserial() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get PDB atom number.
- getPdbSerial() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- getPdbStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getPDBUploadPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getPdbx_align() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_align_begin() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getPdbx_alt_source_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_ambiguous_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_aromatic_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getPdbx_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_auth_seq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_auth_seq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_beg_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_blank_PDB_chainid_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getPdbx_CASP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_component_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_component_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_component_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_data_cutoff_high_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_high_rms_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_low_absF() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getPdbx_db_accession() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_description() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_descriptor() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_diffrn_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_dist_value() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ec() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_end_seq_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getPdbx_formal_charge() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_full_space_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getPdbx_gene_src_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_fragment() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_plasmid() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_gene_src_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_atcc() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_cell() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_cell_line() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_cellular_location() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_culture_collection() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_gene() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_scientific_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_strain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_tissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_tissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_vector() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_host_org_vector_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_ideal_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_ideal_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_initial_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_isotropic_thermal_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_keywords() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_leaving_atom_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ls_cross_valid_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_F() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_I() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_method_to_determine_struct() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_model_Cartn_x_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_model_Cartn_y_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_model_Cartn_z_ideal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_model_coordinates_db_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_missing_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_model_type_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getPdbx_modified() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- getPdbx_modified_date() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_mutation() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_ncbi_taxonomy_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_number_of_molecules() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_ordinal() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getPdbx_organ() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_organelle() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_organism_scientific() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_overall_ESU_R() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_ESU_R_Free() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_phase_error() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_SU_R_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_SU_R_free_Blow_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_SU_R_free_Cruickshank_DPI() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_PDB_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_PDB_id_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getPdbx_PDB_model_num() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getPdbx_plasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_plasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_polymer_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_processing_site() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_ptnr1_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr1_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr1_standard_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr2_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr2_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_alt_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_ptnr3_PDB_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_R_Free_selection_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_ref_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_refine_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_release_status() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaced_by() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_residue_numbering() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_secretion() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_seq_align_beg_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_align_end_ins_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_one_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- getPdbx_seq_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_solvent_ion_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_shrinkage_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_vdw_probe_radii() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPdbx_src_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbx_starting_model() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getPdbx_stereo_config() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getPdbx_stereochem_target_val_spec_case() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_stereochemistry_target_values() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_strand_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_subcomponent_list() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_synonyms() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_TLS_residual_ADP_flag() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getPdbx_type() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPdbx_unique_axis() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getPdbx_value_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPdbx_variant() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
-
- getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getPdbxStructAssemblies() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
-
Data access method for list describing all assemblies
- getPdbxStructAssemblies() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getPdbxStructAssembly(int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getPdbxStructAssembly(int) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
-
get the data for a particular pdbxStructAssembly.
- getPdbxStructAssembly(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getPdbxStructAssemblyGen(int) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getPdbxStructAssemblyGen(int) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
-
get the data for a particular pdbxStructAssemblyGen.
- getPdbxStructAssemblyGen(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
-
- getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getPdbxStructAssemblyGens() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
-
Data access method for list describing all assemblies
- getPdbxStructAssemblyGens() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getPdbxStructOperList() - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- getPdbxStructOperList() - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
-
Get all the possible operators
- getPdbxStructOperList() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getPdbxStructOperLists() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
-
- getPDPDomainNamesForPDB(String) - Method in interface org.biojava.nbio.structure.domain.PDPProvider
-
- getPDPDomainNamesForPDB(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
- getPdpprovider() - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getPenultimateGoTerm(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
-
- getPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- getPercentFreeReflections() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentFreeReflections property.
- getPercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentRamaOutliers property.
- getPercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentRotaOutliers property.
- getPercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the percentRSRZOutliers property.
- getPercId() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getPerDomainEvalue() - Method in class org.forester.protein.BasicDomain
-
- getPerDomainEvalue() - Method in interface org.forester.protein.Domain
-
- getPerDomainEvalue() - Method in class org.forester.surfacing.SimpleDomain
-
- getPerDomainScore() - Method in class org.forester.protein.BasicDomain
-
- getPerDomainScore() - Method in interface org.forester.protein.Domain
-
- getPerDomainScore() - Method in class org.forester.surfacing.SimpleDomain
-
- getPerGenomeDomainPromiscuityStatistics() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- getPerGenomeDomainPromiscuityStatistics() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
This should return a statistic for per domain
promiscuity in a genome.
- getPeriod() - Method in enum org.biojava.nbio.structure.Element
-
Returns the period in the periodic table of this Element.
- getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getPermutation(int) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
-
- getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getPermutationSize() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getPerSequenceEvalue() - Method in class org.forester.protein.BasicDomain
-
- getPerSequenceEvalue() - Method in interface org.forester.protein.Domain
-
- getPerSequenceEvalue() - Method in class org.forester.surfacing.SimpleDomain
-
- getPerSequenceScore() - Method in class org.forester.protein.BasicDomain
-
- getPerSequenceScore() - Method in interface org.forester.protein.Domain
-
- getPerSequenceScore() - Method in class org.forester.surfacing.SimpleDomain
-
- getPfamAccession() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getPhase() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
- getPhase() - Method in class org.forester.phylogeny.iterators.PostOrderStackObject
-
- getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the phi angle.
- getPhi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getPhi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the phi property.
- getPhylogeneticInferenceOptions() - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog
-
- getPhylogeny() - Method in class org.forester.archaeopteryx.TreePanel
-
Get a pointer to the phylogeny
- getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return pivot permutation vector
- getPlasmid_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPlasmid_name() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getPmid() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of PMID field.
- getPMin() - Method in class org.forester.go.etc.OntologizerResult
-
- getPointGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getPoints() - Method in class org.forester.phylogeny.data.Distribution
-
- getPoints() - Method in class org.forester.phylogeny.data.Polygon
-
- getPolygons() - Method in class org.forester.phylogeny.data.Distribution
-
- getPolygonVertices(int, double, Point3d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the vertices of an n-fold polygon of given radius and center
- getPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getPolymers() - Method in class org.biojava.nbio.structure.rcsb.RCSBDescription
-
- getPolymerType() - Method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
-
Gets the associated PolymerType, which are less specific
- getPolymerType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getPopFamily() - Method in class org.forester.go.etc.OntologizerResult
-
- getPopTerm() - Method in class org.forester.go.etc.OntologizerResult
-
- getPopTotal() - Method in class org.forester.go.etc.OntologizerResult
-
- getPos(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getPos1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getPos1() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getPos2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getPos2() - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- getPosition() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getPosition() - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- getPosition() - Method in interface org.biojava.nbio.core.sequence.location.template.Point
-
Returns the position held by this object
- getPosition(ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Gets the 0-based index of residueNumber to the matched atoms
- getPositionInQueue(String, String, String, String) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getPositionInQueue(String, String, String, String, int) - Method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getPreciseDistance(Atom, Atom) - Static method in class org.biojava.nbio.structure.secstruc.SecStruc
-
calculate distance between two atoms.
- getPredicate() - Method in interface org.biojava.nbio.ontology.Triple
-
Return a Term which defines the type of relationship between the subject and object terms.
- getPredicate() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getPredominantGroupType(Chain) - Static method in class org.biojava.nbio.structure.StructureTools
-
Get the predominant
GroupType for a given Chain, following these rules:
if the ratio of number of residues of a certain
GroupType to total
non-water residues is above the threshold
0.95, then that
GroupType is returned
if there is no
GroupType that is above the threshold then the
GroupType
with most members is chosen, logging it
- getPreferredHeight() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Y coordinate size
- getPreferredSize() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- getPreferredSize() - Method in class org.forester.development.MsaRenderer
-
- getPreferredWidth() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
X coordinate size
- getPresentCharacters() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getPresentCharactersAsStringArray() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getPresentCharactersAsStringBuffer() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getPresentCount() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getPreviousExternalNode() - Method in class org.forester.phylogeny.PhylogenyNode
-
Returns a refernce to the next external PhylogenyNode of this
PhylogenyNode.
- getPreviousIDs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getPreviousNames() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getPreviousSymbols() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getPrincipalAxes() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getPrintableNameByType(SequenceRelation.SEQUENCE_RELATION_TYPE) - Static method in class org.forester.phylogeny.data.SequenceRelation
-
- getPrintMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getProbability() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The probability (FATCAT) or Z-score (CE) of the alignment.
- getProcessById(long) - Method in class org.forester.archaeopteryx.tools.ProcessPool
-
- getProcessByIndex(int) - Method in class org.forester.archaeopteryx.tools.ProcessPool
-
- getProcessingInstructions() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getProcessingInstructions() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
This is used to indicate any kind of special processing.
- getProcessPool() - Method in class org.forester.archaeopteryx.MainFrame
-
- getProfile() - Method in class org.biojava.nbio.alignment.FractionalIdentityInProfileScorer
-
- getProfile() - Method in class org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer
-
- getProfile() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getProfile() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getProfile() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getProfile() - Method in interface org.biojava.nbio.alignment.template.Aligner
-
Returns the alignment
Profile produced by this alignment algorithm.
- getProfile() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the profile stored at this node.
- getProfile() - Method in interface org.biojava.nbio.alignment.template.PairInProfileScorer
-
Returns the
Profile from which the aligned pair originated.
- getProfileFuture() - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- getProfileFuture() - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Returns the profile future stored at this node, but does not force the calculation, yet.
- getProfileProfileAligner() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.PartitionRefiner
-
Returns class type of profile-profile alignment subroutine.
- getProfileProfileAligner() - Method in interface org.biojava.nbio.alignment.template.RescoreRefiner
-
Returns class type of profile-profile alignment subroutine.
- getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getProgram() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getProgram() - Method in class org.biojava.nbio.structure.validation.Programs
-
Gets the value of the program property.
- getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getProgram_version() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getPrograms() - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Gets the value of the programs property.
- getProgressiveAlignment(GuideTree<S, C>, Alignments.ProfileProfileAlignerType, GapPenalty, SubstitutionMatrix<C>) - Static method in class org.biojava.nbio.alignment.Alignments
-
Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.
- getProjectedDistance(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the distance from a point to the axis of rotation
- getProjectedPoint(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Projects a given point onto the axis of rotation
- getProperties() - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
Get the properties
- getProperties() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
Implement this to return the Map delegate.
- getProperties() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation
-
- getProperties() - Method in interface org.biojava.nbio.structure.Group
-
return properties.
- getProperties() - Method in class org.biojava.nbio.structure.HetatomImpl
-
return properties.
- getProperties() - Method in class org.biojava.nbio.structure.validation.Program
-
Gets the value of the properties property.
- getProperties() - Method in class org.forester.phylogeny.data.Annotation
-
- getProperties() - Method in class org.forester.phylogeny.data.NodeData
-
- getProperties() - Method in class org.forester.phylogeny.data.PropertiesMap
-
- getPropertiesArray() - Method in class org.forester.phylogeny.data.PropertiesMap
-
- getPropertiesWithGivenReferencePrefix(String) - Method in class org.forester.phylogeny.data.PropertiesMap
-
- getProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
- getProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
-
Retrieve the value of a property by key.
- getProperty(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- getProperty(String) - Method in interface org.biojava.nbio.structure.Group
-
get a single property .
- getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl
-
get a single property .
- getProperty(String) - Method in class org.forester.phylogeny.data.PropertiesMap
-
- getPropertyRefs() - Method in class org.forester.phylogeny.data.PropertiesMap
-
Returns all property refs of this PhylogenyNode as String array.
- getProtein() - Method in class org.biojava.nbio.phosphosite.Site
-
- getProteinCDSSequences() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Return a list of protein sequences based on each CDS sequence
where the phase shift between two CDS sequences is assigned to the
CDS sequence that starts the triplet.
- getProteinChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
-
- getProteinChainCount() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
-
- getProteinDomain(int) - Method in class org.forester.protein.BasicProtein
-
- getProteinDomain(int) - Method in interface org.forester.protein.Protein
-
- getProteinDomainCount(DomainId) - Method in class org.forester.protein.BasicProtein
-
- getProteinDomainCount(DomainId) - Method in interface org.forester.protein.Protein
-
- getProteinDomains() - Method in class org.forester.protein.BasicProtein
-
- getProteinDomains(DomainId) - Method in class org.forester.protein.BasicProtein
-
- getProteinDomains() - Method in interface org.forester.protein.Protein
-
- getProteinDomains(DomainId) - Method in interface org.forester.protein.Protein
-
- getProteinGraph() - Method in class org.biojava.nbio.structure.symmetry.core.SubunitGraph
-
- getProteinId() - Method in class org.forester.protein.BasicProtein
-
- getProteinId() - Method in interface org.forester.protein.Protein
-
- getProteinsEncountered() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getProteinsEncountered() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getProteinSequence() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the ProteinSequence from the RNA sequence
- getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get the ProteinSequene from the RNA sequence with user defined
transcription engine
- getProteinSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the protein sequence
- getProteinSequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
Get the protein sequence with user defined TranscriptEngine
- getProteinSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getProteinSequenceForStructure(Structure, Map<Integer, Group>) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
-
Generates a ProteinSequence corresponding to the sequence of struct,
and maintains a mapping from the sequence back to the original groups.
- getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
-
- getProteinSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
-
- getProteinsIgnoredDueToFilter() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getProteinsIgnoredDueToFilter() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getProteinsStored() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getProteinsStored() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getProvider() - Method in class org.forester.phylogeny.data.Identifier
-
- getProvider() - Method in class org.forester.ws.seqdb.EbiDbEntry
-
- getProvider() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry
-
- getProvider() - Method in class org.forester.ws.seqdb.UniProtEntry
-
- getProvider() - Method in class org.forester.ws.uniprot.EbiDbEntry
-
- getProvider() - Method in interface org.forester.ws.uniprot.SequenceDatabaseEntry
-
- getProvider() - Method in class org.forester.ws.uniprot.UniProtEntry
-
- getProxySequenceReader() - Method in interface org.biojava.nbio.core.sequence.location.template.AccesionedLocation
-
Return the proxy reader used to get sequence for this location.
- getProxySequenceReader() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getPseudoStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc
-
Calculate the psi angle.
- getPsi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getPsi() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the psi property.
- getPsimodId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPsimodId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPsimodName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getPsimodName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getPtnr1_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr1_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_auth_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_auth_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_auth_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_asym_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_atom_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_comp_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_label_seq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPtnr2_symmetry() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- getPublicationDate() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getPublisher() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getPvalue() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getPvalue() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
-
- getPvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getPwdDistanceMethod() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getPx() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getQ() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
-
Generate and return the (economy-sized) orthogonal factor
- getQualifiedName() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getQualifiers() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getQualifiers() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the qualifiers for this feature
- getQualitativeColorPalettes(boolean) - Static method in enum org.jcolorbrewer.ColorBrewer
-
- getQualities() - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
-
- getQualities(int, int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
-
- getQuality() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq
-
Return the quality scores for this FASTQ formatted sequence.
- getQualityAt(int) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
-
- getQuantities() - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
-
- getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
-
- getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getQuery() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getQuery() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getQuery() - Method in class org.biojava.nbio.alignment.SimpleProfilePair
-
- getQuery() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getQuery() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getQuery() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getQuery() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer
-
Returns the first sequence of the pair.
- getQuery() - Method in interface org.biojava.nbio.alignment.template.ProfilePair
-
Returns the first
Profile of the pair.
- getQuery() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer
-
Returns the first profile of the pair.
- getQuery() - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
- getQueryEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
-
- getQueryIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
-
- getQueryStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getR() - Method in class org.biojava.nbio.structure.jama.QRDecomposition
-
Return the upper triangular factor
- getRadius(Atom) - Static method in class org.biojava.nbio.structure.asa.AsaCalculator
-
Gets the van der Waals radius of the given atom following the values defined by
Chothia (1976) J.Mol.Biol.105,1-14
NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates"
slightly the heavy atoms to account for Hydrogens.
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
Returns the radius for drawing polyhedra
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getRadius() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
Returns the radius for drawing the minor rotation axis in the xy-plane
- getRadiusOfGyration() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- getRama() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rama property.
- getRandomDataColumns(int) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRandomDataColumns(int, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRandomNumberGeneratorSeed() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getRandomSleepTime() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getRandomUsername() - Static method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
- getRanges() - Method in class org.biojava.nbio.structure.AtomPositionMap
-
Returns a list of
ResidueRanges corresponding to this entire AtomPositionMap.
- getRanges() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getRanges() - Method in interface org.biojava.nbio.structure.StructureIdentifier
-
- getRanges() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getRanges() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
-
- getRank() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getRank() - Method in class org.forester.ws.seqdb.UniProtTaxonomy
-
- getRank() - Method in class org.forester.ws.uniprot.UniProtTaxonomy
-
- getRealEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the real parts of the eigenvalues
- getRealEnd() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getRealStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getRecordAdditionalAttachments() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getRecordType() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- getRecordType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- getRecordUnidentifiableCompounds() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getReducedCAStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools
-
reduce a structure to a Calpha representation only
- getReducedStructure(Structure, String) - Static method in class org.biojava.nbio.structure.StructureTools
-
Reduce a structure to provide a smaller representation .
- getReducedStructure(Structure, int) - Static method in class org.biojava.nbio.structure.StructureTools
-
Reduce a structure to provide a smaller representation.
- getRef() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of REF field.
- getRef() - Method in class org.forester.phylogeny.data.Annotation
-
- getRef() - Method in class org.forester.phylogeny.data.Property
-
- getRef0() - Method in class org.forester.phylogeny.data.SequenceRelation
-
- getRef1() - Method in class org.forester.phylogeny.data.SequenceRelation
-
- getRef_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getRefAuthor() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRefChainId() - Method in class org.biojava.nbio.structure.Compound
-
Return the ref chain id value.
- getRefComment() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getReference() - Method in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- getReference() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getReference() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
To get a type of reference for the webservice (an URL or citation, for example).
- getReference() - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always returns the first Reference.
- getReference(int) - Method in class org.forester.phylogeny.data.NodeData
-
- getReferences() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getReferences() - Method in class org.forester.phylogeny.data.NodeData
-
- getRefLocation() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRefmacVersion() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the refmacVersion property.
- getRefMedline() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRefn() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of REFN field.
- getRefseqIds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getRefTitle() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- getRegistryInfo() - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- getRelativeAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the relative (complexed) ASA, i.e.
- getRelativeAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
Returns the relative (uncomplexed) ASA, i.e.
- getRelativePercentileClashscore() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentileClashscore property.
- getRelativePercentileDCCRfree() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getRelativePercentilePercentRamaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentilePercentRamaOutliers property.
- getRelativePercentilePercentRotaOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentilePercentRotaOutliers property.
- getRelativePercentilePercentRSRZOutliers() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the relativePercentilePercentRSRZOutliers property.
- getRelativePercentileRNAsuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getRelevantSequenceRelationTypes() - Method in class org.forester.phylogeny.Phylogeny
-
- getRelevantSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
Returns the normalised list of sub locations i.e.
- getRelevantSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
An extension to
Location.getSubLocations() which returns sub-locations
of sub-locations; this will continue until it runs out of those locations.
- getRelevantSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getRelevantSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Will return a SequenceReader object which offers a view of all resolved
locations i.e.
- getReMappedScientificNamesFromGeneTree() - Method in class org.forester.sdi.GSDI
-
- getRemoteBlastInfo() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
A simple method to check the availability of the QBlast service.
- getRemoteTerm() - Method in interface org.biojava.nbio.ontology.RemoteTerm
-
Return the imported term
- getRemoteTerm() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getRemoteTerms() - Method in interface org.biojava.nbio.ontology.OntologyOps
-
Get the set of all remote terms.
- getRenderingFactorWidth() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getRenderingFactorWidth() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- getRenderingSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getRenderingSize() - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
-
- getRenderingSize() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- getRepeatUnitCenters() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getRepeatUnitIndices() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
-
- getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getReplaced(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
if ChemComp is replacing another one, get the old version
otherwise return the same ChemComp again.
- getReplaced(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplacement(String, boolean, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Gets the PDB which superseded oldPdbId.
- getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
if ChemComp is replaced by another one, get the newer version
otherwise return the same ChemComp again.
- getReplacer(String) - Method in class org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplaces() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getReplaces(String, boolean) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the ID of the protein which was made obsolete by newPdbId.
- getRepresentative() - Method in class org.biojava.nbio.structure.cath.CathNode
-
- getRepresentative() - Method in class org.biojava.nbio.structure.Compound
-
Get the representative Chain for this Compound.
- getRepresentative() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- getRepresentativeChain(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getRepresentativeDomains() - Method in interface org.biojava.nbio.structure.domain.DomainProvider
-
- getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.PDBDomainProvider
-
Gets a list of all domain representatives
- getRepresentativeDomains() - Method in class org.biojava.nbio.structure.domain.RemoteDomainProvider
-
- getRepresentatives(String, int) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- GetRepresentatives - Class in org.biojava.nbio.structure.rcsb
-
TODO Move this to Representatives.
- GetRepresentatives() - Constructor for class org.biojava.nbio.structure.rcsb.GetRepresentatives
-
- getRepresentatives(int) - Static method in class org.biojava.nbio.structure.rcsb.GetRepresentatives
-
Returns a representative set of PDB protein chains at the specified sequence
identity cutoff.
- getRepresentatives(Astral.AstralSet) - Static method in class org.biojava.nbio.structure.scop.Astral
-
Get a list of representatives' names for the specified ASTRAL cutoff.
- getRepresentatives(String) - Static method in class org.biojava.nbio.structure.scop.Astral
-
Get a list of representatives' names for the specified ASTRAL cutoff.
- getRepresentatives(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
-
- getResidId() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getResidId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getResidName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getResidName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getResidual() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getResidualVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getResidue() - Method in class org.biojava.nbio.phosphosite.Site
-
- getResidue(int) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
-
Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
- getResidue(int, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
-
Returns the ResidueNumber that is at position positionInRange in
this ResidueRange.
- getResidueAt(int, int) - Method in class org.forester.msa.BasicMsa
-
- getResidueAt(int, int) - Method in interface org.forester.msa.Msa
-
- getResidueAt(int, int) - Method in class org.forester.msa.ResampleableMsa
-
- getResidueAt(int) - Method in class org.forester.sequence.BasicSequence
-
- getResidueAt(int) - Method in interface org.forester.sequence.Sequence
-
- getResidueName() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- getResidueNumber() - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- getResidueNumber() - Method in interface org.biojava.nbio.structure.Group
-
returns a dynamically created ResidueNumber for the group - this
contains the chainId, resNum and insCode of the group.
- getResidueNumber() - Method in class org.biojava.nbio.structure.HetatomImpl
-
returns a dynamically created ResidueNumber for the group - this
contains the chainId, resNum and insCode of the group.
- getResidueRanges() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getResidueRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getResidueRanges() - Method in interface org.biojava.nbio.structure.StructureIdentifier
-
Returns the list of
ResidueRanges that this StructureIdentifier defines.
- getResidueRanges() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getResidueRanges() - Method in class org.biojava.nbio.structure.SubstructureIdentifier
-
- getResidues() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
For each residue in the fasta file, return the ResidueNumber in the
corresponding structure.
- getResidues() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getResidueType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
-
- getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType
-
Get a set of ResidueTypes loosely equivalent to this GroupType.
- getResname() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the resname property.
- getResName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getResName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getResNames() - Method in class org.biojava.nbio.structure.Compound
-
- getResnum() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the resnum property.
- getResnum1() - Method in class org.biojava.nbio.structure.SSBond
-
get residue number for first CYS.
- getResnum2() - Method in class org.biojava.nbio.structure.SSBond
-
get residue number for second CYS.
- getResolution() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getResolution() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getResolver() - Method in class org.biojava.nbio.core.sequence.location.FuzzyPoint
-
- getResourceManager(String) - Static method in class org.biojava.nbio.structure.align.util.ResourceManager
-
- getResScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getResSeq1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getResSeq2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getRestypesNotcheckedForBondAngleGeometry() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the restypesNotcheckedForBondAngleGeometry property.
- getResult(String, String) - Static method in class org.forester.development.HmmerRest
-
- getResult(String) - Static method in class org.forester.development.HmmerRest
-
- getResult(String) - Static method in class org.forester.ws.wabi.RestUtil
-
Method for access REST
- getResult(String, String, String) - Static method in class org.forester.ws.wabi.RestUtil
-
- getResultFile() - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- getReturnFormat() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getReturnFormat() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
The expected format of the response.
- getReverse() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Returns a Sequence which runs in the current reverse order
- getReverse() - Method in enum org.biojava.nbio.core.sequence.Strand
-
- getReverse() - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- getReverseComplement() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
- getReverseComplement() - Method in class org.biojava.nbio.core.sequence.RNASequence
-
Get reverse complement view of the sequence
- getReverseFrames() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
Returns all frames which are in the reverse orientation
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getRfree() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getRight() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getRimResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the interface rim, defined as those residues at
the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff
- getRise() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getRms() - Method in class org.biojava.nbio.structure.align.helper.JointFragments
-
- getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
-
get the RMS of the JointFragments pair frag
- getRms() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getRMS(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.SVDSuperimposer
-
Calculate the RMS (root mean square) deviation of two sets of atoms.
- getRmsd() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getRmsd() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getRmsd() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- getRmsdCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
The cutoff to be used during AFP detection
- getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- getRmsdIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getRmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
RMSD Threshold
- getRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getRmsdThrJoin() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
RMSD threshold for joining of AFPs
- getRnaAminoAcidTranslator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getRnaCompounds() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getRNACompoundSet() - Static method in class org.biojava.nbio.core.sequence.compound.RNACompoundSet
-
- getRNASequence() - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
- getRNASequence(TranscriptionEngine) - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Allow a user to pass in a rules engine to do the DNA to RNA translation
- getRNASequence(Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence
-
Allows the user to pass in the Frame shift.
- getRNASequence(TranscriptionEngine, Frame) - Method in class org.biojava.nbio.core.sequence.DNASequence
-
- getRnaSequenceCreator() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getRnaSuiteness() - Method in class org.biojava.nbio.structure.validation.Entry
-
- getRnaToDna() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getRobustStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getRoot() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the root
GuideTree.Node which corresponds to the full multiple sequence alignment.
- getRoot() - Method in interface org.biojava.nbio.alignment.template.HierarchicalClusterer
-
Returns the root node of the tree resulting from this clustering algorithm.
- getRoot() - Method in class org.forester.phylogeny.Phylogeny
-
Returns the root PhylogenyNode of this Phylogeny.
- getRootURL() - Method in class org.biojava.nbio.structure.scop.ScopMirror
-
Get the URL for the root download directory, or null if none is set.
- getRot() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getRota() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rota property.
- getRotation() - Method in class org.biojava.nbio.structure.SVDSuperimposer
-
Get the Rotation matrix that is required to superimpose the two atom sets.
- getRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getRotationAxis() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get a unit vector along the rotation axis
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
-
Deprecated.
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns rotation group (point group) information representing rotational quaternary symmetry,
see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
Gets the rotation matrix from the last call to
calc_rmsd.
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
Gets the rotation matrix from the last call to
calc_rmsd.
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
- getRotationMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the rotation matrix corresponding to this axis
- getRotationMatrix(double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the rotation matrix corresponding to a rotation about this axis
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- getRotationPos() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get a position on the rotation axis.
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getRotAxisAndAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Given a rotation matrix calculates the rotation axis and angle for it.
- getRotAxisAngle(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getRotAxisType(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Given a transformation matrix containing a rotation returns the type of rotation:
1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation,
6 for 6-fold rotation,
-1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation,
-4 for 4-fold improper rotation and -6 for 6-fold improper rotation
- getRotMax(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getRow(AminoAcidCompound) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getRow(C) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getRow(C) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
- getRow() - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- getRowDimension() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Get row dimension.
- getRowHeader() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRowIdentifiers() - Method in class org.forester.util.GeneralTable
-
- getRowIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRowLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- getRowPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Make a one-dimensional row packed copy of the internal array.
- getRows() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getRows() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getRows() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Get the list of row names.
- getRows() - Method in class org.forester.development.MsaRenderer
-
- getRscc() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rscc property.
- getRscore() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getRscoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getRsr() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rsr property.
- getRsrz() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the rsrz property.
- getS() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the diagonal matrix of singular values
- getSaid() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the said property.
- getSaturation() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
Deprecated.
- getSaturation() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- getSaveAlignmentMenuItem(AFPChain) - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getSaveOutputDir() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getScale() - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getScale() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getScale() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- getScale() - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- getScale() - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- getScalevalue() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
Deprecated.
- getScalevalue() - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- getScid() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the scid property.
- getScientificName() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getScientificName() - Method in class org.forester.ws.seqdb.UniProtTaxonomy
-
- getScientificName() - Method in class org.forester.ws.uniprot.UniProtTaxonomy
-
- getSCOP() - Method in class org.biojava.nbio.structure.gui.util.ScopInstallationInstance
-
- getSCOP() - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Get the current default instance for the default version
- getSCOP(boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
- getSCOP(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
requests a particular version of SCOP.
- getSCOP(String, boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Gets an instance of the specified scop version.
- getScopDescription() - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
-
- getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopDescriptionBySunid(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Return the SCOP description for a node in the hierarchy by its "sunid" id.
- getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScopDescriptionFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDescriptionsXML(List<ScopDescription>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDescriptionXML(ScopDescription) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDomain() - Method in class org.biojava.nbio.structure.scop.server.ScopDomains
-
- getScopDomainFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopDomainsBySunid(Integer) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Get a SCOP domain by its sunid
- getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScopDomainsXML(List<ScopDomain>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDomainXML(ScopDomain) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopDownloadURL() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
Deprecated.
- getScope() - Method in class org.biojava.nbio.ontology.Synonym
-
- getScopId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getScopNode(int) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopNode(int) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopNode(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Access a particular ScopNode.
- getScopNode(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScopNode() - Method in class org.biojava.nbio.structure.scop.server.ScopNodes
-
- getScopNodeFromXML(String) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopNodesXML(List<ScopNode>) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopNodeXML(ScopNode) - Static method in class org.biojava.nbio.structure.scop.server.XMLUtil
-
- getScopSelectPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getScopVersion() - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getScopVersion() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getScopVersion() - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Returns the SCOP version
- getScopVersion() - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getScore() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getScore() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getScore() - Method in class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- getScore() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getScore() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScore() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score resulting from algorithm.
- getScore() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getScore() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- getScore() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
the alignment score
- getScore() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- getScore() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getScore() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- getScore() - Method in interface org.forester.pccx.Coverage
-
- getScore() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
-
- getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- getScoreLogrankTest() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getScoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getScoreMatrix() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the similarity matrix used to construct this guide tree.
- getScoreMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScoreMatrix() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner
-
Returns the entire score matrix built during alignment.
- getScoreMatrix(String) - Static method in class org.biojava.nbio.phylo.ResidueProperties
-
get a ScoreMatrix based on its string name
- getScoreMatrixAsString() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScoreMatrixAsString() - Method in interface org.biojava.nbio.alignment.template.MatrixAligner
-
Returns a depiction of the score matrix as a String.
- getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getScoreMatrixDimensions() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getScores(File) - Method in class org.biojava.nbio.ronn.ORonnModel
-
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
Returns QuatSymmetryScores averaged over all rotations
(except the first rotation, which is the unit operation E)
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getScores() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
Returns QuatSymmetryScores averaged over all rotations
(except the first rotation, which is the unit operation E)
- getScoringMethod() - Method in class org.forester.pccx.ExternalNodeBasedCoverageMethodOptions
-
- getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Get the component of translation parallel to the axis of rotation
- getScriptGenerator() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
-
- getSD() - Method in class org.forester.pccx.ExternalNodeBasedCoverage
-
- getSearchFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
An input file to be used for the DB search
- getSearchMethod() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getSearchParameter() - Method in class org.forester.surfacing.SimpleDomain
-
- getSecond() - Method in class org.biojava.nbio.structure.contact.Pair
-
- getSecondAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- getSecondGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets the GroupAsa for the corresponding residue number of second chain
- getSecondGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.
- getSecondNode() - Method in interface org.forester.phylogeny.Edge
-
- getSecondNode() - Method in class org.forester.phylogeny.PhylogenyBranch
-
- getSecretion() - Method in class org.biojava.nbio.structure.Compound
-
- getSecStruc() - Method in interface org.biojava.nbio.structure.AminoAcid
-
Get secondary structure data .
- getSecStruc() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Get secondary structure data .
- getSecStruc() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getSeedFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getSeedRmsdCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getSegId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getSegmentAtPos(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getSegmentId() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getSegments() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSegments() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getSegments() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- getSelectedAlignmentPos() - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- getSelection() - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- getSelection() - Method in interface org.biojava.nbio.structure.gui.Selection
-
- getSelection() - Method in class org.biojava.nbio.structure.gui.SelectionImpl
-
- getSelection() - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
- getSelectPDBPanel() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getSeparatorSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- getSeq() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the seq property.
- getSeq_align_beg() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_align_end() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getSeq_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getSeqBegin() - Method in class org.biojava.nbio.structure.DBRef
-
Initial sequence number of the PDB sequence segment.
- getSeqEnd() - Method in class org.biojava.nbio.structure.DBRef
-
Ending sequence number of the PDB sequence segment.
- getSeqNum() - Method in class org.biojava.nbio.structure.ResidueNumber
-
- getSeqPos(int, Point) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Convert from a X position in the JPanel to alignment position
- getSeqPos(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
-
start counting at 0...
- getSeqresEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getSeqResGroup(int) - Method in interface org.biojava.nbio.structure.Chain
-
Return the Group at given position,
from within groups in the SEQRES records of the chain, i.e.
- getSeqResGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the Group at given position,
from within groups in the SEQRES records of the chain, i.e.
- getSeqResGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain
-
- getSeqResGroups() - Method in interface org.biojava.nbio.structure.Chain
-
Return a list of all groups in SEQRES records of the chain, i.e.
- getSeqResGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl
-
- getSeqResGroups() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return a list of all groups in SEQRES records of the chain, i.e.
- getSeqResLength() - Method in interface org.biojava.nbio.structure.Chain
-
Return the number of groups in the SEQRES records of the chain, i.e.
- getSeqResLength() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the number of groups in the SEQRES records of the chain, i.e.
- getSeqResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getSeqResSequence() - Method in interface org.biojava.nbio.structure.Chain
-
Return the PDB SEQRES sequence as a one-letter sequence string.
- getSeqResSequence() - Method in class org.biojava.nbio.structure.ChainImpl
-
Return the PDB SEQRES sequence as a one-letter sequence string.
- getSeqResSequence() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getSeqresStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getSeqs() - Method in class org.forester.archaeopteryx.MainFrameApplication
-
- getSeqsFile() - Method in class org.forester.archaeopteryx.MainFrameApplication
-
- getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
- getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
Assumes all compounds were uppercase
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
-
- getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
-
- getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.DNASequenceCreator
-
- getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.FastaSequenceParser
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
- getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Should be able to extend the same concept to a remote URL call or database connection.
- getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator
-
Not sure of use case and currently not supported
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
- getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Should be able to extend the same concept to a remote URL call or database connection.
- getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator
-
Not sure of use case and currently not supported
- getSequence(BufferedReader, int) - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
-
- getSequence(List<AminoAcidCompound>) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
-
- getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.ProteinSequenceCreator
-
- getSequence(String, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
-
- getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
-
- getSequence(List<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.io.RNASequenceCreator
-
- getSequence(String, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
-
- getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
-
- getSequence(List<C>) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface
-
- getSequence(BufferedReader, int) - Method in interface org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
-
- getSequence() - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation
-
- getSequence() - Method in class org.biojava.nbio.data.sequence.FastaSequence
-
Gets the value of sequence
- getSequence() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq
-
Return the sequence for this FASTQ formatted sequence.
- getSequence() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSequence() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getSequence() - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always returns the first Sequence.
- getSequence(int) - Method in class org.forester.phylogeny.data.NodeData
-
- getSequence5PrimeTo3Prime() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction
Returns the DNASequence representative of the 5' and 3' reading based on strand
- getSequenceAlignmentClusters() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getSequenceAlignmentClusters(double) - Method in class org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
-
- getSequenceAlignmentClusters() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
-
- getSequenceAlignmentLength() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getSequenceAsString() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns the sequence as a String
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
- getSequenceAsString() - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns the String representation of the Sequence
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ComplementSequenceView
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.ReversedSequenceView
-
- getSequenceAsString() - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- getSequenceAsString(int) - Method in class org.forester.msa.BasicMsa
-
- getSequenceAsString(int) - Method in interface org.forester.msa.Msa
-
- getSequenceClusterCount() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getSequenceClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getSequenceClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getSequenceCollection() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
-
- getSequenceCount() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSequenceFromString(String) - Method in class org.biojava.nbio.core.util.SequenceTools
-
- getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getSequenceHeaderParser() - Method in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- getSequenceIdentity() - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- getSequenceIdentityThresholds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getSequenceIndexAt(int) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getSequenceIndexAt(int) - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
Returns the index in the original
Sequence corresponding to the given index within an alignment.
- getSequenceMapByIdForPhylogeny(Phylogeny) - Static method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
-
- getSequenceName() - Method in class org.forester.ws.seqdb.EbiDbEntry
-
- getSequenceName() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry
-
- getSequenceName() - Method in class org.forester.ws.seqdb.UniProtEntry
-
- getSequenceName() - Method in class org.forester.ws.uniprot.EbiDbEntry
-
- getSequenceName() - Method in interface org.forester.ws.uniprot.SequenceDatabaseEntry
-
- getSequenceName() - Method in class org.forester.ws.uniprot.UniProtEntry
-
- getSequenceNames() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- getSequencePseudoSymmetryThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- getSequenceRelationQueries() - Method in class org.forester.phylogeny.Phylogeny
-
- getSequenceRelations() - Method in class org.forester.phylogeny.data.Sequence
-
- getSequences() - Method in class org.biojava.nbio.alignment.GuideTree
-
Returns the
Sequences which make up the leaves of this tree.
- getSequences() - Method in class org.biojava.nbio.alignment.io.StockholmStructure
-
- getSequences() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein sequences read from the Fasta file.
- getSequences() - Method in class org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
-
- getSequences() - Method in class org.forester.phylogeny.data.NodeData
-
- getSequenceScore() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Provide place holder for a metric that indicate a score associated with the sequence
- getSequenceString(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getSequenceSymbol() - Method in class org.forester.ws.seqdb.EbiDbEntry
-
- getSequenceSymbol() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry
-
- getSequenceSymbol() - Method in class org.forester.ws.seqdb.UniProtEntry
-
- getSequenceSymbol() - Method in class org.forester.ws.uniprot.EbiDbEntry
-
- getSequenceSymbol() - Method in interface org.forester.ws.uniprot.SequenceDatabaseEntry
-
- getSequenceSymbol() - Method in class org.forester.ws.uniprot.UniProtEntry
-
- getSequenceUsage() - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
-
- getSequentialColorPalettes(boolean) - Static method in enum org.jcolorbrewer.ColorBrewer
-
- getSeqWeight() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
- getSerialversionuid() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getSerNum() - Method in class org.biojava.nbio.structure.SSBond
-
set serial number of this SSBOND in PDB file
- getServer() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getServer() - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
- getServer() - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getServerName() - Static method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Return the String with the PDB server name, including the leading protocol
String (http:// or ftp://).
- getShape() - Method in class org.forester.phylogeny.data.NodeVisualization
-
- getSharedBinaryCombinationsBasedDistances() - Method in class org.forester.surfacing.PairwiseGenomeComparator
-
- getSharedBinaryDomainCombinations() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
- getSharedDomains() - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
- getSharedDomainsBasedDistances() - Method in class org.forester.surfacing.PairwiseGenomeComparator
-
- getShift() - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
Gets the shift from the last call to
calc_rmsd.
- getShift() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
Gets the shift from the last call to
calc_rmsd.
- getShift() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
returns the shift vector that has to be applied on structure to to shift on structure one
- getShorName() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getShortDescription() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getShortDescription() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Get the short description that can be used to describe the feature
- getShortName() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.compound.NucleotideCompound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getShortName() - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getShortName() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getShortName() - Method in enum org.biojava.nbio.structure.xtal.TransformType
-
- getShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets the international short name (as used in PDB),
e.g.
- getShowDBresult() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- getShowPDBMenuItem() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- getSiftsMapping(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
-
- getSimCount() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getSimilarity() - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getSimilarity(double) - Method in class org.biojava.nbio.alignment.template.AbstractScorer
-
- getSimilarity() - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a similarity between 0.0 and 1.0.
- getSimilarity(double) - Method in interface org.biojava.nbio.alignment.template.Scorer
-
Returns score as a similarity between 0.0 and scale.
- getSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Returns the similarity score for the alignment.
- getSimilarity1() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Deprecated.
use getCoverage1() instead
- getSimilarity2() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Deprecated.
use getCoverage2() instead
- getSimilarityScore() - Method in class org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity
-
- getSimilarityScore() - Method in class org.forester.surfacing.CountsBasedPairwiseDomainSimilarity
-
- getSimilarityScore() - Method in interface org.forester.surfacing.PairwiseDomainSimilarity
-
- getSingularValues() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the one-dimensional array of singular values
- getSiteID() - Method in class org.biojava.nbio.structure.Site
-
- getSites() - Method in interface org.biojava.nbio.structure.Structure
-
- getSites() - Method in class org.biojava.nbio.structure.StructureImpl
-
- getSize() - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getSize() - Method in interface org.biojava.nbio.alignment.template.Profile
-
Returns the number of rows in this profile.
- getSize() - Method in class org.biojava.nbio.core.sequence.MultipleSequenceAlignment
-
Get the number of sequences in the MSA
- getSize() - Method in interface org.biojava.nbio.core.sequence.template.LightweightProfile
-
Returns the number of rows in this profile.
- getSize() - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- getSize() - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- getSize() - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix
-
- getSize() - Method in class org.forester.phylogeny.data.NodeVisualization
-
- getSize() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- getSize() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
- getSmallDisplayIcon() - Method in class org.jcolorbrewer.ui.DivergingColorPalettePanel
-
- getSmallDisplayIcon() - Method in class org.jcolorbrewer.ui.QualitativeColorPalettePanel
-
- getSmallDisplayIcon() - Method in class org.jcolorbrewer.ui.SequentialColorPalettePanel
-
- getSmallFont() - Method in class org.forester.archaeopteryx.TreeFontSet
-
- getSmiles() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getSOILD() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSolvent_model_details() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_bsol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_ksol() - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- getSortVariable() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
-
- getSortVariable() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- getSource() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
The feature source
- getSource() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getSource() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
The source of the feature.
- getSource() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Added support for the source of this sequence for GFF3 export
If a sub sequence doesn't have source then check for parent source
- getSource() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getSource() - Method in class org.forester.phylogeny.data.Accession
-
- getSource() - Method in class org.forester.phylogeny.data.Annotation
-
- getSourceId() - Method in class org.forester.phylogeny.data.Sequence
-
- getSourceSeed() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getSourceStructure() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getSpace_group_name_H_M() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getSpace_group_name_Hall() - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- getSpaceGroup() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Get the SpaceGroup
- getSpaceGroup(int) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
-
Gets the space group for the given standard identifier.
- getSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser
-
Get the space group for the given international short name, using
the PDB format, e.g.
- getSparse() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getSpeciationOrDuplicationEventsSum() - Method in class org.forester.sdi.GSDI
-
- getSpeciationsSum() - Method in class org.forester.sdi.GSDI
-
- getSpecies() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getSpecies(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method for display purposes.
- getSpecies() - Method in class org.forester.protein.BasicProtein
-
- getSpecies() - Method in interface org.forester.protein.Protein
-
- getSpecies() - Method in class org.forester.surfacing.BasicCombinableDomains
-
- getSpecies() - Method in class org.forester.surfacing.BasicGenomeWideCombinableDomains
-
- getSpecies() - Method in interface org.forester.surfacing.CombinableDomains
-
Returns the species of this combinable domains.
- getSpecies() - Method in class org.forester.surfacing.DomainLengthsTable
-
- getSpecies() - Method in interface org.forester.surfacing.DomainSimilarity
-
- getSpecies() - Method in interface org.forester.surfacing.GenomeWideCombinableDomains
-
- getSpecies() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getSpeciesCustomOrder() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getSpeciesData() - Method in interface org.forester.surfacing.DomainSimilarity
-
This should return a map, which maps species names to
SpeciesSpecificDomainSimilariyData
- getSpeciesData() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getSpeciesId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getSpeciesId() - Method in class org.forester.species.BasicSpecies
-
- getSpeciesId() - Method in interface org.forester.species.Species
-
- getSpeciesList() - Method in class org.forester.surfacing.DomainLengths
-
- getSpeciesTree() - Method in class org.forester.sdi.SDI
-
Returns the species tree.
- getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
-
- getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler
-
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Location of split files within the directory, as an array of paths.
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getSplitDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getSplitpat1() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getSplitpat2() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getSqFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getSqTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- getSrc_method() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getSSBonds() - Method in interface org.biojava.nbio.structure.Structure
-
Get the list of SSBonds as they have been defined in the PDB files
- getSSBonds() - Method in class org.biojava.nbio.structure.StructureImpl
-
get the list of SSBonds as they have been defined in the PDB files
- getStainTypeFromString(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
-
- getStandardDeviation() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getStandardDeviation() - Method in class org.forester.phylogeny.data.Confidence
-
- getStandardDeviation() - Method in class org.forester.sdi.DistanceCalculator
-
Returns the standard deviation.
- getStandardDeviationOfSimilarityScore() - Method in interface org.forester.surfacing.DomainSimilarity
-
- getStandardDeviationOfSimilarityScore() - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- getStandardErrorFromCommand() - Method in class org.forester.util.SystemCommandExecutor
-
Get the standard error (stderr) from the command you just exec'd.
- getStandardOutputFromCommand() - Method in class org.forester.util.SystemCommandExecutor
-
Get the standard output (stdout) from the command you just exec'd.
- getStart() - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getStart() - Method in interface org.biojava.nbio.alignment.template.AlignedSequence
-
Returns the
Point within an alignment of the first element of the original
Sequence.
- getStart() - Method in interface org.biojava.nbio.alignment.template.ProfileView
-
Returns the column index of the viewed
Profile corresponding to the first element in this view
- getStart() - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
- getStart() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getStart() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Start of the location
- getStart() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getStart() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getStart() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- getStart() - Method in class org.biojava.nbio.structure.ResidueRange
-
- getStart() - Method in class org.forester.archaeopteryx.tools.ProcessRunning
-
- getStart_construct_id() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- getStartCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getStartPage() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getStartTimestamp() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
-
StartupParameters is a bean to store all the possible
command line parameters.
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
-
- getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- getState(int, int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getState(String, int) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getState(String, String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- getState(int, int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getState(String, int) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getState(String, String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- getStatus() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getStatus() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- getStatus(String) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the status of the PDB in question.
- getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus
-
Get the status of the a collection of PDBs in question in a single query.
- getStatus() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getStatus() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getStatusListener() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- getStderr() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getStdev() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the stdev property.
- getStdev() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the stdev property.
- getStdev() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the stdev property.
- getStdev() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the stdev property.
- getStdlow() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getStepSize() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
how many pairs should be requested for alignment from server?
- getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.ChainClusterer
-
- getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getStop() - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- getStop() - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- getStopCodonSequence() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getStoreEmptySeqRes() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
a flag to detrermine if SEQRES should be stored, even if alignSeqREs is disabled.
- getStrain() - Method in class org.biojava.nbio.structure.Compound
-
- getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getStrain() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- getStrand() - Method in class org.biojava.nbio.core.sequence.CDSSequence
-
- getStrand() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
A gene should have Strand
- getStrand() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getStrand() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Strand which the location is located on
- getStrand() - Method in class org.biojava.nbio.core.sequence.TranscriptSequence
-
- getStrata() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
-
- getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager
-
- getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet
-
- getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet
-
- getStringForCompound(AminoAcidCompound) - Method in class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet
-
- getStringForCompound(C) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundSet
-
- getStringForCompound(C) - Method in interface org.biojava.nbio.core.sequence.template.CompoundSet
-
- getStringRepresentation() - Method in enum org.biojava.nbio.core.sequence.Strand
-
- getStrippedExternalGeneTreeNodes() - Method in class org.forester.sdi.GSDI
-
- getStrippedSpeciesTreeNodes() - Method in class org.forester.sdi.GSDI
-
- getStructAssemblies() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getStructAssemblyGens() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getStructOpers() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- getStructure() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getStructure(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Request a Structure based on a name.
- getStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructure(URL) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructure(File) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Handles the actual parsing of the file into a Structure object.
- getStructure() - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
This method will return the parsed protein structure, once the parsing has been finished
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMCIFFileReader
-
- getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- getStructure(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Open filename and return a Structure object.
- getStructure(File) - Method in interface org.biojava.nbio.structure.io.StructureIOFile
-
Read file from File and returns
a Structure object.
- getStructure(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
Loads a structure based on a name.
- getStructure(String) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getStructure(String, PDBFileParser, AtomCache) - Static method in class org.biojava.nbio.structure.StructureTools
-
Flexibly get a structure from an input String.
- getStructure1() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getStructure1() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
-
- getStructure1() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
-
- getStructure2() - Method in class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBDirPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBServerPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.PDBUploadPanel
-
- getStructure2() - Method in class org.biojava.nbio.structure.gui.util.ScopSelectPanel
-
- getStructure2() - Method in interface org.biojava.nbio.structure.gui.util.StructurePairSelector
-
- getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.AlignmentGui
-
- getStructureAlignment() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getStructureAtom(Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getStructureAtomLinkage(Atom, boolean, Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getStructureById(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- getStructureById(String) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
- getStructureById(String) - Method in interface org.biojava.nbio.structure.io.StructureProvider
-
get the structure for a PDB ID
- getStructureForCathDomain(StructureName) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForCathDomain(StructureName, CathDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Returns a
Structure corresponding to the CATH identifier supplied in
structureName, using the specified
CathDatabase.
- getStructureForDomain(ScopDomain) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(ScopDomain, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(ScopDomain, ScopDatabase, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureForDomain(String, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- getStructureGroup(Group, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil
-
- getStructureId() - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- getStructureIds() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getStructurePairAligner() - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- getStructures() - Method in class org.biojava.nbio.structure.io.FastaStructureParser
-
Gets the protein structures mapped from the Fasta file.
- getStudyFamily() - Method in class org.forester.go.etc.OntologizerResult
-
- getStudyTerm() - Method in class org.forester.go.etc.OntologizerResult
-
- getStudyTotal() - Method in class org.forester.go.etc.OntologizerResult
-
- getSubject() - Method in interface org.biojava.nbio.ontology.Triple
-
Return the subject term of this triple
- getSubject() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getSubLocations() - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- getSubLocations() - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Gives access to the sub locations for this location.
- getSubproblems(List<AlignerHelper.Anchor>, int, int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
Convert a list of anchors into a subproblem list.
- getSubProfile(Location) - Method in class org.biojava.nbio.alignment.SimpleProfile
-
- getSubProfile(Location) - Method in interface org.biojava.nbio.alignment.template.Profile
-
- getSubRanges(Structure, String) - Static method in class org.biojava.nbio.structure.StructureTools
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- getSubSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
If circular this will return the sequence represented by the sub
locations joined.
- getSubSequence(Sequence<C>) - Method in interface org.biojava.nbio.core.sequence.location.template.Location
-
Will return a SequenceReader object which represents the outer bounds
of this Location
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- getSubSequence(int, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Returns a sub sequence view
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getSubSequence(Integer, Integer) - Method in interface org.biojava.nbio.core.sequence.template.Sequence
-
Returns a portion of the sequence from the different positions.
- getSubSequence(Integer, Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getSubstitutionMatrix() - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns the substitution matrix.
- getSubstitutionMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
- getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getSubstitutionScore(int, int) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getSubstitutionScoreVector(int) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns score for the alignment of the query column to all target columns
- getSubstitutionScoreVector(int, AlignerHelper.Subproblem) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Returns score for the alignment of the query column to all target columns
- getSubstructureMatchingProteinSequence(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher
-
Get a substructure of
wholeStructure containing only the
Groups that are included in
sequence.
- getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns protein subunit information that was used to determine symmetry information
- getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getSubunitTypeCount() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
-
- getSuggestion(String) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
get a list of suggestions for a userInput
- getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- getSuggestion(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- getSum() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getSum() - Method in interface org.forester.util.DescriptiveStatistics
-
- getSummaryAsString() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getSummaryAsString() - Method in interface org.forester.util.DescriptiveStatistics
-
- getSummaryPos() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
- getSumOfFailures() - Method in class org.forester.surfacing.MappingResults
-
- getSumOfGainsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getSumOfLossesOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getSumOfPresentOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getSumOfSuccesses() - Method in class org.forester.surfacing.MappingResults
-
- getSunID() - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- getSunid() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- getSuperfamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- getSuperGoIds() - Method in class org.forester.go.BasicGoTerm
-
- getSuperGoIds() - Method in interface org.forester.go.GoTerm
-
- getSuperOrthologousNodes(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Returns all Nodes which are connected to external PhylogenyNode n of this
Phylogeny by a path containing only speciation events.
- getSuperOrthologs() - Method in class org.forester.sdi.RIOn
-
- getSurfaceResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the residues belonging to the surface
- getSurname() - Method in class org.biojava.nbio.structure.Author
-
- getSurv() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getSurvivalFitInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getSurvivalInfoList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getSurvivalInfoList() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
The data used to draw the graph
- getSurvivalTimePercentile(String, double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
To get the median percentile for a particular group pass the value of
.50.
- getSwissprotId() - Method in interface org.biojava.nbio.structure.Chain
-
Get the Swissprot id of this chain.
- getSwissprotId() - Method in class org.biojava.nbio.structure.ChainImpl
-
get the Swissprot id of this chains .
- getSym1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getSym2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
-
- getSymbol() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- getSymbol() - Method in class org.forester.phylogeny.data.Sequence
-
- getSymbolSet() - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- getSymDeviation() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getSymmClash() - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Gets the value of the symmClash property.
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
-
String representation of Symmetry, e.g.
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
Returns the symmetry group.
- getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getSymmetryClass(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.HelixSolver
-
- getSymmetryOperations() - Method in interface org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.RotationSolver
-
- getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.SystematicSolver
-
- getSymmetryOrder(Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
- getSymmetryOrder(Map<Integer, Integer>, Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Tries to detect symmetry in an alignment.
- getSymmetryOrder(AFPChain, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Guesses the order of symmetry in an alignment
- getSymop() - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Gets the value of the symop property.
- getSynonym() - Method in class org.forester.ws.seqdb.UniProtTaxonomy
-
- getSynonym() - Method in class org.forester.ws.uniprot.UniProtTaxonomy
-
- getSynonyms() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl
-
- getSynonyms() - Method in interface org.biojava.nbio.ontology.Term
-
Return the synonyms for this term.
- getSynonyms() - Method in class org.biojava.nbio.ontology.Term.Impl
-
- getSynonyms() - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- getSynonyms() - Method in class org.biojava.nbio.structure.Compound
-
- getSynonyms() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getSynonyms() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getSynthetic() - Method in class org.biojava.nbio.structure.Compound
-
- getSystematicName() - Method in interface org.biojava.nbio.protmod.ProteinModification
-
- getSystematicName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl
-
- getT() - Method in class org.biojava.nbio.structure.align.model.AFP
-
- getTabbedPane() - Method in class org.forester.archaeopteryx.MainPanel
-
- getTable(String) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
Returns a table by its name
- getTable(Integer) - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
Returns a table by its identifier i.e.
- getTable() - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
-
- getTables() - Method in class org.biojava.nbio.core.sequence.io.IUPACParser
-
Returns a list of all available IUPAC tables
- getTabPane() - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- getTarget() - Method in class org.biojava.nbio.alignment.FractionalIdentityScorer
-
- getTarget() - Method in class org.biojava.nbio.alignment.FractionalSimilarityScorer
-
- getTarget() - Method in class org.biojava.nbio.alignment.SimpleProfilePair
-
- getTarget() - Method in class org.biojava.nbio.alignment.SimpleSequencePair
-
- getTarget() - Method in class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- getTarget() - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- getTarget() - Method in interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer
-
Returns the second sequence of the pair.
- getTarget() - Method in interface org.biojava.nbio.alignment.template.ProfilePair
-
Returns the second
Profile of the pair.
- getTarget() - Method in interface org.biojava.nbio.alignment.template.ProfileProfileScorer
-
Returns the second profile of the pair.
- getTarget() - Method in interface org.biojava.nbio.alignment.template.SequencePair
-
- getTargetEndIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getTargetIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
-
- getTargetIndex(int) - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Cut
-
- getTargetOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- getTargetSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Returns the Sequence which is our edit.
- getTargetStartIndex() - Method in class org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
-
- getTaxCompBase() - Method in class org.forester.sdi.GSDI
-
- getTaxonomicRank(String) - Static method in class org.forester.ws.wabi.TxSearch
-
- getTaxonomies() - Method in class org.forester.phylogeny.data.NodeData
-
- getTaxonomiesFromCommonName(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools
-
- getTaxonomiesFromCommonName(String, int) - Static method in class org.forester.ws.uniprot.SequenceDbWsTools
-
- getTaxonomiesFromCommonNameStrict(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools
-
- getTaxonomiesFromCommonNameStrict(String, int) - Static method in class org.forester.ws.uniprot.SequenceDbWsTools
-
- getTaxonomiesFromId(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools
-
- getTaxonomiesFromId(String, int) - Static method in class org.forester.ws.uniprot.SequenceDbWsTools
-
- getTaxonomiesFromScientificName(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools
-
- getTaxonomiesFromScientificName(String, int) - Static method in class org.forester.ws.uniprot.SequenceDbWsTools
-
- getTaxonomiesFromScientificNameStrict(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools
-
Does not return "sub-types".
- getTaxonomiesFromScientificNameStrict(String, int) - Static method in class org.forester.ws.uniprot.SequenceDbWsTools
-
Does not return "sub-types".
- getTaxonomiesFromTaxonomyCode(String, int) - Static method in class org.forester.ws.seqdb.SequenceDbWsTools
-
- getTaxonomiesFromTaxonomyCode(String, int) - Static method in class org.forester.ws.uniprot.SequenceDbWsTools
-
- getTaxonomy() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- getTaxonomy() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getTaxonomy() - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always returns the first Taxonomy.
- getTaxonomy(int) - Method in class org.forester.phylogeny.data.NodeData
-
- getTaxonomyCode() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getTaxonomyExtraction() - Method in class org.forester.io.parsers.nhx.NHXParser
-
- getTaxonomyIdentifier(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method for display purposes.
- getTaxonomyIdentifier() - Method in class org.forester.ws.seqdb.EbiDbEntry
-
- getTaxonomyIdentifier() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry
-
- getTaxonomyIdentifier() - Method in class org.forester.ws.seqdb.UniProtEntry
-
- getTaxonomyIdentifier() - Method in class org.forester.ws.uniprot.EbiDbEntry
-
- getTaxonomyIdentifier() - Method in interface org.forester.ws.uniprot.SequenceDatabaseEntry
-
- getTaxonomyIdentifier() - Method in class org.forester.ws.uniprot.UniProtEntry
-
- getTaxonomyScientificName() - Method in class org.forester.ws.seqdb.EbiDbEntry
-
- getTaxonomyScientificName() - Method in interface org.forester.ws.seqdb.SequenceDatabaseEntry
-
- getTaxonomyScientificName() - Method in class org.forester.ws.seqdb.UniProtEntry
-
- getTaxonomyScientificName() - Method in class org.forester.ws.uniprot.EbiDbEntry
-
- getTaxonomyScientificName() - Method in interface org.forester.ws.uniprot.SequenceDatabaseEntry
-
- getTaxonomyScientificName() - Method in class org.forester.ws.uniprot.UniProtEntry
-
- getTempBuffer() - Method in class org.biojava.nbio.ontology.obo.OboFileParser
-
- getTempDir() - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- getTempFactor() - Method in interface org.biojava.nbio.structure.Atom
-
Get temp factor.
- getTempFactor() - Method in class org.biojava.nbio.structure.AtomImpl
-
- getTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Fetch the term with the specified name.
- getTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getTerms() - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getTerms() - Method in interface org.biojava.nbio.ontology.Ontology
-
Return all the terms in this ontology
- getTerms() - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getTest() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
-
- getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
-
- getText() - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- getThePdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
Returns the PDB ID.
- getThreadPool() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Returns current shared thread pool.
- getThreads() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getThree() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- getThree() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getThree_letter_code() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
Should return the 3-prime end of the given Sequence according to
the edit.
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Delete
-
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Insert
-
- getThreePrime(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.Substitute
-
- getThreeState() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getTime() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getTime() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getTime() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getTime() - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- getTime() - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- getTime() - Method in class org.forester.sdi.RIO
-
Returns the time (in ms) needed to run "inferOrthologs".
- getTimeAxisIncrementPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
Get the percentage increment for the time axis
- getTimeout() - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- getTimeout() - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- getTimeStamp() - Method in class org.biojava.nbio.structure.io.PDBFileParser
-
Returns a time stamp.
- getTimeSumSDI() - Method in class org.forester.sdi.SDIR
-
Returns the sum of times (in ms) needed to run method infer of class SDI.
- getTissue() - Method in class org.biojava.nbio.structure.Compound
-
- getTissue() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getTissue_fraction() - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- getTitle() - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- getTitle() - Method in class org.biojava.nbio.structure.Compound
-
- getTitle() - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- getTitle() - Method in class org.biojava.nbio.structure.JournalArticle
-
Get the value of title
- getTitle() - Method in class org.biojava.nbio.structure.PDBHeader
-
- getTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getTmIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- getTMScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Returns the tmScore of the alignment.
- getTMScore(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer
-
- getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.SVDSuperimposer
-
Calculate the TM-Score for the superposition.
- getTMScoreAlternate(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.SVDSuperimposer
-
Calculate the TM-Score for the superposition.
- getTo() - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- getTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- getTo() - Method in class org.forester.phylogeny.data.ProteinDomain
-
- getTo() - Method in class org.forester.protein.BasicDomain
-
- getTo() - Method in interface org.forester.protein.Domain
-
- getTo() - Method in class org.forester.surfacing.SimpleDomain
-
- getToCompoundSet() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator
-
- getTool() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Get the tool identifier for QBlast.
- getTop() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getTopologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getTorsionPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
-
- getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
-
- getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Returns the total area buried upon formation of this interface,
defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:
- getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
Return the average buried surface area for this interface cluster
- getTotalCount() - Method in class org.forester.protein.BasicDomain
-
- getTotalCount() - Method in interface org.forester.protein.Domain
-
- getTotalCount() - Method in class org.forester.surfacing.SimpleDomain
-
- getTotalGains() - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- getTotalGains() - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- getTotalGains() - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- getTotalGains() - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getTotalLength() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- getTotalLength() - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- getTotalLength() - Method in class org.forester.phylogeny.data.DomainArchitecture
-
- getTotalLenIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getTotalLenOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getTotalLosses() - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- getTotalLosses() - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- getTotalLosses() - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- getTotalLosses() - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getTotalRmsdIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
this is the init-RMSD, not the final RMSD after refinement.
- getTotalRmsdOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The RMSD of the final alignment.
- getTotalUnchanged() - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- getTotalUnchanged() - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- getTotalUnchanged() - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- getTotalUnchanged() - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getTraceFlag() - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- getTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getTraces() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getTrans() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getTranscoefpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getTranscript(String) - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the transcript sequence by accession
- getTranscriptionEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getTranscriptionStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- getTranscripts() - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
Get the collection of transcription sequences assigned to this gene
- getTransfAlgebraic(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets a transformation algebraic string given its index.
- getTransfAlgebraic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.AxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns transformation matrix to orient structure
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getTransformation() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getTransformation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets a transformation by index expressed in crystal axes basis.
- getTransformationMap() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser
-
Returns a map of bioassembly transformations
- getTransformationMatrix() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.
- getTransformationMatrix() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- getTransformations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
Gets all transformations except for the identity in crystal axes basis.
- getTransformationsOrthonormal() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Gets all symmetry transformation operators corresponding to this structure's space group
(including the identity, at index 0) expressed in the orthonormal basis.
- getTransformedCoordinates() - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getTransforms() - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
Return the 2 crystal transform operations performed on each of the
molecules of this interface.
- getTransforms() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
- getTransformType() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
Returns the TransformType of this transformation: AU, crystal translation, fractional translation
, 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getTransition(ProteinSequence) - Method in interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
-
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(ProteinSequence) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(String, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(String, IProfeatProperties.ATTRIBUTE) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(String) - Static method in class org.biojava.nbio.aaproperties.profeat.ProfeatProperties
-
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE, IProfeatProperties.TRANSITION) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getTransition(ProteinSequence, IProfeatProperties.ATTRIBUTE) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getTransition(ProteinSequence) - Method in class org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
-
- getTranslatedBbs(Vector3d) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
-
Returns a new BoundingBoxes object containing the same bounds as this
BoundingBoxes object translated by the given translation
- getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
-
- getTranslation() - Method in class org.biojava.nbio.structure.SVDSuperimposer
-
Get the shift vector.
- getTranslScrewComponent() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- getTranslScrewComponent(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
Given a transformation matrix containing a rotation and translation returns the
screw component of the rotation.
- getTransNCS() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the transNCS property.
- getTransparancy() - Method in class org.forester.phylogeny.data.NodeVisualization
-
- getTree(CathDomain) - Method in interface org.biojava.nbio.structure.cath.CathDatabase
-
Return the CATH sub-tree for a particular domain.
- getTree(CathDomain) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- getTree(ScopDomain) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
get the SCOP sub-tree for a particular domain.
- getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- getTreeFontSet() - Method in class org.forester.archaeopteryx.MainPanel
-
- getTreshold(int) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
-
- getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- getTriples(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology
-
Return all triples from this ontology which match the supplied
pattern.
- getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- getTriplet() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getTrustedCutoffs() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
Not always 2.
It may undergo further change.
- getTurn() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- getTwi() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getTwinFraction() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the twinFraction property.
- getTwinL() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the twinL property.
- getTwinL2() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the twinL2 property.
- getTwistedGroups() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- getTwo() - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
- getTwo() - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- getTwoFoldsPerpendicular() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- getTxId(String) - Static method in class org.forester.ws.wabi.TxSearch
-
- getTxName(String) - Static method in class org.forester.ws.wabi.TxSearch
-
- getType() - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
- getType() - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
- getType() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
The feature type
- getType() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getType() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
The type of the feature.
- getType() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- getType() - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
- getType() - Method in interface org.biojava.nbio.structure.Group
-
- getType() - Method in class org.biojava.nbio.structure.HetatomImpl
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- getType() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getType() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- getType() - Method in class org.biojava.nbio.structure.NucleotideImpl
-
- getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getType() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getType() - Method in class org.forester.go.BasicGoRelationship
-
- getType() - Method in class org.forester.go.BasicGoSubset
-
- getType() - Method in class org.forester.go.BasicGoXRef
-
- getType() - Method in class org.forester.go.etc.OntologizerResult
-
- getType() - Method in class org.forester.go.GoNameSpace
-
- getType() - Method in interface org.forester.go.GoRelationship
-
- getType() - Method in interface org.forester.go.GoSubset
-
- getType() - Method in interface org.forester.go.GoXRef
-
- getType() - Method in class org.forester.msa.BasicMsa
-
- getType() - Method in interface org.forester.msa.Msa
-
- getType() - Method in class org.forester.phylogeny.data.Annotation
-
- getType() - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- getType() - Method in class org.forester.phylogeny.data.Confidence
-
- getType() - Method in class org.forester.phylogeny.data.Sequence
-
- getType() - Method in class org.forester.phylogeny.data.SequenceRelation
-
- getType() - Method in class org.forester.phylogeny.data.Uri
-
- getType() - Method in class org.forester.phylogeny.Phylogeny
-
- getType() - Method in class org.forester.sequence.BasicSequence
-
- getType() - Method in interface org.forester.sequence.Sequence
-
- getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- getType_symbol() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- getTypeField() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getU() - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Return upper triangular factor
- getU() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the left singular vectors
- getUltimateGoTerm(GoTerm, Map<GoId, GoTerm>) - Static method in class org.forester.go.GoUtils
-
- getUltraParalogousNodes(PhylogenyNode) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Returns all Nodes which are connected to external PhylogenyNode n of this
Phylogeny by a path containing, and leading to, only duplication events.
- getUltraParalogs() - Method in class org.forester.sdi.RIOn
-
- getUnaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
-
Returns a list of operators for this assembly.
- getUnderlyingCompound() - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- getUnidentifiableAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getUnidentifiableModifiedResidues() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- getUniprot() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- getUniprot() - Method in class org.biojava.nbio.phosphosite.Site
-
- getUniProtAccessionId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getUniprotbaseURL() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
The current UniProt URL to deal with caching issues.
- getUniprotDirectoryCache() - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Local directory cache of XML that can be downloaded
- getUniprotEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getUniProtId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getUniProtPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getUniProtResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- getUniprotStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- getUniqueID() - Method in class org.biojava.nbio.survival.cox.CoxVariables
-
Need a unique id from String
- getUniqueInterfaces() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Returns the list of unique interfaces that the given Structure has upon
generation of all crystal symmetry mates.
- getUniqueInterfaces(double) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Returns the list of unique interfaces that the given Structure has upon
generation of all crystal symmetry mates.
- getUniqueSequenceList() - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- getUnit() - Method in class org.forester.phylogeny.data.Date
-
- getUnit() - Method in class org.forester.phylogeny.data.Property
-
- getUnitsGainedOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getUnitsLostOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getUnitsOnNode(String) - Method in class org.forester.surfacing.DomainParsimonyCalculator
-
- getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getUnknownDataTypeVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getUnweightedStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
-
- getUpper() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- getUpperedBase() - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- getUri(int) - Method in class org.forester.phylogeny.data.Annotation
-
- getUri(int) - Method in interface org.forester.phylogeny.data.MultipleUris
-
- getUri(int) - Method in class org.forester.phylogeny.data.Sequence
-
- getUri(int) - Method in class org.forester.phylogeny.data.Taxonomy
-
- getUris() - Method in class org.forester.phylogeny.data.Annotation
-
- getUris() - Method in interface org.forester.phylogeny.data.MultipleUris
-
- getUris() - Method in class org.forester.phylogeny.data.Sequence
-
- getUris() - Method in class org.forester.phylogeny.data.Taxonomy
-
- getUrl() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
-
- getUrl() - Method in class org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient
-
- getUrl() - Method in interface org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
-
Use QUERY_PLACEHOLDER to indicate position of query variable.
- getUrlString() - Method in class org.forester.archaeopteryx.ArchaeopteryxA
-
- getUsed() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- getUsedAtomNames() - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- getUserCollection() - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Provided for convince if the developer needs to associate data with a sequence
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigHelp() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
The help text for each of these parameters.
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigParameterNames() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
The labels to be displayed to the user for each parameter
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigParameters() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
get the list of parameters that the user can change through the user interface.
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- getUserConfigTypes() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
-
Get the data types of the parameters
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- getUsername() - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- getUserObject() - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- getUserObject() - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- getUserObject() - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
- getV() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition
-
Return the eigenvector matrix
- getV() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Return the right singular vectors
- getValence(V) - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- getValence(int) - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- getValence(V) - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- getValence(int) - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- getValenceElectronCount() - Method in enum org.biojava.nbio.structure.Element
-
Returns the number of valence electrons for this Element.
- getValue(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- getValue(C, C) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- getValue(C, C) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Returns value in matrix for conversion from first
Compound to the second.
- getValue() - Method in class org.biojava.nbio.core.sequence.features.Qualifier
-
- getValue() - Method in class org.biojava.nbio.core.util.CRC64Checksum
-
- getValue() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
-
- getValue() - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- getValue() - Method in class org.forester.archaeopteryx.tools.PhyloInferenceDialog
-
- getValue(int, int) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- getValue(int, int) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix
-
- getValue() - Method in interface org.forester.go.Mapping
-
- getValue() - Method in class org.forester.go.PfamToGoMapping
-
- getValue() - Method in class org.forester.phylogeny.data.Accession
-
- getValue() - Method in class org.forester.phylogeny.data.BranchColor
-
- getValue() - Method in class org.forester.phylogeny.data.BranchWidth
-
- getValue() - Method in class org.forester.phylogeny.data.Confidence
-
- getValue() - Method in class org.forester.phylogeny.data.Date
-
- getValue() - Method in class org.forester.phylogeny.data.Identifier
-
- getValue() - Method in class org.forester.phylogeny.data.Property
-
- getValue() - Method in class org.forester.phylogeny.data.Uri
-
- getValue(int) - Method in class org.forester.util.BasicDescriptiveStatistics
-
- getValue(int, int) - Method in class org.forester.util.BasicTable
-
- getValue(int) - Method in interface org.forester.util.DescriptiveStatistics
-
- getValue(IDENTIFIER_TYPE, IDENTIFIER_TYPE) - Method in class org.forester.util.GeneralTable
-
- getValue_order() - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- getValueAsBoolean() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getValueAsDouble() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getValueAsInt() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getValueAsString() - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
- getValueAsString(int, int) - Method in class org.forester.util.BasicTable
-
- getValueAsString(IDENTIFIER_TYPE, IDENTIFIER_TYPE) - Method in class org.forester.util.GeneralTable
-
- getValuePlusProvider() - Method in class org.forester.phylogeny.data.Identifier
-
- getValues() - Method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
-
- getValues() - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- getVarhaz() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getVariableResiduals() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getVariance() - Method in class org.forester.sdi.DistanceCalculator
-
Returns the variance.
- getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.Fastq
-
Return the FASTQ sequence format variant for this FASTQ formatted sequence.
- getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader
-
- getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqReader
-
- getVariant() - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader
-
- getVariant() - Method in class org.biojava.nbio.structure.Compound
-
- getVDWRadius() - Method in enum org.biojava.nbio.structure.Element
-
Returns the van der Waals radius of this Element.
- getVector() - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- getVector() - Method in class org.forester.phylogeny.data.NodeData
-
- getVector3dScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
- getVersion() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getVersion() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
-
- getVersion() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- getVersion() - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- getVersion() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- getVersion() - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Get the Version information for this Algorithm.
- getVersion() - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- getVersion() - Method in class org.biojava.nbio.structure.validation.Program
-
Gets the value of the version property.
- getVertex(int) - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- getVertex(int) - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- getVertex1() - Method in class org.biojava.nbio.structure.symmetry.utils.Edge
-
- getVertex2() - Method in class org.biojava.nbio.structure.symmetry.utils.Edge
-
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Returns the vertices of an n-fold polygon of given radius and center
- getVertices() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Returns the vertices of an n-fold polygon of given radius and center
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the vertices of an n-fold polygon of given radius and center
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Returns the vertices of an n-fold polygon of given radius and center
- getVertices() - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- getVertices() - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getViewCount() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getViewedProfile() - Method in interface org.biojava.nbio.alignment.template.ProfileView
-
Returns the entire
Profile being viewed
- getViewedSequence() - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- getViewedSequence() - Method in interface org.biojava.nbio.core.sequence.template.SequenceView
-
- getViewer() - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getViewMatrix(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
- getViewName(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
- getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
- getVolume() - Method in class org.biojava.nbio.structure.JournalArticle
-
- getVolume() - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
Returns the volume of this unit cell.
- getWaldTestInfo() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getWarningCount() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- getWarningCount() - Method in class org.forester.io.parsers.tol.TolParser
-
- getWarningMessages() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- getWarningMessages() - Method in class org.forester.io.parsers.tol.TolParser
-
- getWebStartConfig() - Static method in class org.biojava.nbio.structure.align.webstart.WebStartMain
-
- getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- getWeight() - Method in class org.biojava.nbio.structure.rcsb.RCSBPolymer
-
- getWeight() - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- getWeight() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- getWeighted() - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- getWellColor() - Method in class org.forester.development.ResidueRenderer
-
- getWidth() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism
-
Returns the radius of an inscribed sphere, that is tangent to each
of the octahedron's faces
- getWikipediaLink() - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- getWilsonBaniso() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the wilsonBaniso property.
- getWilsonBestimate() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the wilsonBestimate property.
- getWindowSize() - Method in class org.biojava.nbio.core.sequence.views.WindowedSequence
-
Access the current window size
- getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
The window size to look at
- getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- getX() - Method in interface org.biojava.nbio.structure.Atom
-
Get coordinate X.
- getX() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get coordinate X.
- getX() - Method in class org.forester.development.AbstractRenderer
-
- getxAxisTimeCoordinates() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getxAxisTimeValues() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- getXcoord() - Method in class org.forester.phylogeny.PhylogenyNode
-
Used for drawing of Trees.
- getXMLcreationDate() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the xmLcreationDate property.
- getXRef() - Method in class org.forester.go.BasicGoXRef
-
- getXRef() - Method in interface org.forester.go.GoXRef
-
- getXSecondary() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getXtriageInputColumns() - Method in class org.biojava.nbio.structure.validation.Entry
-
Gets the value of the xtriageInputColumns property.
- getXYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc
-
Convert a rotation Matrix to Euler angles.
- getY() - Method in interface org.biojava.nbio.structure.Atom
-
Get coordinate Y.
- getY() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get coordinate Y.
- getY() - Method in class org.forester.development.AbstractRenderer
-
- getYcoord() - Method in class org.forester.phylogeny.PhylogenyNode
-
Used for drawing of Trees.
- getYSecondary() - Method in class org.forester.phylogeny.PhylogenyNode
-
- getZ() - Method in interface org.biojava.nbio.structure.Atom
-
Get coordinate Z.
- getZ() - Method in class org.biojava.nbio.structure.AtomImpl
-
Get coordinate Z.
- getZ() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
- getZ() - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Gets the value of the z property.
- getZ() - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Gets the value of the z property.
- getZ() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- getZ_PDB() - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns the Jmol zoom to fit polyhedron and symmetry axes.
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- getZoom() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
-
- getZscore() - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Gets the value of the zscore property.
- getZscore() - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Gets the value of the zscore property.
- getZYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc
-
Get euler angles for a matrix given in ZYZ convention.
- GFF3FromUniprotBlastHits - Class in org.biojava.nbio.genome.homology
-
- GFF3FromUniprotBlastHits() - Constructor for class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
-
- GFF3Reader - Class in org.biojava.nbio.genome.parsers.gff
-
http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
- GFF3Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Reader
-
- GFF3Writer - Class in org.biojava.nbio.genome.parsers.gff
-
- GFF3Writer() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Writer
-
- Gln - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- GLOBAL_ALIGN1 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- GLOBAL_ALIGN2 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- Glu - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- Gly - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- GO_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
-
- goac - Class in org.forester.application
-
- goac() - Constructor for class org.forester.application.goac
-
- GoAnnotation - Class in org.forester.archaeopteryx.tools
-
- GoAnnotation(MainFrameApplication, TreePanel, Phylogeny) - Constructor for class org.forester.archaeopteryx.tools.GoAnnotation
-
- GOC_STR - Static variable in interface org.forester.go.GoXRef
-
- GoId - Class in org.forester.go
-
- GoId(String) - Constructor for class org.forester.go.GoId
-
- gold - Static variable in class org.biojava.nbio.structure.gui.util.color.ColorUtils
-
- GoNameSpace - Class in org.forester.go
-
- GoNameSpace(GoNameSpace.GoNamespaceType) - Constructor for class org.forester.go.GoNameSpace
-
- GoNameSpace(String) - Constructor for class org.forester.go.GoNameSpace
-
- GoNameSpace.GoNamespaceType - Enum in org.forester.go
-
- GOOGLE_SCHOLAR_LIMITS - Static variable in class org.forester.surfacing.SurfacingConstants
-
- GOOGLE_SCHOLAR_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
-
- GOOGLE_WEB_SEARCH_LINK - Static variable in class org.forester.surfacing.SurfacingConstants
-
- GOParser - Class in org.biojava.nbio.ontology.io
-
Simple parser for the Gene Ontology (GO) flatfile format.
- GOParser() - Constructor for class org.biojava.nbio.ontology.io.GOParser
-
- GoRelationship - Interface in org.forester.go
-
- GoRelationship.Type - Enum in org.forester.go
-
- GOSLIM_ASPERGILLUS_STR - Static variable in interface org.forester.go.GoSubset
-
- GOSLIM_CANDIDA_STR - Static variable in interface org.forester.go.GoSubset
-
- GOSLIM_GENERIC_STR - Static variable in interface org.forester.go.GoSubset
-
- GOSLIM_GOA_STR - Static variable in interface org.forester.go.GoSubset
-
- GOSLIM_PIR_STR - Static variable in interface org.forester.go.GoSubset
-
- GOSLIM_PLANT_STR - Static variable in interface org.forester.go.GoSubset
-
- GOSLIM_POMBE_STR - Static variable in interface org.forester.go.GoSubset
-
- GOSLIM_YEAST_STR - Static variable in interface org.forester.go.GoSubset
-
- GoSubset - Interface in org.forester.go
-
- GoSubset.Type - Enum in org.forester.go
-
- GOSUBSET_PROK_STR - Static variable in interface org.forester.go.GoSubset
-
- GoTerm - Interface in org.forester.go
-
- Gotoh - Class in org.biojava.nbio.structure.align.pairwise
-
a class to perform Gotoh algorithm
- Gotoh(Alignable) - Constructor for class org.biojava.nbio.structure.align.pairwise.Gotoh
-
- GoUtils - Class in org.forester.go
-
- GoXRef - Interface in org.forester.go
-
- GoXRef.Type - Enum in org.forester.go
-
- GradientMapper - Class in org.biojava.nbio.structure.gui.util.color
-
Maps a set of real values onto a gradient.
- GradientMapper() - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- GradientMapper(Color, Color) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- GradientMapper(Color, Color, ColorSpace) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- GradientPanel - Class in org.biojava.nbio.structure.gui.util.color
-
- GradientPanel(ContinuousColorMapper, double, double) - Constructor for class org.biojava.nbio.structure.gui.util.color.GradientPanel
-
- gradients - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- Graph<V> - Interface in org.biojava.nbio.structure.symmetry.utils
-
- Grid - Class in org.biojava.nbio.structure.contact
-
A grid to be used for calculating atom contacts through geometric hashing algorithm.
- Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid
-
Creates a Grid, the cutoff is in Angstroms and can
be specified to a precision of 0.01A
- GridCell - Class in org.biojava.nbio.structure.contact
-
A grid cell to be used in contact calculation via geometric hashing algorithm.
- GridCell() - Constructor for class org.biojava.nbio.structure.contact.GridCell
-
- group() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get the first item (everything before first semicolon, if it has one)
in the attribute field, which is assumed to
be a group identifer.
- group() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
-
Get the group id of the feature.
- Group - Interface in org.biojava.nbio.structure
-
This is the data structure for a single Group of atoms.
- group - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- group1 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
The seven different attributes are
Hydrophobicity (Polar, Neutral, Hydrophobicity)
Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)
Charge (Positive, Neutral, Negative)
Secondary structure (Helix, Strand, Coil)
Solvent accessibility (Buried, Exposed, Intermediate)
- group1 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
-
- group1WorseOutcome - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
-
- group2 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
- group2 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
-
- group3 - Static variable in class org.biojava.nbio.aaproperties.profeat.convertor.Convertor
-
- GroupAsa - Class in org.biojava.nbio.structure.asa
-
A class to store the results of ASA calculations, it can
hold ASA values per atom present in
Group
- GroupAsa(Group) - Constructor for class org.biojava.nbio.structure.asa.GroupAsa
-
- groupByRange(double[], String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
Need to allow a range of values similar to cut in R and a continuous c
- GroupContact - Class in org.biojava.nbio.structure.contact
-
A pair of residues that are in contact
- GroupContact() - Constructor for class org.biojava.nbio.structure.contact.GroupContact
-
- GroupContactSet - Class in org.biojava.nbio.structure.contact
-
A set of residue-residue contacts
- GroupContactSet() - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
-
- GroupContactSet(AtomContactSet) - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet
-
Constructs a GroupContactSet by collapsing the given AtomContactSet into
residue-residue (group-group) contacts.
- GroupIterator - Class in org.biojava.nbio.structure
-
An iterator over all groups of a structure.
- GroupIterator(Structure) - Constructor for class org.biojava.nbio.structure.GroupIterator
-
Constructs a GroupIterator object.
- GroupResults - Class in org.biojava.nbio.survival.kaplanmeier.figure
-
- GroupResults() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
-
- GroupType - Enum in org.biojava.nbio.structure
-
This contains basic categories for Group types.
- groupValues() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a collection of all unique group ids in the list, as defined
by the group() method of the features.
- gsdi - Class in org.forester.application
-
- gsdi() - Constructor for class org.forester.application.gsdi
-
- GSDI - Class in org.forester.sdi
-
- GSDI(Phylogeny, Phylogeny, boolean, boolean, boolean) - Constructor for class org.forester.sdi.GSDI
-
- GTSlikeScore(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
-
- GuanUberbacher<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment.routines
-
Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last
Compound of each
Sequence).
- GuanUberbacher() - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
-
- GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
-
Prepares for a pairwise global sequence alignment.
- GuanUberbacher(S, S, GapPenalty, SubstitutionMatrix<C>, int) - Constructor for class org.biojava.nbio.alignment.routines.GuanUberbacher
-
Prepares for a pairwise global sequence alignment.
- guessOrderFromAngle(double, int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis
-
Returns the rotation order o that gives the lowest value of |2PI / o - theta,
given that the value is strictly lower than threshold, for orders o=1,...,maxOrder.
- guessSequentialAlignment(Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
Takes a potentially non-sequential alignment and guesses a sequential
version of it.
- GUIAlignmentProgressListener - Class in org.biojava.nbio.structure.align.gui
-
a GUI that allows to watch progress as multiple alignments are being processed.
- GUIAlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
-
- GuideTree<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements a data structure for a guide tree used during progressive multiple sequence alignment.
- GuideTree(List<S>, List<PairwiseSequenceScorer<S, C>>) - Constructor for class org.biojava.nbio.alignment.GuideTree
-
Creates a guide tree for use during progressive multiple sequence alignment.
- GuideTree.Node - Class in org.biojava.nbio.alignment
-
Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.
- GuideTreeNode<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template
-
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
- GUIFarmJobRunnable - Class in org.biojava.nbio.structure.align.gui
-
- GUIFarmJobRunnable(FarmJobParameters) - Constructor for class org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable
-
- GuiWrapper - Class in org.biojava.nbio.structure.align.ce
-
A class to wrap some of the strucutre.gui classes using Reflection
- GuiWrapper() - Constructor for class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- GZIP_MAGIC - Static variable in class org.biojava.nbio.core.util.InputStreamProvider
-
The magic number found at the start of a GZIP stream.
- S - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- s_min - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
-
- SABIO_RK_STR - Static variable in interface org.forester.go.GoXRef
-
- said - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
- sampleStandardDeviation() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- sampleStandardDeviation() - Method in interface org.forester.util.DescriptiveStatistics
-
- sampleStandardUnit(double) - Method in class org.forester.util.BasicDescriptiveStatistics
-
- sampleStandardUnit(double, double, double) - Static method in class org.forester.util.BasicDescriptiveStatistics
-
Computes the sample standard unit (z-score).
- sampleStandardUnit(double) - Method in interface org.forester.util.DescriptiveStatistics
-
- sampleVariance() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- sampleVariance() - Method in interface org.forester.util.DescriptiveStatistics
-
- SandboxStyleStructureProvider - Class in org.biojava.nbio.structure.io
-
The "Sandbox" style of organizing files is to have a directory structure like below, i.e.
- SandboxStyleStructureProvider() - Constructor for class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
- SangerFastqReader - Class in org.biojava.nbio.sequencing.io.fastq
-
- SangerFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SangerFastqReader
-
- SangerFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq
-
- SangerFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter
-
- SANITIZE - Static variable in class org.forester.tools.PhylogenyDecorator
-
- sanitizeString(String) - Static method in class org.forester.util.ForesterUtil
-
- SankoffParsimony<STATE_TYPE> - Class in org.forester.evoinference.parsimony
-
IN PROGRESS!
DO NOT USE!
- SankoffParsimony() - Constructor for class org.forester.evoinference.parsimony.SankoffParsimony
-
- save(UserConfiguration) - Method in class org.biojava.nbio.structure.align.webstart.PersistentConfig
-
writes the configuration
- save(OutputStream, char, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- SAVE_ALIGNMENT_XML - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- saveCSV(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Save the worksheet as a csv file
- savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
- savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- savePNGKMNumRisk(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
Combine the KM and Num risk into one image
- saveSurvivalData(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
Save data from survival curve to text file
- saveTXT(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- SAX_FEATURES_VALIDATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- SAX_FEATURES_VALIDATION - Static variable in class org.forester.io.parsers.tol.TolParser
-
- scalarProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Scalar product (dot product).
- scale(Atom, double) - Static method in class org.biojava.nbio.structure.Calc
-
Multiply elements of a by s
- scale(double) - Method in class org.biojava.nbio.structure.math.SparseVector
-
Calculates alpha * a
- scale(double[][], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- scale(double[][], double) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- SCALE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- ScaleableMatrixPanel - Class in org.biojava.nbio.structure.gui
-
A JPanel that can display the underlying distance matrix
data of the protein structure alignment algorithm.
- ScaleableMatrixPanel() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- ScaleableMatrixPanel.GradientRenderer - Class in org.biojava.nbio.structure.gui
-
A renderer for the the gradient dropdown menu at the top of scaleableMatrixPanes.
- ScaleableMatrixPanel.GradientRenderer() - Constructor for class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer
-
- scaleAdd(double, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Perform linear transformation s*X+B, and store the result in b
- scaleColours - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- ScaledSubstitutionMatrix - Class in org.biojava.nbio.alignment.aaindex
-
The biojava-alignment module represents substitution matrices with short
values.
- ScaledSubstitutionMatrix() - Constructor for class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- scaleEquals(Atom, double) - Static method in class org.biojava.nbio.structure.Calc
-
Multiply elements of a by s (in place)
- scan(ProteinSequence) - Method in interface org.biojava.nbio.ws.hmmer.HmmerScan
-
- scan(ProteinSequence) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
-
- scan(ProteinSequence, URL) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
-
Scans a protein sequence for Pfam profile matches.
- ScanSymmetry - Class in org.biojava.nbio.structure.symmetry.analysis
-
- ScanSymmetry() - Constructor for class org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry
-
- SchemaGenerator - Class in org.biojava.nbio.aaproperties.xml
-
- SchemaGenerator(String) - Constructor for class org.biojava.nbio.aaproperties.xml.SchemaGenerator
-
- scid - Variable in class org.biojava.nbio.structure.validation.SymmClash
-
- SCOP - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- SCOP_DOWNLOAD - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- SCOP_DOWNLOAD_ALTERNATE - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- SCOP_VERSION - Static variable in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
-
- SCOPAutoSuggestProvider - Class in org.biojava.nbio.structure.align.gui.autosuggest
-
- SCOPAutoSuggestProvider() - Constructor for class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- ScopCategory - Enum in org.biojava.nbio.structure.scop
-
The various categories provided by SCOP.
- ScopDatabase - Interface in org.biojava.nbio.structure.scop
-
General API how to interact with SCOP
- ScopDescription - Class in org.biojava.nbio.structure.scop
-
Contains data from
dir.des.scop.txt_1.75
- ScopDescription() - Constructor for class org.biojava.nbio.structure.scop.ScopDescription
-
- ScopDescriptions - Class in org.biojava.nbio.structure.scop.server
-
- ScopDescriptions() - Constructor for class org.biojava.nbio.structure.scop.server.ScopDescriptions
-
- ScopDomain - Class in org.biojava.nbio.structure.scop
-
Container for the information for a domain.
- ScopDomain() - Constructor for class org.biojava.nbio.structure.scop.ScopDomain
-
- ScopDomains - Class in org.biojava.nbio.structure.scop.server
-
- ScopDomains() - Constructor for class org.biojava.nbio.structure.scop.server.ScopDomains
-
- ScopFactory - Class in org.biojava.nbio.structure.scop
-
Controls the global ScopDatabase being used.
- ScopFactory() - Constructor for class org.biojava.nbio.structure.scop.ScopFactory
-
- scopIDregex - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
-
- ScopInstallation - Class in org.biojava.nbio.structure.scop
-
This class provides access to the SCOP protein structure classification.
- ScopInstallation(String) - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation
-
Create a new SCOP installation.
- ScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation
-
Create a new SCOP installation, downloading the file to "the right place".
- ScopInstallationInstance - Class in org.biojava.nbio.structure.gui.util
-
- ScopIOException - Exception in org.biojava.nbio.structure.scop
-
Indicates that an I/O error occurred with SCOP lazy initialization.
- ScopIOException() - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
-
- ScopIOException(String) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
-
- ScopIOException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
-
- ScopIOException(Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException
-
- ScopMirror - Class in org.biojava.nbio.structure.scop
-
Helper class to store paths to the four SCOP files
The string "%s" is replaced with the version number.
- ScopMirror(String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
-
Specify all keys individually
- ScopMirror(String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
-
Specify a common root URL which is concatenated with individual filenames
- ScopMirror(String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
-
- ScopMirror() - Constructor for class org.biojava.nbio.structure.scop.ScopMirror
-
Use default MRC location
- ScopNode - Class in org.biojava.nbio.structure.scop
-
- ScopNode() - Constructor for class org.biojava.nbio.structure.scop.ScopNode
-
- ScopNodes - Class in org.biojava.nbio.structure.scop.server
-
- ScopNodes() - Constructor for class org.biojava.nbio.structure.scop.server.ScopNodes
-
- ScopSelectPanel - Class in org.biojava.nbio.structure.gui.util
-
- ScopSelectPanel() - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel
-
- ScopSelectPanel(boolean) - Constructor for class org.biojava.nbio.structure.gui.util.ScopSelectPanel
-
- scopVersion - Variable in class org.biojava.nbio.structure.scop.ScopInstallation
-
- score - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- score() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get score.
- score - Variable in class org.biojava.nbio.ronn.Jronn.Range
-
- scoreMatrices - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- ScoreMatrix - Class in org.biojava.nbio.phylo
-
- Scorer - Interface in org.biojava.nbio.alignment.template
-
Defines an algorithm which computes a score.
- scores - Variable in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Dynamic programming score matrix
The first dimension has the length of the first (query) sequence + 1
The second has the length of the second (target) sequence + 1
The third has length 1 for linear gap penalty and 3 for affine/constant gap
(one each for match/substitution, deletion, insertion)
- scoresToRanges(float[], float) - Static method in class org.biojava.nbio.ronn.Jronn
-
Convert raw scores to ranges.
- ScoringMethodForExternalNode - Interface in org.forester.pccx
-
- scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- scroll - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- SDI - Class in org.forester.sdi
-
- SDI(Phylogeny, Phylogeny) - Constructor for class org.forester.sdi.SDI
-
Constructor which sets the gene tree and the species tree to be compared.
- SDI.TaxonomyComparisonBase - Enum in org.forester.sdi
-
- sdi_dir - Class in org.forester.application
-
- sdi_dir() - Constructor for class org.forester.application.sdi_dir
-
- sdi_r - Class in org.forester.application
-
- sdi_r() - Constructor for class org.forester.application.sdi_r
-
- SDIException - Exception in org.forester.sdi
-
- SDIException() - Constructor for exception org.forester.sdi.SDIException
-
- SDIException(String) - Constructor for exception org.forester.sdi.SDIException
-
- SDIR - Class in org.forester.sdi
-
- SDIR() - Constructor for class org.forester.sdi.SDIR
-
Default contructor which creates an "empty" object..
- SDIse - Class in org.forester.sdi
-
- SDIse(Phylogeny, Phylogeny) - Constructor for class org.forester.sdi.SDIse
-
Constructor which sets the gene tree and the species tree to be compared.
- searchData(String, Phylogeny, boolean, boolean) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- searchDataLogicalAnd(String[], Phylogeny, boolean, boolean) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- searchLineage(List<String>, List<TxSearch.RANKS>) - Static method in class org.forester.ws.wabi.TxSearch
-
- searchLineage(List<String>, List<TxSearch.RANKS>, String) - Static method in class org.forester.ws.wabi.TxSearch
-
- searchParam(String, TxSearch.TAX_NAME_CLASS, TxSearch.TAX_RANK, int, boolean) - Static method in class org.forester.ws.wabi.TxSearch
-
- searchSimple(String) - Static method in class org.forester.ws.wabi.TxSearch
-
- SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO - Static variable in class org.forester.application.surfacing
-
- SecStruc - Class in org.biojava.nbio.structure.secstruc
-
Assign secondary structure to a Structure object.
- SecStruc() - Constructor for class org.biojava.nbio.structure.secstruc.SecStruc
-
- SecStrucGroup - Class in org.biojava.nbio.structure.secstruc
-
- SecStrucGroup() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- SecStrucState - Class in org.biojava.nbio.structure.secstruc
-
- SecStrucState() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucState
-
- SecStrucType - Enum in org.biojava.nbio.structure.secstruc
-
- sectp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- SEED - Static variable in class org.biojava.nbio.core.util.Hashcoder
-
An initial value for a hashCode, to which we add
contributions from fields.
- Segment - Class in org.biojava.nbio.structure.domain.pdp
-
- Segment() - Constructor for class org.biojava.nbio.structure.domain.pdp.Segment
-
- SegmentComparator - Class in org.biojava.nbio.structure.domain.pdp
-
- SegmentComparator() - Constructor for class org.biojava.nbio.structure.domain.pdp.SegmentComparator
-
- select(WorkSheet, String) - Method in interface org.biojava.nbio.survival.kaplanmeier.figure.CensorStatusSelect
-
- SELECT_EQR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- selectByAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a list of all features that include the specified attribute key/value pair.
- selectByAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a list of all features that include the specified attribute key.
- selectByGroup(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a list of all features that have the specified group id, as defined by
the group() method of the features.
- selectByType(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a list of all features that are of the specified type, as defined by
the type() method of the features.
- selectByUserData(String, Object) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a list of all features that include the specified key/value pair in their userMap().
- selectByUserData(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a list of all features that include the specified key in their userMap().
- selectElements(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
-
- Selection - Interface in org.biojava.nbio.structure.gui
-
- SelectionImpl - Class in org.biojava.nbio.structure.gui
-
- SelectionImpl() - Constructor for class org.biojava.nbio.structure.gui.SelectionImpl
-
- selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- selectionLocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- selectionLocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
-
- selectionLocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
-
- selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- selectionUnlocked() - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- selectionUnlocked() - Method in interface org.biojava.nbio.structure.gui.events.AlignmentPositionListener
-
- selectionUnlocked() - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
-
- selectOverlapping(String, Location, boolean) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a list of all features that overlap the specified location on the specified
sequence.
- selectParentElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
-
- SelectPDBPanel - Class in org.biojava.nbio.structure.align.gui
-
A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
- SelectPDBPanel() - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- SelectPDBPanel(boolean) - Constructor for class org.biojava.nbio.structure.align.gui.SelectPDBPanel
-
- selectSingleElement(Element, String) - Static method in class org.biojava.nbio.core.util.XMLHelper
-
- sendAFPChainToServer(String, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
- sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
- sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Sends the Blast request via the Put command of the CGI-BIN interface.
- sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
-
Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object
- sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
-
Doing the actual analysis on the instantiated service using specified parameters on the string representation
of the Sequence object
- sendDeleteRequest(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Sends a delete request for given request id.
- sendMultiAFPChainToServer(String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- sendMultiAFPChainToServer(String, String, String, String) - Static method in class org.biojava.nbio.structure.align.client.JFatCatClient
-
- sendResultsToServer(List<String>) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
- sentResultsToServer(int, String) - Method in class org.biojava.nbio.structure.align.client.CountProgressListener
-
- sentResultsToServer(int, String) - Method in interface org.biojava.nbio.structure.align.events.AlignmentProgressListener
-
- sentResultsToServer(int, String) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
-
- SEPARATOR - Static variable in interface org.forester.protein.BinaryDomainCombination
-
- seq - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
- SEQ_TYPE_DNA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
-
- SEQ_TYPE_PROTEIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
-
- SEQ_TYPE_RNA - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
-
- seqArraySize(int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
- seqFont - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- seqIsLikelyToBeAa(String) - Static method in class org.forester.util.ForesterUtil
-
- seqname() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get the sequence name.
- seqname() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
-
Get the sequence name.
- SeqRes2AtomAligner - Class in org.biojava.nbio.structure.io
-
Aligns the SEQRES residues to the ATOM residues.
- SeqRes2AtomAligner() - Constructor for class org.biojava.nbio.structure.io.SeqRes2AtomAligner
-
- SEQRESRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid
-
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
- Sequence<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
-
Main interface for defining a collection of Compounds and accessing them
using biological indexes
- sequence(String) - Method in interface org.biojava.nbio.sequencing.io.fastq.ParseListener
-
Notify this parse listener of a sequence line.
- SEQUENCE - Static variable in class org.forester.archaeopteryx.TreeColorSet
-
- SEQUENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- Sequence - Class in org.forester.phylogeny.data
-
- Sequence() - Constructor for class org.forester.phylogeny.data.Sequence
-
- Sequence - Interface in org.forester.sequence
-
- Sequence.TYPE - Enum in org.forester.sequence
-
- SEQUENCE_ACCESSION - Static variable in class org.forester.io.parsers.nhx.NHXtags
-
- SEQUENCE_COLOR - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_DOMAIN_ARCHITECURE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_LOCATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_MOL_SEQ - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_MOL_SEQ_ALIGNED_ATTR - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_NAME - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_RELATION - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_RELATION_DISTANCE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_RELATION_ID_REF0 - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_RELATION_ID_REF1 - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_RELATION_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_RELATION_TYPE_ORTHOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_RELATION_TYPE_OTHER - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_RELATION_TYPE_PARALOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_RELATION_TYPE_UNKNOWN - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_RELATION_TYPE_XENOLOGY - Static variable in class org.forester.phylogeny.data.SequenceRelation
-
- SEQUENCE_SOURCE_ID - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_SYMBOL - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_SYMBOL_PATTERN - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
-
- SEQUENCE_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlMapping
-
- SEQUENCE_TYPES - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
-
- SequenceAlignmentCluster - Class in org.biojava.nbio.structure.symmetry.core
-
- SequenceAlignmentCluster(QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- sequenceAndQualityLengthsMatch() - Method in class org.biojava.nbio.sequencing.io.fastq.FastqBuilder
-
Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
- SequenceAsStringHelper<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
-
This is a common method that can be used across multiple storage/proxy implementations to
handle Negative strand and other interesting elements of sequence data.
- SequenceAsStringHelper() - Constructor for class org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper
-
- SequenceComparator - Class in org.biojava.nbio.core.sequence
-
Used to sort sequences
- SequenceComparator() - Constructor for class org.biojava.nbio.core.sequence.SequenceComparator
-
- SequenceCreatorInterface<C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
-
- SequenceDatabaseEntry - Interface in org.forester.ws.seqdb
-
- SequenceDatabaseEntry - Interface in org.forester.ws.uniprot
-
- SequenceDataRetriver - Class in org.forester.archaeopteryx.tools
-
- SequenceDataRetriver(MainFrameApplication, TreePanel, Phylogeny) - Constructor for class org.forester.archaeopteryx.tools.SequenceDataRetriver
-
- SequenceDbWsTools - Class in org.forester.ws.seqdb
-
- SequenceDbWsTools() - Constructor for class org.forester.ws.seqdb.SequenceDbWsTools
-
- SequenceDbWsTools - Class in org.forester.ws.uniprot
-
- SequenceDbWsTools() - Constructor for class org.forester.ws.uniprot.SequenceDbWsTools
-
- SequenceDbWsTools.Db - Enum in org.forester.ws.seqdb
-
- SequenceDbWsTools.Db - Enum in org.forester.ws.uniprot
-
- SequenceDisplay - Class in org.biojava.nbio.structure.gui
-
A sequence display that can show the results of a protein structure alignment.
- SequenceDisplay(StructurePairAligner) - Constructor for class org.biojava.nbio.structure.gui.SequenceDisplay
-
- sequenceEquality(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
A case-sensitive manner of comparing two sequence objects together.
- sequenceEqualityIgnoreCase(Sequence<C>, Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
A case-insensitive manner of comparing two sequence objects together.
- SequenceFileProxyLoader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
-
This class represents the storage container of a sequence stored in a fasta file where
the initial parsing of the file we store the offset and length of the sequence.
- SequenceFileProxyLoader(File, SequenceParserInterface, long, int, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- SequenceHeaderParserInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava.nbio.core.sequence.io.template
-
- SequenceIdParser - Class in org.forester.util
-
- SequenceLocation<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava.nbio.core.sequence.location
-
A location in a sequence that keeps a reference to its parent sequence
- SequenceLocation(int, int, S) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
-
- SequenceLocation(int, int, S, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
-
- SequenceLocation(int, int, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
-
- SequenceLocation(Point, Point, S, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SequenceLocation
-
- SequenceMixin - Class in org.biojava.nbio.core.sequence.template
-
Provides a set of static methods to be used as static imports when needed
across multiple Sequence implementations but inheritance gets in the way.
- SequenceMixin() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin
-
- SequenceMixin.SequenceIterator<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
-
A basic sequence iterator which iterates over the given Sequence by
biological index.
- SequenceMixin.SequenceIterator(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator
-
- SequenceMouseListener - Class in org.biojava.nbio.structure.gui.util
-
a mouse listener for the AbstractChainRenderer class
it listens to all mouse events and triggeres appropriate
SequenceListener and FeatureListener events
- SequenceMouseListener(SequenceDisplay) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceMouseListener
-
- SequenceOptimizationHints - Class in org.biojava.nbio.core.sequence
-
A static class that provides optimization hints for memory or performance handling of sequence data.
- SequenceOptimizationHints() - Constructor for class org.biojava.nbio.core.sequence.SequenceOptimizationHints
-
- SequenceOptimizationHints.SequenceCollection - Enum in org.biojava.nbio.core.sequence
-
- SequenceOptimizationHints.SequenceUsage - Enum in org.biojava.nbio.core.sequence
-
- SequencePair<S extends Sequence<C>,C extends Compound> - Interface in org.biojava.nbio.alignment.template
-
Defines a data structure for the results of pairwise sequence alignment.
- SequenceParser - Class in org.forester.io.parsers.phyloxml.data
-
- SequenceParserInterface - Interface in org.biojava.nbio.core.sequence.io.template
-
- SequenceProxyView<C extends Compound> - Class in org.biojava.nbio.core.sequence.template
-
- SequenceProxyView() - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- SequenceProxyView(Sequence<C>) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- SequenceProxyView(Sequence<C>, Integer, Integer) - Constructor for class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
Main constructor for working with SequenceProxyViews
- SequenceReader<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
-
- SequenceRelation - Class in org.forester.phylogeny.data
-
- SequenceRelation() - Constructor for class org.forester.phylogeny.data.SequenceRelation
-
- SequenceRelation.SEQUENCE_RELATION_TYPE - Enum in org.forester.phylogeny.data
-
- SequenceRelationParser - Class in org.forester.io.parsers.phyloxml.data
-
- SequenceScalePanel - Class in org.biojava.nbio.structure.gui.util
-
A class that draws a Sequence as a rectangle, a scale display over it.
- SequenceScalePanel(int) - Constructor for class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- SequenceTools - Class in org.biojava.nbio.core.util
-
- SequenceTools() - Constructor for class org.biojava.nbio.core.util.SequenceTools
-
- SequenceUtil - Class in org.biojava.nbio.data.sequence
-
Utility class for operations on sequences
- SequenceView<C extends Compound> - Interface in org.biojava.nbio.core.sequence.template
-
- SequenceWriter - Class in org.forester.io.writers
-
- SequenceWriter() - Constructor for class org.forester.io.writers.SequenceWriter
-
- SequenceWriter.SEQ_FORMAT - Enum in org.forester.io.writers
-
- SequentialColorPalettePanel - Class in org.jcolorbrewer.ui
-
Creates a color palette of sequential colors defined by ColorBrewer
- SequentialColorPalettePanel() - Constructor for class org.jcolorbrewer.ui.SequentialColorPalettePanel
-
- seqWeight - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- Ser - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- SerializableCache<K,V> - Class in org.biojava.nbio.structure.domain
-
A class that provides all that is necessary to create a Serializable Cache
- SerializableCache(String) - Constructor for class org.biojava.nbio.structure.domain.SerializableCache
-
set cacheFileName to null to disable caching
- serialize(File) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- serializedCache - Variable in class org.biojava.nbio.structure.domain.SerializableCache
-
- serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.ChooseDirAction
-
- serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor
-
- serialVersionUID - Static variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathDomain
-
- serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathFragment
-
- serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathNode
-
- serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathSegment
-
- serialVersionUID - Static variable in exception org.biojava.nbio.structure.io.PDBParseException
-
- serialVersionUID - Static variable in exception org.biojava.nbio.structure.StructureException
-
- serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
-
- serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
-
- serialVersionUID - Static variable in class org.forester.archaeopteryx.FontChooser
-
- SERVER_LOCATION - Static variable in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
- set(int, int, double) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Set a single element.
- set(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- set(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- setA(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setAAIndexProvider(AAIndexProvider) - Static method in class org.biojava.nbio.alignment.aaindex.AAindexFactory
-
- setAbbreviateScientificTaxonNames(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setAbsoluteMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setAbsolutePercentialRNAsuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
- setAbsolutePercentileClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the absolutePercentileClashscore property.
- setAbsolutePercentileDCCRfree(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
- setAbsolutePercentilePercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the absolutePercentilePercentRamaOutliers property.
- setAbsolutePercentilePercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the absolutePercentilePercentRotaOutliers property.
- setAbsolutePercentilePercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the absolutePercentilePercentRSRZOutliers property.
- setAbsorpt_coefficient_mu(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_correction_T_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_correction_T_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_correction_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_process_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setAccept1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setAccept2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setAcceptedAtomNames(String[]) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
by default the parser will read in all atoms (unless using the CAonly switch).
- setAccession(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
-
The last accession passed to this routine will always be the one used.
- setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setAccession(AccessionID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setAccession(Accession) - Method in class org.forester.phylogeny.data.Sequence
-
- setAccession(String) - Method in class org.forester.protein.BasicProtein
-
- setAccessionNr(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setAcentricOutliers(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the acentricOutliers property.
- setAddress(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- setAfpAftIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAfpBefIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
- setAFPChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- setAfpChain(AFPChain) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- setAfpChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAfpChainList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAfpChainTwiBin(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAfpChainTwiList(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAfpChainTwiNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAfpDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setAfpDisCut0(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setAfpIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAfpSet(List<AFP>) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Set the set of AFPs for this alignment.
- setAlgorithm(StructureAlignment) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
-
- setAlgorithm(StructureAlignment) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAligMap(List<AlignedPosition>) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- setAligMat(AligMatEl[][]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setAligMat(int, int, AligMatEl) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setAligMat(AligMatEl[][]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setAlign_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- setAlignementOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
- setAlignementOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
-
Method to set the value for a specific alignment parameter using a key to store in a map.
- setAlignment(int[][][]) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- setAlignment1(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- setAlignment2(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- setAlignmentFractionThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setAlignmentLengthFraction(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- setAlignmentMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setAlignmentNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Set the number of alignments to fetch
- setAlignmentOption(BlastAlignmentParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the value of specified parameter
- setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Sets the alignment output format to get from the QBlast service
- setAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
we only keep the first alternative...
- setAlignPairs(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlignScoreUpdate(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlignSeqRes(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
define if the SEQRES in the structure should be aligned with the ATOM records
if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
- setAliLenth(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setAllNodesToNotCollapse() - Method in class org.forester.phylogeny.Phylogeny
-
Sets all Nodes of this Phylogeny to not-collapsed.
- setAllowDomainsToBeIgnored(boolean) - Method in class org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
-
- setAllowNonUniqueQuery(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setAlnbeg1(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlnbeg2(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlnLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlnseq1(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlnseq2(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlnsymb(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setAlpha(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setAlt_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setAltAligNumber(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- setAltcode(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the altcode property.
- setAlternativeAlignment(AlternativeAlignment) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- setAlternativeAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
-
- setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- setAltLoc(Character) - Method in interface org.biojava.nbio.structure.Atom
-
Set alternate Location.
- setAltLoc(Character) - Method in class org.biojava.nbio.structure.AtomImpl
-
set alternate Location.
- setAltShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setAminoacid(List<AminoAcidComposition>) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
-
- setAminoType(Character) - Method in interface org.biojava.nbio.structure.AminoAcid
-
Set the name of the AA, in single letter code .
- setAminoType(Character) - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Set the name of the AA, in single letter code .
- setAnchors(int[]) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
Sets the starting list of anchors before running the alignment routine.
- setAngle_alpha(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setAngle_alpha_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setAngle_beta(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setAngle_beta_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setAngle_gamma(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setAngle_gamma_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setAngleDiff(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setAngleThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setAniso_B(String[][]) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setAnnotation(Annotation) - Method in class org.biojava.nbio.ontology.Term.Impl
-
- setAnnotationType(AbstractSequence.AnnotationType) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setApprovedName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setApprovedSymbol(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setArchitectureId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setArrowCursor() - Method in class org.forester.archaeopteryx.MainPanel
-
- setArrowCursor() - Method in class org.forester.archaeopteryx.TreePanel
-
- setAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- setAsas(double[], double[], int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- setAssembly_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- setAssignments(Map<String, String>) - Method in class org.biojava.nbio.structure.domain.AssignmentXMLSerializer
-
- setAsym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setAsym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setAsym_id_list(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- setAsymUnit(Structure) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
-
- setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
-
- setAsymUnit(Structure) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
-
- setAtcc(String) - Method in class org.biojava.nbio.structure.Compound
-
- setAtom(String) - Method in class org.biojava.nbio.structure.validation.Clash
-
Sets the value of the atom property.
- setAtom(String) - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Sets the value of the atom property.
- setAtom0(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Sets the value of the atom0 property.
- setAtom0(String) - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Sets the value of the atom0 property.
- setAtom1(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Sets the value of the atom1 property.
- setAtom1(String) - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Sets the value of the atom1 property.
- setAtom2(String) - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Sets the value of the atom2 property.
- setAtom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setAtom_id_1(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- setAtom_id_2(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- setAtomAsaCs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- setAtomAsaUs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa
-
- setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- setAtomCache(AtomCache) - Method in interface org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
-
- setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider
-
- setAtomCache(AtomCache) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider
-
- setAtomCache(AtomCache) - Static method in class org.biojava.nbio.structure.StructureIO
-
- setAtomCaThreshold(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
the maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
- setAtomGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain
-
Set all Groups with observed density in the chain, i.e.
- setAtomGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set all Groups with observed density in the chain, i.e.
- setAtomicNumber(int) - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- setAtomLinkages(Set<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
Set atom linkages
- setAtomLinkages(Set<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- setAtomName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- setAtoms(List<Atom>) - Method in interface org.biojava.nbio.structure.Group
-
Set the atoms of this group.
- setAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Set the atoms of this group.
- setAtoms(List<ChemCompAtom>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setAtoms(String) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Sets the value of the atoms property.
- setAtoms(String) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Sets the value of the atoms property.
- setAttemptedValidationSteps(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the attemptedValidationSteps property.
- setAuth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setAuth_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setAuth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setAuth_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setAuth_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setAuth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setAuth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setAuth_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setAuthority(String) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setAuthorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setAuthors(String) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Deprecated.
Use #setFetchBehavior()
- setAutoSuggestProvider(AutoSuggestProvider) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
-
- setAvgoccu(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the avgoccu property.
- setAxisAngle(AxisAngle4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setAxisTransformation(RotationAxisAligner) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- setAxisTypes(int[]) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setB(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setB_iso_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setB_iso_mean(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setB_iso_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setB_iso_or_equiv(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setB_iso_or_equiv_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setBackground(Color) - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Set the background color for the window.
- setBackgroundColorGradient(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setBackgroundColorGradient(boolean) - Method in class org.forester.archaeopteryx.Options
-
- setBadRmsd(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setBaseFontFamilyName(String) - Method in class org.forester.archaeopteryx.Configuration
-
- setBaseFontSize(int) - Method in class org.forester.archaeopteryx.Configuration
-
- setBbs(Structure, Matrix4d[], boolean) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox
-
- setBend(boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setBeta(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setBetweenCompounds(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setBinaryCharacters(BinaryCharacters) - Method in class org.forester.phylogeny.data.NodeData
-
- setBinaryOperators(List<OrderedPair<String>>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
-
- setBioAssemblies(Map<Integer, BioAssemblyInfo>) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setBioBegin(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setBioEnd(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- setBiol_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setBiologicalAssembly(boolean) - Method in interface org.biojava.nbio.structure.Structure
-
Set a flag to indicate if this structure is a biological assembly
- setBiologicalAssembly(boolean) - Method in class org.biojava.nbio.structure.StructureImpl
-
Sets a flag to indicate if this structure is a biological assembly
- setBiologicalUnit(String) - Method in class org.biojava.nbio.structure.Compound
-
- setBioStart(Integer) - Method in class org.biojava.nbio.core.sequence.template.SequenceProxyView
-
- setBioUnitDataProvider(String) - Static method in class org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
-
- setBlastAdvancedOptions(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
This method is to be used if a request is to use non-default values at submission.
- setBlastDatabase(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the database to be used with blastall
- setBlastExpect(double) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the EXPECT parameter to be use with blastall
- setBlastFromToPosition(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the QUERY_FROM and QUERY_TO parameters to be use by blast.
- setBlastGapCosts(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the GAPCOSTS parameter
- setBlastMatrix(BlastMatrixEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the value for the MATRIX parameter to use for blastall
- setBlastProgram(BlastProgramEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the program to be used with blastall
- setBlastWordSize(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
-
Sets the WORD_SIZE parameter to be use with blastall
- setBlock2Afp(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockGap(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockNumClu(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockNumIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockNumSpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockResList(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockResSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockRotationMatrix(Matrix[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockScore(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockShiftVector(Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setBlockSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setbondLengthTolerance(double) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- setBonds(List<ChemCompBond>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setBootstrapConfidence(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method.
- setBootstrapSamples(int) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setBorderColor(Color) - Method in class org.forester.phylogeny.data.NodeVisualization
-
- setBranchColor(BranchColor) - Method in class org.forester.phylogeny.data.BranchData
-
- setBranchColorValue(PhylogenyNode, Color) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- setBranchData(BranchData) - Method in class org.forester.phylogeny.PhylogenyNode
-
- setBranchWidth(BranchWidth) - Method in class org.forester.phylogeny.data.BranchData
-
- setBranchWidthValue(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method
- setBravLattice(BravaisLattice) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setBtype(BridgeType) - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- setBulkSolventB(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the bulkSolventB property.
- setBulkSolventK(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the bulkSolventK property.
- setC(Atom) - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- setC(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setC1(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- setCA(Atom) - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- setCa1Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- setCa2(Atom[]) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- setCa2Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setCache(AtomCache) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- setCacheDoubleValues(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- setCacheLocation(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- setCacheLocation(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- setCachePath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
set the location at which utility data should be cached.
- setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setCallbackFunction(String, String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- setCartn_x(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setCartn_x_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setCartn_y(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setCartn_y_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setCartn_z(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setCartn_z_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setCategory(String) - Method in class org.biojava.nbio.ontology.Synonym
-
- setCategory(ModificationCategory) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
- setCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- setCATH(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setCath(CathDatabase) - Static method in class org.biojava.nbio.structure.cath.CathFactory
-
Sets the default (singleton) CathDatabase.
- setCathDownloadUrl(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- setCathVersion(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- setCCP4Version(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the ccp4Version property.
- setCdsEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setCdsStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setCell(String) - Method in class org.biojava.nbio.structure.Compound
-
- setCell_setting(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- setCellColor(ContinuousColorMapper) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- setCellLine(String) - Method in class org.biojava.nbio.structure.Compound
-
- setCellularLocation(String) - Method in class org.biojava.nbio.structure.Compound
-
- setCenter1(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setCenter2(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setCentered(boolean) - Method in class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- setCentricOutliers(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the centricOutliers property.
- setChain(Chain) - Method in interface org.biojava.nbio.structure.Group
-
Sets the back-reference to its parent Chain.
- setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceMouseListener
-
- setChain(Chain) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- setChain(Chain) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Sets the back-reference to its parent Chain.
- setChain(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the chain property.
- setChain1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setChain2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setChainId(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- setChainId(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- setChainID(String) - Method in interface org.biojava.nbio.structure.Chain
-
Set the name of this chain (Chain id in PDB file ).
- setChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set the name of this chain (Chain id in PDB file ).
- setChainId(String) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- setChainId(String) - Method in class org.biojava.nbio.structure.DBRef
-
The chain ID of the corresponding chain.
- setChainId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setChainId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Sets the chain identified this transformation should be applied to.
- setChainId(String) - Method in class org.biojava.nbio.structure.ResidueNumber
-
- setChainID1(String) - Method in class org.biojava.nbio.structure.SSBond
-
- setChainID2(String) - Method in class org.biojava.nbio.structure.SSBond
-
- setChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setChainRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The RMSD of the chain of AFPs.
- setChains(List<Chain>) - Method in class org.biojava.nbio.structure.Compound
-
Set the chains for this Compound
- setChains(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
-
Set the chains of a structure, if this is a NMR structure,
this will only set model 0.
- setChains(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
-
Set the chains for a model
- setChains(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setChains(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setCharacter(int, String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- setCharacter(int, String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- setCharge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.Group
-
Set the Chemical Component that closer describes this group.
- setChemComp(ChemComp) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- setChemCompProvider(ChemCompProvider) - Static method in class org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
-
- setChild1(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the first child PhylogenyNode of this PhylogenyNode to n.
- setChild2(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the second child PhylogenyNode of this PhylogenyNode to n.
- setChildNode(int, PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
-
Inserts PhylogenyNode n at the specified position i into the list of
child nodes.
- setChildren(List<Integer>) - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Set the children features
- setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Set the children features
- setChrLoc(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setChromosomeNumber(int) - Method in class org.biojava.nbio.core.sequence.ChromosomeSequence
-
- setCid(BigInteger) - Method in class org.biojava.nbio.structure.validation.Clash
-
Sets the value of the cid property.
- setCircular(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Set the radius of a circumscribed sphere, that goes
through all vertices
- setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Set the radius of a circumscribed sphere, that goes
through all vertices
- setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Set the radius of a circumscribed sphere, that goes
through all vertices
- setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Set the radius of a circumscribed sphere, that goes
through all vertices
- setClashmag(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Clash
-
Sets the value of the clashmag property.
- setClashmag(BigDecimal) - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Sets the value of the clashmag property.
- setClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the clashscore property.
- setClassId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setClassId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setClassification(String) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
set the number of the cluster this alignment belongs to.
- setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setCluster(StructureInterfaceCluster) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setClusterValue(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setCode(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- setCoeff(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setCoefficient(String, CoxCoefficient) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setCol(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- setCollapse(boolean) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets whether this PhylogenyNode should be drawn as collapsed.
- setColor(Color) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- setColor(Color) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
Apply this color to the current Selection
- setColor(Color) - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Set the current color in the color chooser.
- setColor(int, int, int) - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Set the current color in the color chooser.
- setColorBrewer(ColorBrewer) - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Set the current color in the color chooser.
- setColorBrewer(ColorBrewer) - Method in class org.jcolorbrewer.ui.ColorPanelSelectionModel
-
- setColorizeBranches(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setColorLabelsSameAsParentBranch(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setColorLabelsSameAsParentBranch(boolean) - Method in class org.forester.archaeopteryx.Options
-
- setColorMap(Map<String, Color>) - Static method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- setColorSpace(ColorSpace, LinearColorInterpolator.InterpolationDirection[]) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
-
Sets the ColorSpace to use for interpolation.
- setColorSpace(ColorSpace) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
-
- setCols(List<AminoAcidCompound>) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setComment(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
- setComment(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setComment(String) - Method in class org.forester.go.BasicGoTerm
-
- setCommon_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setCommonName(String) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- setComp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- setComplexFeaturesAppendMode(InsdcParser.complexFeaturesAppendEnum) - Method in class org.biojava.nbio.core.sequence.location.InsdcParser
-
- setCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
-
- setCompound(Compound) - Method in interface org.biojava.nbio.structure.Chain
-
Set the Compound
- setCompound(Compound) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set the Compound
- setCompoundAt(char, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Converts from char to Compound and sets it at the given biological index
- setCompoundAt(C, int) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Sets the compound at the specified biological index
- setCompounds(List<Compound>) - Method in interface org.biojava.nbio.structure.Structure
-
Set the Compounds
- setCompounds(List<Compound>) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Class is immutable & so this is unsupported
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Unsupported
- setCompoundSet(CompoundSet<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setCompoundSet(CompoundSet<C>) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader
-
- setCompoundSet(CompoundSet<NucleotideCompound>) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- setCondition(ModificationCondition) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
- setConfidence(Confidence) - Method in class org.forester.phylogeny.data.Annotation
-
- setConfidence(Confidence) - Method in class org.forester.phylogeny.data.Event
-
- setConfidence(Confidence) - Method in class org.forester.phylogeny.data.SequenceRelation
-
- setConfidence(Confidence) - Method in class org.forester.phylogeny.Phylogeny
-
- setConfidence(PhylogenyNode, double) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method.
- setConfidence(PhylogenyNode, double, String) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method.
- setConn(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setConn_type_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setConnectedFrom(int) - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- setConnectedTo(int) - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- setConnections(List<Map<String, Integer>>) - Method in interface org.biojava.nbio.structure.Structure
-
sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
- setConnections(List<Map<String, Integer>>) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setContacts(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setContacts(AtomContactSet) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setContacts(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader
-
- setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- setContents(String, ArrayList) - Method in class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- setContents(String) - Method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
Once the sequence is retrieved set the contents and make sure everything this is valid
- setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- setContents(List<C>) - Method in class org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader
-
- setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.BitSequenceReader
-
Class is immutable & so this is unsupported
- setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.JoiningSequenceReader
-
- setContents(String) - Method in class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Unsupported
- setContents(String) - Method in interface org.biojava.nbio.core.sequence.template.SequenceReader
-
- setContents(String) - Method in class org.biojava.nbio.core.sequence.views.RnaSequenceView
-
- setContig(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
-
- setCoords(double[]) - Method in interface org.biojava.nbio.structure.Atom
-
Set the coordinates.
- setCoords(double[]) - Method in class org.biojava.nbio.structure.AtomImpl
-
Set the coordinates.
- setCopiedAndPastedNodes(Set<Integer>) - Method in class org.forester.archaeopteryx.MainPanel
-
- setCorrelation_coeff_Fo_to_Fc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setCorrelation_coeff_Fo_to_Fc_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setCovered(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setCoxInfo(ArrayList<String>, CoxInfo, String, LinkedHashMap<String, String>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- setCPPoint(Integer) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- setCreate_co(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setCreateAtomBonds(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
Should we create bonds between atoms when parsing a file?
- setCrystalCell(CrystalCell) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Set the crystal cell
- setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setCrystallographicInfo(PDBCrystallographicInfo) - Method in interface org.biojava.nbio.structure.Structure
-
Set crystallographic information for this structure
- setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.StructureImpl
-
Sets crystallographic information for this structure
- setCrystals_number(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setCurrentSequence(String) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
Method open nucleotide stream for sequence with given name.
- setCurrentSequencePosition(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
- setCustomChain1(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
sets a chain in a custom, user provided file
- setCustomFile1(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
set the file path for a custom, user provided file, not a standard PDB file.
- setCut_sites(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- setCuts(int, AlignerHelper.Subproblem, AlignerHelper.Last[][], AlignerHelper.Cut[]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
- setCutsPerSection(int) - Method in class org.biojava.nbio.alignment.routines.GuanUberbacher
-
Sets the number of cuts added to each section during each pass.
- setData(List<String>) - Method in class org.biojava.nbio.structure.scop.server.ListStringWrapper
-
- setData(TreeSet<String>) - Method in class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper
-
- setData(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper
-
- setDataAnisotropy(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the dataAnisotropy property.
- setDatabase(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
- setDatabase(String) - Method in class org.biojava.nbio.structure.DBRef
-
Specifies the database value.
- setDatabaseReferences(DatabaseReferenceInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setDataCompleteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the dataCompleteness property.
- setDate(Date) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setDate(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- setDate(Date) - Method in class org.forester.phylogeny.data.NodeData
-
- setDate_original(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- setDb_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setDb_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setDb_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setDb_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setDbAccession(String) - Method in class org.biojava.nbio.structure.DBRef
-
Sequence database accession code.
- setDbComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setDbIdCode(String) - Method in class org.biojava.nbio.structure.DBRef
-
Sequence database identification code.
- setDbReferences(Set<StockholmStructure.DatabaseReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setDBRefs(List<DBRef>) - Method in interface org.biojava.nbio.structure.Structure
-
Set the list of database references for this structure
- setDBRefs(List<DBRef>) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setDbSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef
-
Initial sequence number of the
database seqment.
- setDbSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef
-
The begin of the sequence position in the database
- setDCCR(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the dccr property.
- setDCCRefinementProgram(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the dccRefinementProgram property.
- setDCCRfree(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the dccRfree property.
- setDcl(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setDebug(boolean) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
Deprecated.
- setDefault() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI
-
- setDefault() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
- setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Sets a default Jmol script used for coloring.
- setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- setDefaultColoring(String) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- setDefaultCutsPerSection(int) - Static method in class org.biojava.nbio.alignment.routines.GuanUberbacher
-
Sets the default number of cuts added to each section during each pass.
- setDefaultExtensionPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
Sets the default gap extension penalty.
- setDefaultNodeFill(NodeVisualization.NodeFill) - Method in class org.forester.archaeopteryx.Configuration
-
- setDefaultNodeShape(NodeVisualization.NodeShape) - Method in class org.forester.archaeopteryx.Configuration
-
- setDefaultNodeShapeSize(short) - Method in class org.forester.archaeopteryx.Configuration
-
- setDefaultOpenPenalty(int) - Static method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
Sets the default gap open penalty.
- setDefaultText(String) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
-
- setDefinition(String) - Method in class org.forester.go.BasicGoTerm
-
- setDegreeFreedom(double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setDensityCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDepDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setDesc(String) - Method in class org.forester.phylogeny.data.Annotation
-
- setDesc(String) - Method in class org.forester.phylogeny.data.Date
-
- setDescription(String) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setDescription(String) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- setDescription(String) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Sets the description of this matrix.
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Set the description that can be used to describe the feature
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setDescription(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- setDescription(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- setDescription(String) - Method in class org.biojava.nbio.ontology.AbstractTerm
-
- setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm
-
- setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- setDescription(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- setDescription(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
set the description of this ontology
- setDescription(String) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl
-
- setDescription(String) - Method in interface org.biojava.nbio.ontology.Term
-
set the description of the term;
- setDescription(String) - Method in class org.biojava.nbio.ontology.Triple.Impl
-
- setDescription(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
- setDescription(String) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- setDescription(String) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- setDescription(String) - Method in class org.biojava.nbio.structure.cath.CathNode
-
- setDescription(String) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- setDescription(String) - Method in class org.biojava.nbio.structure.Site
-
sets the REMARK 800 description of the site
- setDescription(String) - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
-
- setDescription(String) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
-
- setDescription(String) - Method in class org.forester.phylogeny.Phylogeny
-
- setDescription(String) - Method in class org.forester.protein.BasicProtein
-
- setDescription(String) - Method in class org.forester.surfacing.MappingResults
-
- setDescription(String) - Method in class org.forester.util.BasicDescriptiveStatistics
-
- setDescription(String) - Method in interface org.forester.util.DescriptiveStatistics
-
- setDescription2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Set the textual description for protein 2.
- setDescriptionNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Sets the number of descriptions to fetch
- setDescriptor(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setDetailedness(DomainSimilarityCalculator.Detailedness) - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- setDetails(String) - Method in class org.biojava.nbio.structure.Compound
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- setDetails(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setDf(int) - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
-
- setDiagonalDistance(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDiagonalDistance2(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDirection(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setDirectionTowards(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyBranch
-
- setDiscreteValues(WorkSheet) - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
-
- setDisCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- setDisFilter(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setDisplayAsPhylogram(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayColors(SortedMap<String, Color>) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayConfidenceValues(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayInternalData(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayNodeNames(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplaySequenceAcc(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplaySequenceNames(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplaySequenceRelations(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplaySequenceSymbols(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayTaxonomyCode(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayTaxonomyCommonNames(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayTaxonomyImages(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisplayTaxonomyScientificNames(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setDisSmooth(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setDist(int[][]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- setDist(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Clash
-
Sets the value of the dist property.
- setDist(BigDecimal) - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Sets the value of the dist property.
- setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- setDisTable1(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setDisTable2(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContact
-
- setDistance(double) - Method in class org.biojava.nbio.structure.secstruc.DistEn
-
- setDistance(Double) - Method in class org.forester.phylogeny.data.SequenceRelation
-
- setDistanceIncrement(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
A matrix with ca1length rows and ca2length columns.
- setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
The distance matrix this alignment is based on
- setDistanceToParent(double) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the length of the branch leading to the _parent of this
PhylogenyNode to double d.
- setDistanceToParent(double) - Method in interface org.forester.phylogeny.PhylogenyNodeI
-
- setDistanceUnit(String) - Method in class org.forester.phylogeny.Phylogeny
-
- setDistribution(Distribution) - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always sets the first Distribution.
- setDistribution(int, Distribution) - Method in class org.forester.phylogeny.data.NodeData
-
- setDNAType(DNASequence.DNAType) - Method in class org.biojava.nbio.core.sequence.DNASequence
-
- setDoAngleCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDoDensityCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDoDistanceCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDoi(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
Set the value of doi
- setDoi(String) - Method in class org.forester.phylogeny.data.Reference
-
- setDomainArchitecture(DomainArchitecture) - Method in class org.forester.phylogeny.data.Sequence
-
- setDomainCounter(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setDomainId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setDomainName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setDomainProvider(DomainProvider) - Static method in class org.biojava.nbio.structure.domain.DomainProviderFactory
-
- setDomains(SortedSet<HmmerDomain>) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setDomainsIgnoredDueToEval(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setDomainsIgnoredDueToIndividualScoreCutoff(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setDomainSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setDonor1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setDonor2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setDoRMSCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setDownloadAll(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider
-
By default this provider will download only some of the
ChemComp files.
- setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- setDuplications(int) - Method in class org.forester.phylogeny.data.Event
-
- setDVar(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setDynamicallyHideData(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setEcNums(List<String>) - Method in class org.biojava.nbio.structure.Compound
-
- setEdited(boolean) - Method in class org.forester.archaeopteryx.TreePanel
-
- setEditorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setEDSR(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the edsr property.
- setEDSResolution(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the edsResolution property.
- setEDSResolutionLow(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the edsResolutionLow property.
- setElement(List<Element>) - Method in class org.biojava.nbio.aaproperties.xml.ElementTable
-
- setElement(Element) - Method in interface org.biojava.nbio.structure.Atom
-
Set element of the atom name, e.g.
- setElement(Element) - Method in class org.biojava.nbio.structure.AtomImpl
-
Set element of the atom name, e.g.
- setElement1(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
-
Sets the first element of an ordered pair.
- setElement2(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair
-
Sets the second element of an ordered pair.
- setEmail(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Set the email for QBlast.
- setEnd(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- setEnd(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- setEnergy(double) - Method in class org.biojava.nbio.structure.secstruc.DistEn
-
- setEnergy(double) - Method in class org.biojava.nbio.structure.secstruc.HBond
-
- setEngineered(String) - Method in class org.biojava.nbio.structure.Compound
-
- setEnsemblGeneId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setEnt(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the ent property.
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- setEntity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setEntityId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- setEntry(Entry) - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Sets the value of the entry property.
- setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- setEntry_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- setEquivalent(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- setEvalCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setEvalue(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setEValueMaximum(double) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setEValueMaximum(double) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- setEvCode(String) - Method in class org.biojava.nbio.structure.Site
-
sets the REMARK 800 EVIDENCE CODE for the site.
- setEvent(Event) - Method in class org.forester.phylogeny.data.NodeData
-
- setEvidence(String) - Method in class org.forester.phylogeny.data.Annotation
-
- setExonCount(int) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setExonEnds(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setExonStarts(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setExpectedExecutionTime(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
- setExperimentalTechnique(String) - Method in class org.biojava.nbio.structure.PDBHeader
-
Adds the experimental technique to the set of experimental techniques of this header.
- setExpression_system_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setExpressionSystem(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemAtccNumber(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemCell(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemCellLine(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemCellularLocation(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemGene(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemOrgan(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemOrganelle(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemOtherDetails(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemPlasmid(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemStrain(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemTaxId(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemTissue(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemVariant(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemVector(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExpressionSystemVectorType(String) - Method in class org.biojava.nbio.structure.Compound
-
- setExtensionPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
- setExtensionPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
Sets penalty given when an already open gap elongates by a single element
- setExtractPfamTaxonomyCodesInNhParsing(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setFalseDiscoveryRate(float) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setFamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setFarmJob(FarmJob) - Method in class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener
-
- setFatCatOutput(boolean) - Method in class org.biojava.nbio.structure.align.gui.MySaveFileListener
-
- setFeatureRetriever(FeatureRetriever) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Set the behavior for fetching files from the server
- setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Set the behavior for fetching files from the server.
- setFetchCurrent(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Deprecated.
Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)
- setFetchCurrent(boolean) - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
Deprecated.
Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
- setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Deprecated.
Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)
- setFetchFileEvenIfObsolete(boolean) - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
Deprecated.
Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
- setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
- setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- setFile1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setFile2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setFileFormat(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- setFileLocation(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
-
- setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
- setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
-
- setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.PDBFileParser
-
- setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.PDBFileReader
-
- setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
- setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.StructureProvider
-
Set the parameters that should be used for file parsing
- setFileParsingParams(FileParsingParameters) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- setFillColor(Color) - Method in class org.forester.phylogeny.data.NodeVisualization
-
- setFillType(NodeVisualization.NodeFill) - Method in class org.forester.phylogeny.data.NodeVisualization
-
- setFirstGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setFlaggedStatusOfOutlierWells(boolean) - Method in class org.forester.development.MsaRenderer
-
- setFlaggedStatusOfSelectedWells(boolean) - Method in class org.forester.development.MsaRenderer
-
- setFlexible(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- setFlippableSidechain(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the flippableSidechain property.
- setFocusAfpList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setFocusAfpn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setFocusRes1(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setFocusRes2(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setFocusResn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setFoFcCorrelation(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the foFcCorrelation property.
- setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setFoldId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setFont(Font) - Method in class org.forester.archaeopteryx.FontChooser
-
- setFormat(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setFormat(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setFormula(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the residue formula.
- setFormula(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setFormula(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setFormula_weight(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setFormula_weight(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setFragCompat(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setFragLen(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setFragLen(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- setFragLen(int) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setFragLenSq(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setFragment(String) - Method in class org.biojava.nbio.structure.Compound
-
- setFragmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- setFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setFragmentMiniDistance(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
- setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- setFragScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setFrom(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- setFrom(int) - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- setFromFtp(JCheckBox) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
-
- setGamma(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell
-
- setGapCreate(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setGapExtCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setGapExtCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setGapExtend(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setGapExtend(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- setGapExtend(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setGapExtension(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- setGapExtension(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setGapExtRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setGapExtRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setGapLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setGapOpen(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- setGapOpen(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- setGapOpen(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- setGapOpen(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setGapOpenCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setGapOpenCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setGapOpenRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setGapOpenRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setGapPenalty(GapPenalty) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Sets the gap penalties.
- setGenbankDirectoryCache(String) - Method in class org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader
-
- setGene(String) - Method in class org.biojava.nbio.structure.Compound
-
- setGene_src_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGene_src_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGene_src_dev_stage(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGene_src_genus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGene_src_species(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGene_src_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGene_src_tissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGene_src_tissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setGenebankId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setGeneLosses(int) - Method in class org.forester.phylogeny.data.Event
-
- setGeneName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setGeneSymb(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setGenus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setGFAccessionNumber(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFAuthors(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFClan(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFDBComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFDefinition(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFGatheringThreshs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFIdentification(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFKeywords(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFMembership(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFNoiseCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFNumSequences(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFPfamAccession(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFPreviousIDs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFRefComment(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFSearchMethod(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFSourceSeed(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFSourceStructure(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFTrustedCutoffs(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFTypeField(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGFWikipediaLink(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setGoAnnotationOutput(DomainSimilarityCalculator.GoAnnotationOutput) - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- setGoIdToTermMap(Map<GoId, GoTerm>) - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- setGoNamespaceLimit(GoNameSpace) - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- setGoSubsets(List<GoSubset>) - Method in class org.forester.go.BasicGoTerm
-
- setGraph(Graph<V>) - Method in class org.biojava.nbio.structure.symmetry.utils.ComponentFinder
-
- setGroup(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setGroup(Group) - Method in interface org.biojava.nbio.structure.Atom
-
Set the back-reference to its parent Group.
- setGroup(Group) - Method in class org.biojava.nbio.structure.AtomImpl
-
Set the back-reference to its parent Group.
- setGroup_PDB(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setGroups(Set<StructureGroup>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- setGroups(Set<StructureGroup>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- setGroups(List<Group>) - Method in class org.biojava.nbio.structure.Site
-
- setGuessRootedness(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser
-
- setH(Atom) - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- setHazardRatio(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setHazardRatioHiCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setHazardRatioLoCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setHeaderOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
Parse only the PDB file header out of the files
- setHeaderVars(String) - Method in class org.biojava.nbio.structure.Compound
-
- setHeight(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
- setHelixRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setHelixRmsdToRiseRatio(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setHetero(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- setHetero(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setHgncId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setHide(boolean) - Method in class org.biojava.nbio.survival.data.HeaderInfo
-
- setHmmAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setHmmDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setHmmFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setHmmName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setHmmTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setHomologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setHost_org_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setHost_org_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setHost_org_genus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setHost_org_species(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setHost_org_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setIclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- setIcode(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the icode property.
- setId(String) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
- setId(long) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setId(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setId(long) - Method in class org.biojava.nbio.structure.AtomImpl
-
Set the Hibernate database ID.
- setId(Long) - Method in interface org.biojava.nbio.structure.Chain
-
Set the ID used by Hibernate.
- setId(Long) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set the ID used by Hibernate.
- setId(Long) - Method in class org.biojava.nbio.structure.Compound
-
set the ID used by Hibernate
- setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- setId(Long) - Method in class org.biojava.nbio.structure.DBRef
-
Set the ID used by Hibernate.
- setId(String) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- setId(long) - Method in class org.biojava.nbio.structure.HetatomImpl
-
the Hibernate database ID
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setId(int) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- setId(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setId(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
- setId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Sets the identifier for this biological assembly transformation.
- setId(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setId(Long) - Method in interface org.biojava.nbio.structure.Structure
-
set the ID used by Hibernate
- setId(Long) - Method in class org.biojava.nbio.structure.StructureImpl
-
set the ID used by Hibernate
- setId(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setId(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setId(String) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
- setId(int) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the Id of this PhylogenyNode to i.
- setIdbnsBegin(char) - Method in class org.biojava.nbio.structure.DBRef
-
Insertion code of initial residue of the segment, if PDB is the
reference.
- setIdbnsEnd(char) - Method in class org.biojava.nbio.structure.DBRef
-
Insertion code of the ending
residue of the segment, if PDB is
the reference.
- setIdCode(String) - Method in class org.biojava.nbio.structure.DBRef
-
Set the idCode for this entry.
- setIdCode(String) - Method in class org.biojava.nbio.structure.PDBHeader
-
The PDB code for this protein structure.
- setIdenticalSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setIdentifier(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
- setIdentifier(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- setIdentifier(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- setIdentifier(int, String) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- setIdentifier(int, String) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- setIdentifier(int, String) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- setIdentifier(int, String) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix
-
- setIdentifier(int, Object) - Method in class org.forester.msa.BasicMsa
-
- setIdentifier(int, Object) - Method in interface org.forester.msa.Msa
-
- setIdentifier(Identifier) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setIdentifier(Identifier) - Method in class org.forester.phylogeny.Phylogeny
-
- setIdentity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setIdxlist(List<int[]>) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
-
Stores the alignment between the residues of several fragments.
- setIgnoreDufs(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setIgnoreDufs(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- setIgnoreEngulfedDomains(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
To ignore domains which are completely engulfed by domains (individual
ones or stretches of overlapping ones) with better support values.
- setIgnoreEngulfedDomains(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
To ignore domains which are completely engulfed by domains (individual
ones or stretches of overlapping ones) with better support values.
- setIgnoreQuotes(boolean) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser
-
- setIgnoreQuotes(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser
-
- setIgnoreVirusLikeIds(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setIgnoreVirusLikeIds(boolean) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- setImageMap(Hashtable<String, BufferedImage>) - Method in class org.forester.archaeopteryx.TreePanel
-
- setInChI(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setInChIKey(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setIndentPhyloxml(boolean) - Method in class org.forester.io.writers.PhylogenyWriter
-
- setIndex(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- setIndex(Integer) - Method in class org.biojava.nbio.survival.data.HeaderInfo
-
- setIndexColumnName(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setIndicator(byte) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the _indicator value of this PhylogenyNode to i.
- setIndicatorsToZero() - Method in class org.forester.phylogeny.Phylogeny
-
Sets the indicators of all Nodes of this Phylogeny to 0.
- setIndividualDomainScoreCutoffs(Map<String, String>) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
Sets the individual domain score cutoff values (for example, gathering
thresholds from Pfam).
- setIndividualScoreCutoffs(Map<String, Double>) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
Sets the individual score cutoff values (for example, gathering
thresholds from Pfam).
- setInitialK(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setInitials(String) - Method in class org.biojava.nbio.structure.Author
-
- setInputMatrixType(SymmetricalDistanceMatrixParser.InputMatrixType) - Method in class org.forester.io.parsers.SymmetricalDistanceMatrixParser
-
- setInsCode(Character) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- setInsCode(Character) - Method in class org.biojava.nbio.structure.ResidueNumber
-
- setInsCode1(String) - Method in class org.biojava.nbio.structure.SSBond
-
- setInsCode2(String) - Method in class org.biojava.nbio.structure.SSBond
-
- setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Sets the radius of an inscribed sphere, that is tangent to each
of the icosahedron's faces
- setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Sets the radius of an inscribed sphere, that is tangent to each
of the octahedron's faces
- setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism
-
Sets the radius of an inscribed sphere, that is tangent to each
of the icosahedron's faces
- setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Sets the radius of an inscribed sphere, that is tangent to each
of the tetrahedron's faces
- setInsertBegin(char) - Method in class org.biojava.nbio.structure.DBRef
-
Initial insertion code of the PDB sequence segment.
- setInsertEnd(char) - Method in class org.biojava.nbio.structure.DBRef
-
Ending insertion code of the PDB sequence segment.
- setInstalledDomainDescription(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- setInstalledDomainList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- setInstalledDomall(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- setInstalledNodeList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation
-
- setInt_Tables_number(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- setIntermediateFilesBase(String) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setInternalChainID(String) - Method in interface org.biojava.nbio.structure.Chain
-
Set the internal chain ID that is used in mmCif files
- setInternalChainID(String) - Method in class org.biojava.nbio.structure.ChainImpl
-
- setInterpolationDirection(int, LinearColorInterpolator.InterpolationDirection) - Method in class org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator
-
- setInterpolator(ColorInterpolator) - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- setIoTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setIoTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setIoverSigma(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the ioverSigma property.
- setIsAminoAcid(boolean) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- setIsFlaggingStatusChangedToFalse() - Method in class org.forester.development.MsaRenderer
-
- setIsMarked(boolean) - Method in class org.forester.development.ResidueRenderer
-
- setIsotopes(List<Isotope>) - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- setIsPublished(Boolean) - Method in class org.biojava.nbio.structure.JournalArticle
-
Sets the publication state of a JournalArticle - TO BE PUBLISHED == false
- setIsSelected(boolean) - Method in class org.forester.development.ResidueRenderer
-
- setJclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- setJmolPanel(JmolPanel) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- setJoinFast(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setJoinPlo(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setJoinRMSCutoff(double) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.PDBHeader
-
Set the associated publication as defined by the JRNL records in a PDB
file.
- setJournalArticle(JournalArticle) - Method in interface org.biojava.nbio.structure.Structure
-
Set the associated publication as defined by the JRNL records in a PDB
file.
- setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.StructureImpl
-
set the associated publication as defined by the JRNL records in a PDB
file.
- setJournalName(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setKaplanMeierFigure(KaplanMeierFigure) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
-
Pick up needed info and details from the KM Figure
- setKappa(float) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics) - Method in class org.forester.surfacing.BasicCombinableDomains
-
- setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics) - Method in interface org.forester.surfacing.CombinableDomains
-
This is to set descriptive statistics for the confidence (i.e.
- setKeyDomainCount(int) - Method in class org.forester.surfacing.BasicCombinableDomains
-
- setKeyDomainCount(int) - Method in interface org.forester.surfacing.CombinableDomains
-
Sets how many times the key domain is present in a given species genome.
- setKeyDomainProteinsCount(int) - Method in class org.forester.surfacing.BasicCombinableDomains
-
- setKeyDomainProteinsCount(int) - Method in interface org.forester.surfacing.CombinableDomains
-
Sets how many proteins with the key domain are present in a given species
genome.
- setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
- setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- setLabel_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setLabel_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setLabel_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setLabel_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setLabel_entity_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setLabel_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- setLength(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- setLength(int) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
-
- setLength1(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setLength2(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setLength_a(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setLength_a_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setLength_b(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setLength_b_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setLength_c(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setLength_c_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setLfrom(int) - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- setLigRSRnbrMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the ligRSRnbrMean property.
- setLigRSRnbrStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the ligRSRnbrStdev property.
- setLigRSRnumnbrs(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the ligRSRnumnbrs property.
- setLigRSRZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the ligRSRZ property.
- setLikeSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setLineage(List<String>) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setLinearPredictor(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaGeneWriter
-
- setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
-
- setLineLength(int) - Method in class org.biojava.nbio.core.sequence.io.GenbankWriter
-
- setLineSeparator(String) - Method in class org.biojava.nbio.core.sequence.io.FastaWriter
-
Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
- setLink(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the linked PhylogenyNode of this PhylogenyNode to n.
- setLoadChemCompInfo(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
Sets if chemical component defintions should be loaded from the web
- setLocal(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- setLocalSymmetry(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
- setLocation(AbstractLocation) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setLocation(AbstractLocation) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
The new location for this feature.
- setLocation(String) - Method in class org.forester.phylogeny.data.Sequence
-
- setLocationInAlignment(Location) - Method in interface org.biojava.nbio.alignment.template.MutableAlignedSequence
-
- setLocus(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- setLongName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- setLongName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- setLongName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- setLongName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- setLookAndFeel() - Static method in class org.biojava.nbio.structure.align.webstart.AligUIManager
-
- setLowercaseToNull(ProteinSequence, Object[]) - Static method in class org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
-
- setLs_d_res_high(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_d_res_low(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_matrix_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_number_parameters(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_number_reflns_all(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_number_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_number_reflns_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_number_reflns_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_number_restraints(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_percent_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_percent_reflns_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_all(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_free_error(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_free_error_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_redundancy_reflns_obs(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_wR_factor_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLs_wR_factor_R_work(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setLto(int) - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- setM(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setMacromolecularSize(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
- setMappingSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- setMapProperty(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
-
- setMarkedOfAllWellsToFalse() - Method in class org.forester.development.MsaRenderer
-
- setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- setMass(double) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- setMatrix(short[][]) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
sets the distance matrix to be displayed
- setMatrix(Matrix) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- setMatrix(Matrix) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Set a submatrix.
- setMatrix(int[], int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Set a submatrix.
- setMatrix(int[], int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Set a submatrix.
- setMatrix(int, int, int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Set a submatrix.
- setMatrix11(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix12(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix13(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix21(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix22(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix23(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix31(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix32(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatrix33(double) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setMatTransform(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- setMax(short) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setMax(double) - Method in class org.forester.development.MsaRenderer
-
- setMax(BigDecimal) - Method in class org.forester.phylogeny.data.Date
-
- setMaxAllowedOverlap(int) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setMaxAllowedOverlap(int) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- setMaxAtoms(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
the maximum numbers of atoms to load in a protein structure (prevents memory overflows)
- setMaxGap(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setMaxGapFrag(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setMaxGapSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Set the Max gap size parameter.
- setMaxGapSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
CE specific parameter: set the Max gap size parameter G (during AFP extension).
- setMaximumLocalCombinations(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setMaximumLocalResults(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setMaximumLocalSubunits(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setMaxIter(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setMaxIterations(int) - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- setMaxNrIterationsForOptimization(int) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Set the maximum nr of times the (slow) optimiziation of alignment should iterate.
- setMaxNrSuggestions(int) - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
set the maximum number of suggestions to return
- setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- setMaxNrSuggestions(int) - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
set the maximum RMSD cutoff to be applied during alignment optimization.
- setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
(jCE specific): maximum RMSD that shall be calculated for the alignment.
- setMaxPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setMaxrefine(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setMaxRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setMaxSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- setMaxTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setMaxTra(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
set the maximum number of Twists that are allowed...
- setMaxTra(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- setMaxTra(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Set the maximum number of Twists that are allowed...
- setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Sets the value of the mean property.
- setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Sets the value of the mean property.
- setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Sets the value of the mean property.
- setMean(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Sets the value of the mean property.
- setMean(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setMeanColor(Color) - Method in class org.forester.development.MsaRenderer
-
- setMembers(List<StructureInterface>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- setMetaDataColumns(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Clears existing meta data columns and sets new ones
- setMetaDataColumnsAfterColumn() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setMetaDataColumnsAfterColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setMetaDataFilter(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setMetaDataRows(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setMetaDataRowsAfterRow() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setMetaDataRowsAfterRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setMethod(String) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- setMethod(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setMethod_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Exptl
-
- setMethod_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron
-
Sets the radius of radius of a sphere, that is tangent to each
of the icosahedron's edges
- setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron
-
Sets the radius of radius of a sphere, that is tangent to each
of the octahedron's edges
- setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron
-
Sets the radius of radius of a sphere, that is tangent to each
of the tetrahedron's edges
- setMin(short) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setMin(double) - Method in class org.forester.development.MsaRenderer
-
- setMin(BigDecimal) - Method in class org.forester.phylogeny.data.Date
-
- setMinConfidenceValue(double) - Method in class org.forester.archaeopteryx.Configuration
-
- setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters
-
- setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
-
- setMindiff(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Sets the value of the mindiff property.
- setMindiff(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Sets the value of the mindiff property.
- setMinimumHelixAngle(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setMinimumHelixRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setMinimumSequenceLengthFraction(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setMinLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setMinRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setMinSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster
-
- setMinTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setMisCut(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setMisLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setMisScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setMod_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- setModDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setModel(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure
-
A convenience function if one wants to edit and replace the
models in a structure.
- setModel(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setModel(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the model property.
- setModel_Cartn_x(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setModel_Cartn_y(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setModel_Cartn_z(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setModelNumber(int) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- setModification(ProteinModification) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound
-
- setModification(ProteinModification) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
-
- setModType(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setMogulIgnore(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the mogulIgnore property.
- setMolecularSequence(String) - Method in class org.forester.phylogeny.data.Sequence
-
- setMolecularSequenceAligned(boolean) - Method in class org.forester.phylogeny.data.Sequence
-
- setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- setMolecularWeight(Float) - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- setMolecularWeight(Float) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- setMoleculeIds(Pair<String>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setMolecules(Pair<Atom[]>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setMolId(int) - Method in class org.biojava.nbio.structure.Compound
-
Set the molecule identifier, called entity_id in mmCIF dictionary.
- setMolName(String) - Method in class org.biojava.nbio.structure.Compound
-
- setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setMon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setMon_nstd_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setMon_nstd_parent_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setMsaPrgParameters(String) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setMsaProcessingMaxAllowedGapRatio(double) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setMsaProcessingMinAllowedLength(int) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setMutation(String) - Method in class org.biojava.nbio.structure.Compound
-
- setN(Atom) - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- setNaiveVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- setName(String) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- setName(String) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setName(String) - Method in class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
- setName(String) - Method in interface org.biojava.nbio.alignment.template.SubstitutionMatrix
-
Sets the name (short description) of this matrix.
- setName(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier
-
- setName(String) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
- setName(String) - Method in class org.biojava.nbio.ontology.IntegerOntology
-
- setName(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl
-
- setName(String) - Method in interface org.biojava.nbio.ontology.Ontology
-
Set the name for this ontology
- setName(String) - Method in class org.biojava.nbio.ontology.Synonym
-
- setName(String) - Method in interface org.biojava.nbio.structure.Atom
-
Set atom name, e.g.
- setName(String) - Method in class org.biojava.nbio.structure.AtomImpl
-
Set atom name, e.g.
- setName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setName(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- setName(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setName(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- setName(String) - Method in interface org.biojava.nbio.structure.Structure
-
Set biological name of Structure .
- setName(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setName(String) - Method in class org.biojava.nbio.structure.validation.Program
-
Sets the value of the name property.
- setName(String) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setName(String) - Method in class org.forester.phylogeny.data.Sequence
-
- setName(String) - Method in class org.forester.phylogeny.Phylogeny
-
Sets the name of this Phylogeny to s.
- setName(String) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the name of this node.
- setName(String) - Method in interface org.forester.phylogeny.PhylogenyNodeI
-
- setName(String) - Method in class org.forester.protein.BasicProtein
-
- setName1(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- setName1(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setName2(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair
-
- setName2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
-
- setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
-
- setNatomsEDS(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the natomsEDS property.
- setNaturalPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setNcbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- setNclose(int) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
-
- setNcsOperators(Matrix4d[]) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Set the NCS operators.
- setNcuts(int) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites
-
- setNdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setNdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setNdom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setNeedsQuotes(boolean) - Method in class org.biojava.nbio.core.sequence.features.Qualifier
-
- setNeutronsNum(int) - Method in class org.biojava.nbio.aaproperties.xml.Isotope
-
- setNmr(boolean) - Method in interface org.biojava.nbio.structure.Structure
-
Deprecated.
- setNmr(boolean) - Method in class org.biojava.nbio.structure.StructureImpl
-
Deprecated.
- setNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathNode
-
- setNodeIdentifier(Identifier) - Method in class org.forester.phylogeny.data.NodeData
-
- setNodeLabelDirection(Options.NODE_LABEL_DIRECTION) - Method in class org.forester.archaeopteryx.Configuration
-
- setNodeName(String) - Method in class org.forester.phylogeny.data.NodeData
-
- setNodeVisualizations(List<NodeVisualization>) - Method in class org.forester.phylogeny.data.NodeData
-
- setNormAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setNotesList(ArrayList<String>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setNotObserved(Boolean) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setNrAlignments(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setNrCPU(int) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalc
-
does not do anything here...
- setNrCPUs(int) - Method in class org.biojava.nbio.structure.align.gui.AlignmentCalcDB
-
- setNrCPUs(int) - Method in interface org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
-
- setNreported(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setNseg(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- setnStart(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setNucleicAcidChainCount(int) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- setNullValue(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- setNum(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- setNum(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
-
- setNumberOfDigitsAfterCommaForBranchLengthValue(short) - Method in class org.forester.archaeopteryx.Configuration
-
- setNumberOfDigitsAfterCommaForConfidenceValues(short) - Method in class org.forester.archaeopteryx.Configuration
-
- setNumCells(int) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder
-
Set the number of neighboring crystal cells that will be used in the search for contacts
- setNumFreeReflections(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the numFreeReflections property.
- setNumHReduce(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the numHReduce property.
- setNumHReduce(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the numHReduce property.
- setNumMillerIndices(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the numMillerIndices property.
- setNumobs(BigInteger) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Sets the value of the numobs property.
- setNumobs(BigInteger) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Sets the value of the numobs property.
- setNumRes(String) - Method in class org.biojava.nbio.structure.Compound
-
- setNumSequences(int) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setO(Atom) - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- setObs(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Sets the value of the obs property.
- setObs(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Sets the value of the obs property.
- setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
[Optional] This method changes the behavior when obsolete entries
are requested.
- setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
[Optional] This method changes the behavior when obsolete entries
are requested.
- setObsval(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Sets the value of the obsval property.
- setObsval(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Sets the value of the obsval property.
- setOccupancy(double) - Method in interface org.biojava.nbio.structure.Atom
-
Set occupancy.
- setOccupancy(double) - Method in class org.biojava.nbio.structure.AtomImpl
-
- setOccupancy(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setOccupancy_esd(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setOccupancy_max(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOccupancy_min(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOccurrenceType(ModificationOccurrenceType) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
- setOffset(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setOligomeric_count(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- setOligomeric_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly
-
- setOmega(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setOmimId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setOne_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Sets the type of bioassembly to be colored.
- setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- setOpenPenalty(int) - Method in class org.biojava.nbio.alignment.SimpleGapPenalty
-
- setOpenPenalty(int) - Method in interface org.biojava.nbio.alignment.template.GapPenalty
-
Sets penalty given when a deletion or insertion gap first opens
- setOper_expression(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen
-
- setOperator(Matrix4d) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- setOptAln(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setOptLen(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setOptLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The length of the optimal alignment.
- setOptRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setOrder(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setOrgan(String) - Method in class org.biojava.nbio.structure.Compound
-
- setOrganelle(String) - Method in class org.biojava.nbio.structure.Compound
-
- setOrganism(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setOrganism_common_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- setOrganism_scientific(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- setOrganismCommon(String) - Method in class org.biojava.nbio.structure.Compound
-
- setOrganismScientific(String) - Method in class org.biojava.nbio.structure.Compound
-
- setOrganismTaxId(String) - Method in class org.biojava.nbio.structure.Compound
-
- setOrientation(Character) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setOriginal(Group) - Method in class org.biojava.nbio.structure.secstruc.SecStrucGroup
-
- setOriginalHeader(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setORmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Set the Original RMSD threshold from which the alignment optimization is started
- setOrthologousSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setOutFile(SynchronizedOutFile) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- setOutFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setOutFile(String) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- setOutputDir(File) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- setOutputFormat(BlastOutputFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Sets the stream output format to get from the QBlast service
If
HTML format is selected, also adds the following parameters (which are removed if another output
format is chosen):
- setOutputOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
- setOutputOption(BlastOutputParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
-
Sets the value of specified output parameter
- setOutputOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
-
Method to set the value for a specific output parameter using a key to store in a map.
- setOutputPDB(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
When writing the results to a file, don;t write as XML but write aligned PDB file
- setOverall_FOM_free_R_set(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOverall_FOM_work_R_set(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOverall_SU_B(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOverall_SU_ML(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOverall_SU_R_Cruickshank_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOverall_SU_R_free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setOwab(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the owab property.
- setP1(int) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setP2(int) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setPaintDefaults(Graphics2D) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
set some default rendering hints, like text antialiasing on
- setPair(Profile<S, C>, Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableProfilePair
-
- setPair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableSequencePair
-
- setPair(PdbPair) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- setPair(Pair<Atom>) - Method in class org.biojava.nbio.structure.contact.AtomContact
-
- setPair(Pair<Group>) - Method in class org.biojava.nbio.structure.contact.GroupContact
-
- setPairs(SortedSet<PdbPair>) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage
-
- setParameter(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- setParameter(double) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
-
- setParameter(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeMain
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
-
- setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.StructureAlignment
-
Set the default parameters for this algorithm to use
- setParametersForPainting(int, int, boolean) - Method in class org.forester.archaeopteryx.TreePanel
-
Set parameters for printing the displayed tree
- setParams(FarmJobParameters) - Method in class org.biojava.nbio.structure.align.FarmJob
-
- setParams(StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
-
set the parameters to be used for the algorithm
- setParent(Structure) - Method in interface org.biojava.nbio.structure.Chain
-
Set the back-reference to its parent Structure.
- setParent(Structure) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set the back-reference to its parent Structure.
- setParent(Structure) - Method in class org.biojava.nbio.structure.DBRef
-
Set the structure object that this DBRef relates to.
- setParent(PhylogenyNode) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the _parent PhylogenyNode of this PhylogenyNode to n.
- setParent(PhylogenyNode) - Method in interface org.forester.phylogeny.PhylogenyNodeI
-
- setParentDNASequence(AbstractSequence<NucleotideCompound>, Integer, Integer) - Method in class org.biojava.nbio.core.sequence.ProteinSequence
-
A Protein sequence can be stand alone or loaded from a transcript
sequence.
- setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
A feature can be the child or contained by a parent feature.
- setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setParentFeature(FeatureInterface<S, C>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Set the parent feature
- setParentId(String) - Method in class org.biojava.nbio.structure.cath.CathNode
-
- setParentSequence(AbstractSequence<?>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setParentSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- setParseBioAssembly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
Should the biological assembly info (REMARK 350) be parsed from the PDB file?
- setParseCAOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
the flag if only the C-alpha atoms of the structure should be parsed.
- setParseSecStruc(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
a flag to tell the parser to parse the Author's secondary structure assignment from the file
default is set to false, i.e.
- setPartialOn3prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setPartialOn5prime(boolean) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setPartner(int) - Method in class org.biojava.nbio.structure.secstruc.HBond
-
- setPath(IndexPair[]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setPath(IndexPair[]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setPath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
Set the path that is used to cache PDB files.
- setPath(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
-
Sets the path for the directory where PDB files are read/written
- setPath(String) - Method in class org.biojava.nbio.structure.io.SandboxStyleStructureProvider
-
directory where to find PDB files
- setPathSize(int) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setPathSize(int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setPathToClustalOmega(File) - Method in class org.forester.archaeopteryx.Configuration
-
- setPathToFastME(File) - Method in class org.forester.archaeopteryx.Configuration
-
- setPathToMafft(File) - Method in class org.forester.archaeopteryx.Configuration
-
- setPdb1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
- setPdb1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setPdb2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
mandatory argument to set the second PDB (and optionally chain ID) to be aligned.
- setPdb2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult
-
- setPdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPdb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_mon_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPdbAln(String[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setPdbccId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the Protein Data Bank Chemical Component ID.
- setPdbccName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the Protein Data Bank Chemical Component name.
- setPDBCode(String) - Method in interface org.biojava.nbio.structure.Structure
-
Set PDB code of structure .
- setPDBCode(String) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setPDBDirField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
-
- setPdbDirSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
Deprecated.
Ignored (4.0.0)
- setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
mandatory argument to set the location of PDB files.
- setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration
-
- setPDBFlag(boolean) - Method in interface org.biojava.nbio.structure.Group
-
Flag if group has 3D data .
- setPDBFlag(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl
-
flag if group has 3D data.
- setPDBHeader(PDBHeader) - Method in interface org.biojava.nbio.structure.Structure
-
Set the the header information for this PDB file
- setPDBHeader(PDBHeader) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setPdbId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setPdbId(String) - Method in class org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
-
- setPdbId(String) - Method in interface org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
-
Tell the provider for which PDB ID the quaternary structure should be returned.
- setPdbId(String) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- setPdbId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setPDBName(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- setPDBName(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
set three character name of AminoAcid.
- setPDBName(String) - Method in interface org.biojava.nbio.structure.Group
-
Set the PDB 3-letter name for this group.
- setPDBName(String) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Set three character name of Group .
- setPdbPath(String) - Static method in class org.biojava.nbio.structure.StructureIO
-
Utility method to set the location where PDB files can be found
- setPDBResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- setPdbResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setPdbResNum(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setPDBresnum1(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- setPDBresnum2(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- setPDBRevisionNumber(BigInteger) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the pdbRevisionNumber property.
- setPDBserial(int) - Method in interface org.biojava.nbio.structure.Atom
-
Set PDB atom number.
- setPDBserial(int) - Method in class org.biojava.nbio.structure.AtomImpl
-
Set PDB atom number.
- setPdbSerial(int) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier
-
- setPdbx_align(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_align_begin(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setPdbx_alt_source_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_ambiguous_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_aromatic_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_aromatic_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- setPdbx_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_auth_seq_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_auth_seq_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_beg_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_beg_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_blank_PDB_chainid_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- setPdbx_CASP_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- setPdbx_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_component_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_component_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_component_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_data_cutoff_high_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_data_cutoff_high_rms_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_data_cutoff_low_absF(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_db_accession(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setPdbx_db_accession(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_db_align_beg_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_db_align_end_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_description(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setPdbx_description(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_descriptor(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- setPdbx_diffrn_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_dist_value(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ec(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setPdbx_end_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_end_seq_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_formal_charge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setPdbx_formal_charge(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setPdbx_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_full_space_group_name_H_M(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- setPdbx_gene_src_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_fragment(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_gene(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_plasmid(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_plasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_scientific_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_gene_src_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_atcc(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_cell(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_cell_line(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_cellular_location(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_culture_collection(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_gene(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_scientific_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_strain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_tissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_tissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_vector(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_host_org_vector_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_ideal_coordinates_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_ideal_coordinates_missing_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_initial_date(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_isotropic_thermal_model(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_keywords(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_leaving_atom_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ls_cross_valid_method(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_ls_sigma_F(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_ls_sigma_I(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_method_to_determine_struct(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_model_Cartn_x_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_model_Cartn_y_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_model_Cartn_z_ideal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_model_coordinates_db_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_model_coordinates_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_model_coordinates_missing_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_model_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- setPdbx_model_type_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- setPdbx_modified(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- setPdbx_modified_date(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_mutation(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setPdbx_ncbi_taxonomy_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_number_of_molecules(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
-
- setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_ordinal(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- setPdbx_organ(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_organelle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_organism_scientific(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_overall_ESU_R(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_overall_ESU_R_Free(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_overall_phase_error(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_overall_SU_R_Blow_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_overall_SU_R_free_Blow_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_overall_SU_R_free_Cruickshank_DPI(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_PDB_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_PDB_id_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setPdbx_PDB_model_num(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setPdbx_plasmid_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_plasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_polymer_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_processing_site(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_ptnr1_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr1_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr1_standard_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr2_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr2_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr3_label_alt_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr3_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr3_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr3_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr3_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_ptnr3_PDB_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_R_Free_selection_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_ref_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_refine_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_release_status(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_replaced_by(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_replaces(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_residue_numbering(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_secretion(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_seq_align_beg_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_seq_align_end_ins_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_seq_one_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- setPdbx_seq_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_solvent_ion_probe_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_solvent_shrinkage_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_solvent_vdw_probe_radii(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_src_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPdbx_src_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbx_starting_model(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_stereo_config(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setPdbx_stereo_config(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- setPdbx_stereochem_target_val_spec_case(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_stereochemistry_target_values(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_strand_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_subcomponent_list(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_synonyms(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_TLS_residual_ADP_flag(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setPdbx_type(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPdbx_unique_axis(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setPdbx_value_order(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPdbx_variant(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setPdbxStructAssemblies(List<PdbxStructAssemblyGen>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
-
- setPdbxStructAssemblies(List<PdbxStructAssembly>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
-
- setPdbxStructOperLists(List<PdbxStructOperList>) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
-
- setPdpprovider(PDPProvider) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- setPercentage(Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- setPercentFreeReflections(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the percentFreeReflections property.
- setPercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the percentRamaOutliers property.
- setPercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the percentRotaOutliers property.
- setPercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the percentRSRZOutliers property.
- setPercId(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- setPerformBootstrapResampling(boolean) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setPermutationSize(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setPhi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setPhi(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the phi property.
- setPhylogenyGraphicsType(Options.PHYLOGENY_GRAPHICS_TYPE) - Method in class org.forester.archaeopteryx.Configuration
-
- setPlasmid_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPlasmid_name(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setPmid(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
Set the value of pmid
- setPolyhedron(Polyhedron) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- setPolymerType(PolymerType) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setPos(int, int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- setPos1(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setPos1(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- setPos2(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setPos2(int) - Method in class org.biojava.nbio.structure.gui.util.AlignedPosition
-
- setPosition(int) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- setPreferredResult(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- setPreferredSize() - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- setPreviousNames(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setPreviousSymbols(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setPrimitiveMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setPrintCE(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
Display the output string in CE style
- setPrintConnections(boolean) - Method in class org.biojava.nbio.structure.io.FileConvert
-
enable/disable printing of connections
connections are sometimes buggy in PDB files
so there are some cases where one might turn this off.
- setPrintFatCat(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setPrintLineWidth(float) - Method in class org.forester.archaeopteryx.Configuration
-
- setPrintXML(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setProbability(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setProfile(Profile<S, C>) - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
-
- setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SimpleProfileProfileAligner
-
- setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.SmithWaterman
-
- setProfile(List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
- setProfile(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Stores the given profile.
- setProfileFuture(Future<ProfilePair<S, C>>) - Method in class org.biojava.nbio.alignment.GuideTree.Node
-
- setProfileFuture(Future<ProfilePair<S, C>>) - Method in interface org.biojava.nbio.alignment.template.GuideTreeNode
-
Stores the given profile future.
- setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- setProgram(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- setProgram_version(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- setPrograms(Programs) - Method in class org.biojava.nbio.structure.validation.WwPDBValidationInformation
-
Sets the value of the programs property.
- setProperties(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.core.sequence.features.DBReferenceInfo
-
- setProperties(Map<String, Object>) - Method in interface org.biojava.nbio.structure.Group
-
Properties of this amino acid.
- setProperties(Map<String, Object>) - Method in class org.biojava.nbio.structure.HetatomImpl
-
Properties of this amino acid.
- setProperties(String) - Method in class org.biojava.nbio.structure.validation.Program
-
Sets the value of the properties property.
- setProperties(PropertiesMap) - Method in class org.forester.phylogeny.data.Annotation
-
- setProperties(PropertiesMap) - Method in class org.forester.phylogeny.data.NodeData
-
- setProperty(Object, Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation
-
- setProperty(Object, Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation
-
Set the value of a property.
- setProperty(String, Object) - Method in interface org.biojava.nbio.structure.Group
-
set a single property .
- setProperty(String, Object) - Method in class org.biojava.nbio.structure.HetatomImpl
-
set a single property .
- setProtein(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setProvider(String) - Method in class org.forester.ws.seqdb.EbiDbEntry
-
- setProvider(String) - Method in class org.forester.ws.uniprot.EbiDbEntry
-
- setProxySequenceReader(SequenceReader<C>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Very important method that allows external mappings of sequence data and features.
- setPseudoSymmetric(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.Subunits
-
- setPsi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setPsi(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the psi property.
- setPsimodId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the PSI-MOD ID.
- setPsimodName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the PSI-MOD name.
- setPtnr1_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr1_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr1_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr1_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr1_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr1_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr1_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr1_symmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_auth_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_auth_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_auth_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_label_asym_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_label_atom_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_label_comp_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_label_seq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPtnr2_symmetry(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- setPublicationDate(int) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setPublished(boolean) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setPublisher(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setPvalue(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setPvalue(Double) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setPwdDistanceMethod(PairwiseDistanceCalculator.PWD_DISTANCE_METHOD) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setPx(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setQualifiers(HashMap<String, Qualifier>) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- setQualifiers(HashMap<String, Qualifier>) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setQualifiers(HashMap<String, Qualifier>) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Set the qualifiers
- setQualities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QualityFeature
-
- setQuantities(List<Number>) - Method in class org.biojava.nbio.core.sequence.features.QuantityFeature
-
- setQuery(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- setQuery(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- setQuery(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableProfilePair
-
Sets the first
Profile of the pair.
- setQuery(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableSequencePair
-
- setRama(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the rama property.
- setRandomize(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- setRandomize(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- setRandomNumberGeneratorSeed(long) - Method in class org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
-
- setRandomNumberSeed(long) - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- setRandomNumberSeed(long) - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- setRanges(List<String>) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setRank(String) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setRecordAdditionalAttachments(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- setRecordType(String) - Method in interface org.biojava.nbio.structure.AminoAcid
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- setRecordType(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- setRecordUnidentifiableCompounds(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
-
- setReduceInitialFragments(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setRef(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
Set the value of the ref.
- setRef0(Sequence) - Method in class org.forester.phylogeny.data.SequenceRelation
-
- setRef1(Sequence) - Method in class org.forester.phylogeny.data.SequenceRelation
-
- setRef_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setRefAuthor(StringBuffer) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- setRefChainId(String) - Method in class org.biojava.nbio.structure.Compound
-
Return the ref chain id value.
- setReference(int, Reference) - Method in class org.forester.phylogeny.data.NodeData
-
- setReference(Reference) - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always sets the first Reference.
- setReferences(Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setRefLocation(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- setRefmacVersion(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the refmacVersion property.
- setRefMedline(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- setRefn(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
Set the value of the refn
- setRefseqIds(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setRefTitle(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- setRelativePercentileClashscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the relativePercentileClashscore property.
- setRelativePercentileDCCRfree(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
- setRelativePercentilePercentRamaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the relativePercentilePercentRamaOutliers property.
- setRelativePercentilePercentRotaOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the relativePercentilePercentRotaOutliers property.
- setRelativePercentilePercentRSRZOutliers(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the relativePercentilePercentRSRZOutliers property.
- setRelativePercentileRNAsuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
- setRelevantSequenceRelationTypes(Collection<SequenceRelation.SEQUENCE_RELATION_TYPE>) - Method in class org.forester.phylogeny.Phylogeny
-
- setRenderingFactorWidth(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- setRenderingFactorWidth(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- setRenderingHeight(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
-
- setRenderingHeight(double) - Method in interface org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
-
- setRenderingHeight(double) - Method in class org.forester.archaeopteryx.phylogeny.data.RenderableVector
-
- setRepeatUnits(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setReplaces(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- setReplaceUnderscores(boolean) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser
-
- setReplaceUnderscores(boolean) - Method in class org.forester.io.parsers.nhx.NHXParser
-
- setReplaceUnderscoresInNhParsing(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setRepresentative(String) - Method in class org.biojava.nbio.structure.cath.CathNode
-
- setRerootable(boolean) - Method in class org.forester.phylogeny.Phylogeny
-
- setResidId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the RESID ID.
- setResidName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the RESID name.
- setResidual(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setResidualVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
Set the residual value for the variable for this sample.
- setResidue(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setResidueAt(int, int, char) - Method in class org.forester.msa.BasicMsa
-
- setResidueAt(int, int, char) - Method in interface org.forester.msa.Msa
-
- setResidueAt(int, int, char) - Method in class org.forester.msa.ResampleableMsa
-
- setResidueName(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
Including insertion code
- setResidueNumber(int) - Method in class org.biojava.nbio.protmod.structure.StructureGroup
-
- setResidueNumber(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.AtomInfo
-
- setResidueNumber(ResidueNumber) - Method in interface org.biojava.nbio.structure.Group
-
sets the ResidueNumber for this Group
- setResidueNumber(String, Integer, Character) - Method in interface org.biojava.nbio.structure.Group
-
Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.
- setResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- setResidueNumber(String, Integer, Character) - Method in class org.biojava.nbio.structure.HetatomImpl
-
- setResidues(List<SiftsResidue>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- setResidueType(ResidueType) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setResname(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the resname property.
- setResNames(String) - Method in class org.biojava.nbio.structure.Compound
-
- setResnum(BigInteger) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the resnum property.
- setResnum1(String) - Method in class org.biojava.nbio.structure.SSBond
-
- setResnum2(String) - Method in class org.biojava.nbio.structure.SSBond
-
- setResolution(Double) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setResolution(float) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setResScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setRestypesNotcheckedForBondAngleGeometry(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the restypesNotcheckedForBondAngleGeometry property.
- setResultFile(File) - Method in class org.biojava.nbio.structure.align.MultiThreadedDBSearch
-
- setReturnGainLossMatrix(boolean) - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- setReturnGainLossMatrix(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- setReturnGainLossMatrix(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- setReturnInternalStates(boolean) - Method in class org.forester.evoinference.parsimony.DolloParsimony
-
- setReturnInternalStates(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
- setReturnInternalStates(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
- setReturnType(HmmPfamOutputParser.ReturnType) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setReturnType(HmmscanPerDomainTableParser.ReturnType) - Method in class org.forester.io.parsers.HmmscanPerDomainTableParser
-
- setRfree(float) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setRms(double) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
-
- setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
the rms in the structurally equivalent regions
- setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setRmsdCenters(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
The cutoff to be used during AFP detection
- setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
-
- setRmsdIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setRmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setRmsdThrJoin(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setRnaSuiteness(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
- setRobustStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setRoot(PhylogenyNode) - Method in class org.forester.phylogeny.Phylogeny
-
- setRooted(boolean) - Method in class org.forester.phylogeny.Phylogeny
-
Sets whether this Phylogeny is rooted or not.
- setRot(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setRota(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the rota property.
- setRotationGroup(RotationGroup) - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- setRotationMatrix(double[][]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
- setRow(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair
-
- setRow(String, int) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- setRowHeader(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
- setRows(List<AminoAcidCompound>) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setRscc(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the rscc property.
- setRscore(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setRscoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setRsr(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the rsr property.
- setRsrz(BigDecimal) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the rsrz property.
- setRunBackground(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setSaid(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the said property.
- setSaturation(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
Deprecated.
- setSaturation(float) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- setSaveOutputDir(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setScale(int) - Method in class org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix
-
- setScale(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- setScale(float) - Method in class org.biojava.nbio.structure.gui.util.CoordManager
-
- setScale(float) - Method in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- setScale(int) - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- setScalevalue(float) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
Deprecated.
- setScalevalue(double) - Method in class org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper
-
- setScid(BigInteger) - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Sets the value of the scid property.
- setScientificName(String) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setScientificName(PhylogenyNode, String) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- setScopDatabase(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Set the default scop version
- setScopDatabase(String, boolean) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Set the default scop version
- setScopDatabase(ScopDatabase) - Static method in class org.biojava.nbio.structure.scop.ScopFactory
-
Set the default scop version and instance
- setScopDescription(List<ScopDescription>) - Method in class org.biojava.nbio.structure.scop.server.ScopDescriptions
-
- setScopDomain(List<ScopDomain>) - Method in class org.biojava.nbio.structure.scop.server.ScopDomains
-
- setScopDownloadURL(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- setScope(int) - Method in class org.biojava.nbio.ontology.Synonym
-
- setScopId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setScopNode(List<ScopNode>) - Method in class org.biojava.nbio.structure.scop.server.ScopNodes
-
- setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.CachedRemoteScopInstallation
-
- setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- setScopVersion(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase
-
Sets the scop version used.
- setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
-
- setScore(double) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setScore(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable
-
- setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
-
- setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- setScore(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setScore(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
-
- setScoreLogrankTest(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setScoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setScorePoint(int, int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Calculate the optimal alignment score for the given sequence positions with an affine or constant gap penalty
- setScorePoint(int, int, int, int, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Calculates the optimal alignment score for the given sequence positions and a linear gap penalty
- setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setScoreVector(int, AlignerHelper.Subproblem, int, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score global alignment for a given position in the query sequence
- setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score global alignment for a given position in the query sequence
- setScoreVector(int, AlignerHelper.Subproblem, int, int[], boolean, int[][][]) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score global alignment for a given position in the query sequence for a linear gap penalty
- setScoreVector(int, int, int, int, int, int[], boolean, int[][][], boolean) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score global alignment for a given position in the query sequence for a linear gap penalty
- setScoreVector(int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score local alignment for a given position in the query sequence
- setScoreVector(int, int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score local alignment for a given position in the query sequence
- setScoreVector(int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score local alignment for a given position in the query sequence for a linear gap penalty
- setScoreVector(int, int, int, int, int, int[], boolean, int[][][], int[], int) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Score local alignment for a given position in the query sequence for a linear gap penalty
- setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Set the scoring strategy to use.
- setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- setSearchFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setSecondGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setSecretion(String) - Method in class org.biojava.nbio.structure.Compound
-
- setSecStruc(Map<String, String>) - Method in interface org.biojava.nbio.structure.AminoAcid
-
Set the secondary structure as a Map.
- setSecStruc(Map<String, String>) - Method in class org.biojava.nbio.structure.AminoAcidImpl
-
Set the secondary structure as a Map.
- setSecStruc(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setSeedFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setSeedRmsdCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setSegId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- setSegmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- setSegments(List<CathSegment>) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setSegments(List<Segment>) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- setSegments(List<SiftsSegment>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.JMatrixPanel
-
- setSelectedAlignmentPos(int) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- setSelection(Selection) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- setSelection(List<AtomInfo>) - Method in interface org.biojava.nbio.structure.gui.Selection
-
- setSelection(List<AtomInfo>) - Method in class org.biojava.nbio.structure.gui.SelectionImpl
-
- setSelection(Selection) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
- setSeparatorSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
-
- setSeq(String) - Method in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
Sets the value of the seq property.
- setSeq_align_beg(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setSeq_align_end(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- setSeq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setSeq_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef
-
Initial sequence number of the PDB sequence segment.
- setSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef
-
Ending sequence number of the PDB sequence segment.
- setSeqNum(Integer) - Method in class org.biojava.nbio.structure.ResidueNumber
-
- setSeqResGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain
-
Set the list of SeqResGroups for this chain.
- setSeqResGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl
-
Set the list of SeqResGroups for this chain.
- setSeqResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setSequence(Sequence<C>) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
- setSequence(S) - Method in class org.biojava.nbio.core.sequence.location.SequenceLocation
-
- setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- setSequence(int, Sequence) - Method in class org.forester.phylogeny.data.NodeData
-
- setSequence(Sequence) - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always sets the first Sequence.
- setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
-
- setSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- setSequenceIdentity(double) - Method in class org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
-
- setSequenceIdentityThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
-
- setSequenceIdentityThresholds(double[]) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setSequencePseudoSymmetryThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setSequenceRelationQueries(Collection<Sequence>) - Method in class org.forester.phylogeny.Phylogeny
-
- setSequences(List<AlignedSequence<S, C>>) - Method in interface org.biojava.nbio.alignment.template.MutableProfile
-
- setSequenceScore(Double) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setSequenceString(String) - Method in class org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
-
- setSequenceUsage(SequenceOptimizationHints.SequenceUsage) - Static method in class org.biojava.nbio.core.sequence.SequenceOptimizationHints
-
- setSequentialAlignment(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
Set whether this alignment has the normal topology, ie the residues
aligned in each block increase sequentially over the original protein.
- setSeqWeight(double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
- setSerNum(int) - Method in class org.biojava.nbio.structure.SSBond
-
get serial number of this SSBOND in PDB file
- setServer(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setServer(String) - Method in class org.biojava.nbio.structure.domain.RemotePDPProvider
-
- setServer(String) - Method in class org.biojava.nbio.structure.scop.RemoteScopInstallation
-
- setShape(NodeVisualization.NodeShape) - Method in class org.forester.phylogeny.data.NodeVisualization
-
- setShortAlign(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
- setShortDescription(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setShortDescription(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Set the short description that can be used to describe the feature
- setShortName(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- setShortName(String) - Method in class org.biojava.nbio.core.sequence.compound.CodonCompound
-
- setShortName(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractCompound
-
- setShortName(String) - Method in interface org.biojava.nbio.core.sequence.template.Compound
-
- setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound
-
- setShortName(String) - Method in class org.biojava.nbio.core.sequence.transcription.Table.Codon
-
- setShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setShow3d(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- setShowBranchLengthValues(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setShowDBresult(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setShowDefaultNodeShapes(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setShowDomainLabels(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setShowDomainLabels(boolean) - Method in class org.forester.archaeopteryx.Options
-
- setShowMenu(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters
-
- setShowScale(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setSimCount(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setSimilarity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setSiteID(String) - Method in class org.biojava.nbio.structure.Site
-
- setSites(List<Site>) - Method in interface org.biojava.nbio.structure.Structure
-
- setSites(List<Site>) - Method in class org.biojava.nbio.structure.StructureImpl
-
- setSize(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
-
- setSize(double) - Method in class org.forester.phylogeny.data.NodeVisualization
-
- setSmiles(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setSOLID(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setSolvent_model_details(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setSolvent_model_param_bsol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setSolvent_model_param_ksol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Refine
-
- setSource(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Set the feature source
- setSource(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setSource(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Change the source of the FeatureInterface.
- setSource(String) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
Added support for the source of this sequence for GFF3 export
- setSource(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
-
- setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusCharactersParser
-
- setSource(Object) - Method in class org.forester.io.parsers.nexus.NexusPhylogeniesParser
-
- setSource(Object) - Method in class org.forester.io.parsers.nexus.PaupLogParser
-
- setSource(Object) - Method in class org.forester.io.parsers.nhx.NHXParser
-
This sets the source to be parsed.
- setSource(Object) - Method in interface org.forester.io.parsers.PhylogenyParser
-
- setSource(Object) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- setSource(Object) - Method in class org.forester.io.parsers.tol.TolParser
-
- setSource(String) - Method in class org.forester.phylogeny.data.Annotation
-
- setSourceId(String) - Method in class org.forester.phylogeny.data.Sequence
-
- setSpace_group_name_H_M(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- setSpace_group_name_Hall(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- setSpaceGroup(SpaceGroup) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo
-
Set the SpaceGroup
- setSparse(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setSpeciations(int) - Method in class org.forester.phylogeny.data.Event
-
- setSpecies(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setSpeciesId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setSpeciesOrder(List<Species>) - Method in class org.forester.surfacing.PrintableDomainSimilarity
-
- setSqFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setSqTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
-
- setSrc_method(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setSSBonds(List<SSBond>) - Method in interface org.biojava.nbio.structure.Structure
-
Set the list of SSBonds for this structure
- setSSBonds(List<SSBond>) - Method in class org.biojava.nbio.structure.StructureImpl
-
set the list of SSBonds for this structure
- setStandard(boolean) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setStandardDeviation(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setStandardDeviation(double) - Method in class org.forester.phylogeny.data.Confidence
-
- setStart(Point) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setStart(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- setStart(String) - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- setStart(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- setStart(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- setStart_construct_id(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
-
- setStartPage(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setStartTimestamp(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
-
- setState(int, int, S) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- setState(String, int, S) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- setState(String, String, S) - Method in class org.forester.evoinference.matrix.character.BasicCharacterStateMatrix
-
- setState(int, int, S) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- setState(String, int, S) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- setState(String, String, S) - Method in interface org.forester.evoinference.matrix.character.CharacterStateMatrix
-
- setStatus(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setStatus(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
-
- setStatus(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Sets the value of the stdev property.
- setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Sets the value of the stdev property.
- setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Sets the value of the stdev property.
- setStdev(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Sets the value of the stdev property.
- setStdlow(ArrayList<Double>) - Method in class org.biojava.nbio.survival.cox.StrataInfo
-
- setSteps(AlignerHelper.Last[][][], boolean, int[], AlignerHelper.Last, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Find alignment path through traceback matrix
- setSteps(AlignerHelper.Last[][][], int[][][], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Find global alignment path through traceback matrix
- setSteps(AlignerHelper.Last[][][], int[], List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Static method in class org.biojava.nbio.alignment.routines.AlignerHelper
-
Find local alignment path through traceback matrix
- setStepSize(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setStop(String) - Method in class org.biojava.nbio.structure.cath.CathFragment
-
- setStop(String) - Method in class org.biojava.nbio.structure.cath.CathSegment
-
- setStoreEmptySeqRes(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
- setStoringScoreMatrix(boolean) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.
- setStrain(String) - Method in class org.biojava.nbio.structure.Compound
-
- setStrain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setStrain(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
-
- setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.GeneSequence
-
- setStrand(Strand) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setStrata(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
-
- setStrictSCOP(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
When strictSCOP is enabled, SCOP domain identifiers (eg 'd1gbga_') are matched literally to the SCOP database.
- setStringSequence(String) - Method in class org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit
-
- setStruct(Struct) - Method in class org.biojava.nbio.structure.io.mmcif.ChemCompConsumer
-
- setStruct(Struct) - Method in interface org.biojava.nbio.structure.io.mmcif.MMcifConsumer
-
- setStruct(Struct) - Method in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- setStructure(Structure) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
-
- setStructure(Structure) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- setStructure(Structure) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
- setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
-
- setStructure1(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener
-
- setStructure2(Structure) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- setStructureAlignmentJmol(StructureAlignmentJmol) - Method in class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel
-
- setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
-
- setStyle(RenderStyle) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- setStyle(RenderStyle) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
Apply this style to the current selection
- setSubLocations(List<Location>) - Method in class org.biojava.nbio.core.sequence.location.template.AbstractLocation
-
- setSubstitutionMatrix(SubstitutionMatrix<C>) - Method in class org.biojava.nbio.alignment.template.AbstractMatrixAligner
-
Sets the substitution matrix.
- setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
- setSubunitRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setSumExtNodes(int) - Method in class org.forester.phylogeny.PhylogenyNode
-
Sets the total number of external Nodes originating from this
PhylogenyNode to i (int).
- setSumOfFailures(int) - Method in class org.forester.surfacing.MappingResults
-
- setSumOfSuccesses(int) - Method in class org.forester.surfacing.MappingResults
-
- setSunID(int) - Method in class org.biojava.nbio.structure.scop.ScopDescription
-
- setSunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode
-
- setSuperfamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain
-
- setSurname(String) - Method in class org.biojava.nbio.structure.Author
-
- setSurvivalData(ArrayList<String>, SurvFitInfo, Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
Allow setting of points in the figure where weighted correction has been
done and percentage has already been calculated.
- setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
The data will set the max time which will result in off time points for
tick marks
- setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Double, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
-
- setSurvivalInfo(ArrayList<String>, ArrayList<SurvivalInfo>, String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
-
- setSurvivalInfoList(ArrayList<SurvivalInfo>) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setSwissprotId(String) - Method in interface org.biojava.nbio.structure.Chain
-
Set the Swissprot id of this chain.
- setSwissprotId(String) - Method in class org.biojava.nbio.structure.ChainImpl
-
set the Swissprot id of this chains .
- setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.AminoAcidComposition
-
- setSymbol(String) - Method in class org.biojava.nbio.aaproperties.xml.Element
-
- setSymbol(String) - Method in class org.forester.phylogeny.data.Sequence
-
- setSymDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- setSymop(String) - Method in class org.biojava.nbio.structure.validation.SymmClash
-
Sets the value of the symop property.
- setSynonyms(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setSynonyms(Set<Object>) - Method in class org.biojava.nbio.ontology.Term.Impl
-
- setSynonyms(List<String>) - Method in class org.biojava.nbio.structure.Compound
-
- setSynthetic(String) - Method in class org.biojava.nbio.structure.Compound
-
- setSystematicName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder
-
Set the systematic name.
- setT(double[]) - Method in class org.biojava.nbio.structure.align.model.AFP
-
- setTabPane(JTabbedPane) - Method in class org.biojava.nbio.structure.align.gui.DBSearchGUI
-
- setTarget(S) - Method in class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
-
- setTarget(Profile<S, C>) - Method in class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
-
- setTarget(Profile<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableProfilePair
-
Sets the second
Profile of the pair.
- setTarget(AlignedSequence<S, C>) - Method in interface org.biojava.nbio.alignment.template.MutableSequencePair
-
- setTaxonomy(TaxonomyID) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setTaxonomy(int, Taxonomy) - Method in class org.forester.phylogeny.data.NodeData
-
- setTaxonomy(Taxonomy) - Method in class org.forester.phylogeny.data.NodeData
-
Convenience method -- always sets the first Taxonomy.
- setTaxonomyCode(String) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setTaxonomyCode(PhylogenyNode, String) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
Convenience method to set the taxonomy code of a phylogeny node.
- setTaxonomyColorize(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setTaxonomyColorizeNodeShapes(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setTaxonomyExtraction(PhylogenyMethods.TAXONOMY_EXTRACTION) - Method in class org.forester.io.parsers.nhx.NHXParser
-
- setTempFactor(double) - Method in interface org.biojava.nbio.structure.Atom
-
Set temp factor .
- setTempFactor(double) - Method in class org.biojava.nbio.structure.AtomImpl
-
- setText(String) - Method in class org.biojava.nbio.structure.align.gui.AlignmentTextPanel
-
- setText(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
-
- setText(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- setTextField(JTextField) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- setThreadPool(ThreadPoolExecutor) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Sets thread pool to any given ThreadPoolExecutor to allow use of an alternative execution style.
- setThreadPoolCPUsAvailable(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Sets thread pool to reserve a given number of processor cores for foreground or other use.
- setThreadPoolCPUsFraction(float) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Sets thread pool to a given fraction of the available processors.
- setThreadPoolDefault() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Sets thread pool to default of 1 background thread for each processor core.
- setThreadPoolSingle() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Sets thread pool to a single background thread.
- setThreadPoolSize(int) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Sets thread pool to given size.
- setThreads(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setThree_letter_code(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setThreeState(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setTime(int) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setTime(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setTimeout(int) - Method in class org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
-
- setTissue(String) - Method in class org.biojava.nbio.structure.Compound
-
- setTissue(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setTissue_fraction(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
-
- setTitle(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- setTitle(String) - Method in class org.biojava.nbio.structure.Compound
-
- setTitle(String) - Method in class org.biojava.nbio.structure.gui.BiojavaJmol
-
- setTitle(String) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- setTitle(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- setTitle(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
Set the value of title
- setTitle(String) - Method in class org.biojava.nbio.structure.PDBHeader
-
- setTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setTmIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
-
- setTMScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setTo(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
-
- setTo(int) - Method in class org.biojava.nbio.structure.secstruc.Ladder
-
- setTool(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
-
Set the tool identifier for QBlast.
- setTopologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setTorsionPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
-
- setTotalArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setTotalLength(int) - Method in class org.forester.phylogeny.data.DomainArchitecture
-
- setTotalLenIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setTotalLenOpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setTotalRmsdIni(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
this is the init-RMSD, not the final RMSD after refinement.
- setTotalRmsdOpt(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
The RMSD of the final alignment.
- setTraceFlag(boolean) - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
- setTraceRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setTraceTmScoreMin(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setTrans(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setTranscriptionEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setTranscriptionStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
-
- setTransfAlgebraic(List<String>) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
-
- setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Helix
-
- setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation
-
- setTransformationMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
Sets the transformation using a 4x4 transformation matrix
- setTransformId(int) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform
-
- setTransforms(Pair<CrystalTransform>) - Method in class org.biojava.nbio.structure.contact.StructureInterface
-
- setTransforms(List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo
-
- setTranslation(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
-
- setTransNCS(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the transNCS property.
- setTransparancy(double) - Method in class org.forester.phylogeny.data.NodeVisualization
-
- setTree(Phylogeny) - Method in class org.forester.archaeopteryx.TreePanel
-
Set a phylogeny tree.
- setTree(Phylogeny) - Method in class org.forester.sdi.DistanceCalculator
-
Sets the rooted Phylogeny t for which the mean distance to the root and
its variance and standard deviation are calculated.
- setTreeAndExtNodes(Phylogeny, ArrayList<PhylogenyNode>) - Method in class org.forester.sdi.DistanceCalculator
-
Sets the rooted Phylogeny t and the external Nodes ext_nodes for which
the mean distance to their lowest common ancestor and its variance and
standard deviation are calculated.
- setTreeAndExtNodes(Phylogeny, Vector<PhylogenyNode>) - Method in class org.forester.sdi.DistanceCalculator
-
Sets the rooted Phylogeny t and the external Nodes ext_nodes for which
the mean distance to their lowest common ancestor and its variance and
standard deviation are calculated.
- setTryAllCPs(Boolean) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters
-
- setTurn(boolean[]) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState
-
- setTwi(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setTwinFraction(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the twinFraction property.
- setTwinL(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the twinL property.
- setTwinL2(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the twinL2 property.
- setTwistedGroups(Group[]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
-
- setType(String) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Set the feature type
- setType(String) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setType(String) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
Change the type of this feature.
- setType(StainType) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
-
- setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemComp
-
- setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor
-
- setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Entity
-
- setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
-
- setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
-
- setType(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setType(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- setType(String) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setType(String) - Method in class org.forester.phylogeny.data.Annotation
-
- setType(String) - Method in class org.forester.phylogeny.data.BinaryCharacters
-
- setType(String) - Method in class org.forester.phylogeny.data.Confidence
-
- setType(String) - Method in class org.forester.phylogeny.data.Sequence
-
- setType(SequenceRelation.SEQUENCE_RELATION_TYPE) - Method in class org.forester.phylogeny.data.SequenceRelation
-
- setType(String) - Method in class org.forester.phylogeny.Phylogeny
-
- setType_symbol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.AtomSite
-
- setType_symbol(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom
-
- setUnaryOperators(List<String>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver
-
- setUncertain(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- setUniprot(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
-
- setUniprot(String) - Method in class org.biojava.nbio.phosphosite.Site
-
- setUniProtAccessionId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setUniprotbaseURL(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- setUniprotDirectoryCache(String) - Static method in class org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader
-
- setUniProtPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setUniProtResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- setUnit(String) - Method in class org.forester.phylogeny.data.Date
-
- setUnitv(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setUnknown(boolean) - Method in class org.biojava.nbio.core.sequence.location.SimplePoint
-
- setUnweightedStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
-
- setUpdateRemediatedFiles(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setUpdateRemediatedFiles(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
- setUris(List<Uri>) - Method in class org.forester.phylogeny.data.Annotation
-
- setUris(List<Uri>) - Method in interface org.forester.phylogeny.data.MultipleUris
-
- setUris(List<Uri>) - Method in class org.forester.phylogeny.data.Sequence
-
- setUris(List<Uri>) - Method in class org.forester.phylogeny.data.Taxonomy
-
- setUseAccessors(boolean) - Method in class org.forester.go.PfamToGoParser
-
- setUseBranchesWidths(boolean) - Method in class org.forester.archaeopteryx.Configuration
-
- setUsed(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
-
- setUsedAtomNames(String[]) - Method in class org.biojava.nbio.structure.align.StrucAligParameters
-
- setUseLast(boolean) - Method in class org.forester.evoinference.parsimony.FitchParsimony
-
This sets whether to use the first or last state in the sorted
states at the undecided internal nodes.
- setUseLast(boolean) - Method in class org.forester.evoinference.parsimony.SankoffParsimony
-
This sets whether to use the first or last state in the sorted
states at the undecided internal nodes.
- setUseMean(boolean) - Method in class org.forester.development.MsaRenderer
-
- setUseMmCif(boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache
-
- setUserCollection(Collection<Object>) - Method in class org.biojava.nbio.core.sequence.template.AbstractSequence
-
- setUsername(String) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.AbstractFeature
-
Allow the user to associate an object with the feature.
- setUserObject(Object) - Method in class org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo
-
- setUserObject(Object) - Method in interface org.biojava.nbio.core.sequence.features.FeatureInterface
-
- setValidateAgainstSchema(String) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- setValidateAgainstSchema(String) - Method in class org.forester.io.parsers.tol.TolParser
-
- setValue(String) - Method in class org.biojava.nbio.core.sequence.features.Qualifier
-
- setValue(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl
-
- setValue(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray
-
- setValue(int, int, double) - Method in class org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
-
- setValue(int, int, double) - Method in interface org.forester.evoinference.matrix.distance.DistanceMatrix
-
- setValue(String) - Method in class org.forester.io.parsers.phyloxml.XmlElement
-
[Careful, this does not call "new String(...)"]
- setValue(Color) - Method in class org.forester.phylogeny.data.BranchColor
-
- setValue(double) - Method in class org.forester.phylogeny.data.Confidence
-
- setValue(BigDecimal) - Method in class org.forester.phylogeny.data.Date
-
- setValue(String) - Method in class org.forester.phylogeny.data.Property
-
- setValue(String) - Method in class org.forester.phylogeny.data.Reference
-
- setValue(int, int, E) - Method in class org.forester.util.BasicTable
-
- setValue(IDENTIFIER_TYPE, IDENTIFIER_TYPE, VALUE_TYPE) - Method in class org.forester.util.GeneralTable
-
- setValue_order(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond
-
- setVariableResiduals(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setVariant(String) - Method in class org.biojava.nbio.structure.Compound
-
- setVector(double[]) - Method in class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList
-
- setVector(List<Double>) - Method in class org.forester.phylogeny.data.NodeData
-
- setVerbose(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobParameters
-
- setVerbose(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.JmolPanel
-
- setVerbose(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- setVerbose(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
-
- setVerbose(boolean) - Method in class org.forester.io.parsers.HmmPfamOutputParser
-
- setVersion(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- setVersion(int) - Method in class org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser
- setVersion(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain
-
- setVersion(String) - Method in class org.biojava.nbio.structure.cath.CathDomain
-
- setVersion(String) - Method in class org.biojava.nbio.structure.validation.Program
-
Sets the value of the version property.
- setVertices(List<V>) - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- setVertices(List<V>) - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- setVolume(String) - Method in class org.biojava.nbio.structure.JournalArticle
-
- setWaitCursor() - Method in class org.forester.archaeopteryx.MainPanel
-
- setWaitCursor() - Method in class org.forester.archaeopteryx.TreePanel
-
- setWaitForAlignments(boolean) - Method in class org.biojava.nbio.structure.align.client.FarmJobRunnable
-
- setWaldTestInfo(WaldTestInfo) - Method in class org.biojava.nbio.survival.cox.CoxInfo
-
- setWeight(Double) - Method in class org.biojava.nbio.structure.rcsb.RCSBLigand
-
- setWeight(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
-
- setWeighted(boolean) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
-
- setWilsonBaniso(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the wilsonBaniso property.
- setWilsonBestimate(BigDecimal) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the wilsonBestimate property.
- setWinSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters
-
- setWinSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- setX(double) - Method in interface org.biojava.nbio.structure.Atom
-
Set the X coordinate.
- setX(double) - Method in class org.biojava.nbio.structure.AtomImpl
-
- setXcoord(float) - Method in class org.forester.phylogeny.PhylogenyNode
-
Used for drawing of Trees.
- setXMLcreationDate(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the xmLcreationDate property.
- setXSecondary(float) - Method in class org.forester.phylogeny.PhylogenyNode
-
- setXtriageInputColumns(String) - Method in class org.biojava.nbio.structure.validation.Entry
-
Sets the value of the xtriageInputColumns property.
- setY(double) - Method in interface org.biojava.nbio.structure.Atom
-
Set the Y coordinate.
- setY(double) - Method in class org.biojava.nbio.structure.AtomImpl
-
- setYcoord(float) - Method in class org.forester.phylogeny.PhylogenyNode
-
Used for drawing of Trees.
- setYSecondary(float) - Method in class org.forester.phylogeny.PhylogenyNode
-
- setZ(double) - Method in interface org.biojava.nbio.structure.Atom
-
Set the Z coordinate.
- setZ(double) - Method in class org.biojava.nbio.structure.AtomImpl
-
- setZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.AngleOutlier
-
Sets the value of the z property.
- setZ(BigDecimal) - Method in class org.biojava.nbio.structure.validation.BondOutlier
-
Sets the value of the z property.
- setZ(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
-
- setZ_PDB(String) - Method in class org.biojava.nbio.structure.io.mmcif.model.Cell
-
- setZippedInputstream(boolean) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlParser
-
- setZippedInputstream(boolean) - Method in class org.forester.io.parsers.tol.TolParser
-
- setZoom(int) - Method in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- setZoom(int) - Method in interface org.biojava.nbio.structure.gui.StructureViewer
-
Set the Zoom level
- setZscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
Sets the value of the zscore property.
- setZscore(BigDecimal) - Method in class org.biojava.nbio.structure.validation.MogBondOutlier
-
Sets the value of the zscore property.
- shift(Structure, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
shift a structure with a vector.
- shift(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Shift a vector.
- shift(Group, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Shift a Group with a vector.
- shiftAtAlignmentLocation(Location, int) - Method in interface org.biojava.nbio.alignment.template.MutableAlignedSequence
-
- shiftAtSequenceLocation(Location, int) - Method in interface org.biojava.nbio.alignment.template.MutableAlignedSequence
-
- shiftCA2(AFPChain, Atom[], Matrix, Atom, Group[]) - Static method in class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
-
only shift CA positions.
- ShortSegmentRemover - Class in org.biojava.nbio.structure.domain.pdp
-
- ShortSegmentRemover() - Constructor for class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
-
- shouldCreateAtomBonds() - Method in class org.biojava.nbio.structure.io.FileParsingParameters
-
Should we create bonds between atoms when parsing a file?
- show(BufferedReader, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
-
- show(File, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
-
- show(URL, UserConfiguration) - Method in class org.biojava.nbio.structure.align.gui.DBResultTable
-
- show() - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Show the dialog box.
- showAboutDialog() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
show some info about this gui
- showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
-
- showAlignmentGUI() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- showAlignmentImage(AFPChain, Atom[], Atom[], Object) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- showAlignmentImage(AFPChain, Atom[], Atom[], StructureAlignmentJmol) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
- showAlignmentImage(AFPChain, String) - Static method in class org.biojava.nbio.structure.align.gui.DisplayAFP
-
- showAlternative(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
-
- showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
Returns a Jmol script to show axes
- showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
Returns a Jmol script to show axes
- showAxes() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- showCompound() - Method in class org.biojava.nbio.structure.Compound
-
- showConsole(boolean) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- showDBResults(StartupParameters) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
- showDialog() - Method in class org.biojava.nbio.structure.align.gui.AboutDialog
-
- showDialog() - Static method in class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
-
- showDialog() - Method in class org.biojava.nbio.structure.align.gui.HelpDialog
-
- showDialog() - Method in class org.biojava.nbio.structure.align.gui.SystemInfo
-
- showDialog(Component, String) - Method in class org.forester.archaeopteryx.FontChooser
-
- showDialog() - Method in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Shows the dialog box and waits for the user to press OK or
Cancel.
- showDistanceMatrix(int) - Method in class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
-
- showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener
-
open a URL in the browser that was used to launch SPICE
- showDocument(String) - Static method in class org.biojava.nbio.structure.align.webstart.BrowserOpener
-
open a URL in the browser that was used to launch SPICE
- showDocument(URL) - Static method in class org.biojava.nbio.structure.align.webstart.JNLPProxy
-
- showErrorMessage(Component, String) - Static method in class org.forester.archaeopteryx.AptxUtil
-
- showHeader() - Method in class org.biojava.nbio.structure.Compound
-
Print some debug statements to System.out
- showMemoryMonitor() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- ShowPDBIDListener - Class in org.biojava.nbio.structure.align.gui
-
- ShowPDBIDListener() - Constructor for class org.biojava.nbio.structure.align.gui.ShowPDBIDListener
-
- showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
-
- showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
-
- showPolyhedron() - Method in class org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
-
- showProgressBar() - Static method in class org.biojava.nbio.structure.align.gui.StructureLoaderThread
-
- showSource() - Method in class org.biojava.nbio.structure.Compound
-
- showStructure(Structure) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper
-
Shows a structure in Jmol
- showSuggest() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
-
Force the suggestions to be displayed (Useful for buttons
e.g.
- showSystemInfo() - Static method in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- showUrl(String) - Method in class org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener
-
- showWhole() - Method in class org.forester.archaeopteryx.MainFrame
-
- shuffle(Sequence<C>) - Static method in class org.biojava.nbio.core.sequence.template.SequenceMixin
-
Implements sequence shuffling by first materializing the given
Sequence into a
List, applying
Collections.shuffle(List) and then returning the shuffled
elements in a new instance of
SequenceBackingStore which behaves
as a
Sequence.
- shuffleColumnsAndThenRows(ArrayList<String>, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Randomly shuffle the columns and rows.
- shuffleColumnValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Need to shuffle column values to allow for randomized testing.
- shuffleRowValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Need to shuffle rows values to allow for randomized testing.
- shutdown() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Disables new tasks from being submitted and closes the thread pool cleanly.
- shutdownAndAwaitTermination() - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Closes the thread pool.
- sideChainScoringType - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- SiftsChainEntry - Class in org.biojava.nbio.structure.io.sifts
-
An entry in the chain-level SIFTS mapping between UniProt and the PDB.
- SiftsChainEntry(String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsChainEntry
-
- SiftsChainToUniprotMapping - Class in org.biojava.nbio.structure.io.sifts
-
A mapping between UniProt entries and PDB chains.
- SiftsEntity - Class in org.biojava.nbio.structure.io.sifts
-
- SiftsEntity() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- SiftsEntity(String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity
-
- SiftsMappingProvider - Class in org.biojava.nbio.structure.io.sifts
-
- SiftsMappingProvider() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
-
- SiftsResidue - Class in org.biojava.nbio.structure.io.sifts
-
- SiftsResidue() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsResidue
-
- SiftsSegment - Class in org.biojava.nbio.structure.io.sifts
-
- SiftsSegment() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- SiftsSegment(String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment
-
- SiftsXMLParser - Class in org.biojava.nbio.structure.io.sifts
-
- SiftsXMLParser() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsXMLParser
-
- SigEva - Class in org.biojava.nbio.structure.align.fatcat.calc
-
- SigEva() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.SigEva
-
- signatureName - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
-
- SIMILARITY_COLOR - Static variable in class org.biojava.nbio.structure.align.gui.MenuCreator
-
- SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements a data structure for a
Sequence within an alignment.
- SimpleAlignedSequence(S, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- SimpleAlignedSequence(S, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- SimpleAlignedSequence(AlignedSequence<S, C>, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleAlignedSequence
-
- SimpleDomain - Class in org.forester.surfacing
-
- SimpleDomain(String) - Constructor for class org.forester.surfacing.SimpleDomain
-
- SimpleGapPenalty - Class in org.biojava.nbio.alignment
-
Implements a data structure for the gap penalties used during a sequence alignment routine.
- SimpleGapPenalty() - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty
-
Creates a new set of gap penalties using the defaults.
- SimpleGapPenalty(int, int) - Constructor for class org.biojava.nbio.alignment.SimpleGapPenalty
-
Creates a new set of gap penalties.
- SimpleGraph<V> - Class in org.biojava.nbio.structure.symmetry.utils
-
A simple nondirected graph implementation based on a list of edges for each vertex
- SimpleGraph() - Constructor for class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- SimpleLocation - Class in org.biojava.nbio.core.sequence.location
-
Very basic implementation of the Location interface which defines a series
of simple constructors.
- SimpleLocation(int, int) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(int, int, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, boolean, AccessionID) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(int, int, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava.nbio.core.sequence.location.SimpleLocation
-
- SimpleMMcifConsumer - Class in org.biojava.nbio.structure.io.mmcif
-
A MMcifConsumer implementation that build a in-memory representation of the
content of a mmcif file as a BioJava Structure object.
- SimpleMMcifConsumer() - Constructor for class org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer
-
- SimpleMMcifParser - Class in org.biojava.nbio.structure.io.mmcif
-
A simple mmCif file parser
- SimpleMMcifParser() - Constructor for class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
-
- SimplePoint - Class in org.biojava.nbio.core.sequence.location
-
Basic implementation of the Point interface.
- SimplePoint() - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint
-
- SimplePoint(int) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint
-
- SimplePoint(int, boolean, boolean) - Constructor for class org.biojava.nbio.core.sequence.location.SimplePoint
-
- SimpleProfile<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements a data structure for the results of sequence alignment.
- SimpleProfile(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfile
-
Creates a pair profile for the given already aligned sequences.
- SimpleProfile(S) - Constructor for class org.biojava.nbio.alignment.SimpleProfile
-
Creates a profile from a single sequence.
- SimpleProfile(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleProfile
-
Creates a pair profile for the given sequences.
- SimpleProfile(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleProfile
-
Creates a pair profile for the given profiles.
- SimpleProfile(Collection<AlignedSequence<S, C>>) - Constructor for class org.biojava.nbio.alignment.SimpleProfile
-
Creates a profile for the already aligned sequences.
- SimpleProfilePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements a data structure for the results of the alignment of a pair of
Profiles.
- SimpleProfilePair(Profile<S, C>, Profile<S, C>, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleProfilePair
-
Creates a pair profile for the given profiles.
- SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
- SimpleProfileProfileAligner() - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
-
- SimpleProfileProfileAligner(Profile<S, C>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
-
Prepares for a profile-profile alignment.
- SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
-
Prepares for a profile-profile alignment run concurrently.
- SimpleProfileProfileAligner(Profile<S, C>, Future<ProfilePair<S, C>>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
-
Prepares for a profile-profile alignment run concurrently.
- SimpleProfileProfileAligner(Future<ProfilePair<S, C>>, Profile<S, C>, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SimpleProfileProfileAligner
-
Prepares for a profile-profile alignment run concurrently.
- SimpleSequencePair<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements a data structure for the results of pairwise sequence alignment.
- SimpleSequencePair(AlignedSequence<S, C>, AlignedSequence<S, C>) - Constructor for class org.biojava.nbio.alignment.SimpleSequencePair
-
Creates a pair profile for the given already aligned sequences.
- SimpleSequencePair(S, S, List<AlignedSequence.Step>, List<AlignedSequence.Step>) - Constructor for class org.biojava.nbio.alignment.SimpleSequencePair
-
Creates a pair profile for the given sequences with a global alignment.
- SimpleSequencePair(S, S, List<AlignedSequence.Step>, int, int, List<AlignedSequence.Step>, int, int) - Constructor for class org.biojava.nbio.alignment.SimpleSequencePair
-
Creates a pair profile for the given sequences with a local alignment.
- SimpleSubstitutionMatrix<C extends Compound> - Class in org.biojava.nbio.alignment
-
Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one
Compound in a sequence for another.
- SimpleSubstitutionMatrix(CompoundSet<C>, File) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
Creates a substitution matrix by reading in a file.
- SimpleSubstitutionMatrix(CompoundSet<C>, Reader, String) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
Creates a substitution matrix by parsing some input.
- SimpleSubstitutionMatrix(CompoundSet<C>, String, String) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
Creates a substitution matrix by parsing a String.
- SimpleSubstitutionMatrix(CompoundSet<C>, short, short) - Constructor for class org.biojava.nbio.alignment.SimpleSubstitutionMatrix
-
Creates an identity substitution matrix from match and replace values.
- SingleCompoundSequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.storage
-
An implementation of the SequenceReader interface which for every
call will return only 1 compound (given to it during construction; a String
is also valid but will require a CompoundSet).
- SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Public constructor to be used with String based constructor
- SingleCompoundSequenceReader(C, CompoundSet<C>, int) - Constructor for class org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader
-
Build the object with a compound rather than a String
- SingleLinkageClusterer - Class in org.biojava.nbio.core.util
-
An implementation of a single linkage clusterer
See http://en.wikipedia.org/wiki/Single-linkage_clustering
- SingleLinkageClusterer(double[][], boolean) - Constructor for class org.biojava.nbio.core.util.SingleLinkageClusterer
-
- singleLocationPattern - Static variable in class org.biojava.nbio.core.sequence.location.InsdcParser
-
parse a location.
- SingularValueDecomposition - Class in org.biojava.nbio.structure.jama
-
Singular Value Decomposition.
- SingularValueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.SingularValueDecomposition
-
Construct the singular value decomposition.
- Site - Class in org.biojava.nbio.phosphosite
-
Created by ap3 on 31/10/2014.
- Site() - Constructor for class org.biojava.nbio.phosphosite.Site
-
- Site - Class in org.biojava.nbio.structure
-
Holds the data of sites presented in PDB files.
- Site() - Constructor for class org.biojava.nbio.structure.Site
-
- Site(String, List<Group>) - Constructor for class org.biojava.nbio.structure.Site
-
- site2 - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
-
- size() - Method in class org.biojava.nbio.core.util.FlatFileCache
-
- size() - Method in class org.biojava.nbio.core.util.SoftHashMap
-
- size() - Method in class org.biojava.nbio.ontology.utils.SmallMap
-
- size() - Method in class org.biojava.nbio.structure.contact.AtomContactSet
-
- size() - Method in class org.biojava.nbio.structure.contact.GroupContactSet
-
- size() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
- size() - Method in interface org.biojava.nbio.structure.Group
-
Get number of atoms.
- size() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- SIZE - Static variable in class org.biojava.nbio.structure.gui.util.SequenceScalePanel
-
- size() - Method in class org.biojava.nbio.structure.HetatomImpl
-
Get number of atoms.
- size() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
Returns the number of mapped entries.
- size() - Method in class org.biojava.nbio.structure.math.SparseVector
-
- size() - Method in class org.biojava.nbio.structure.math.SymbolTable
-
How many keys are in the table?
- size() - Method in interface org.biojava.nbio.structure.Structure
-
Return number of Chains in this Structure.
- size(int) - Method in interface org.biojava.nbio.structure.Structure
-
Return number of chains of model.
- size() - Method in class org.biojava.nbio.structure.StructureImpl
-
return number of chains , if NMR return number of chains of first model .
- size(int) - Method in class org.biojava.nbio.structure.StructureImpl
-
return number of chains of model.
- size() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
-
- size() - Method in interface org.biojava.nbio.structure.symmetry.utils.Graph
-
- size() - Method in class org.biojava.nbio.structure.symmetry.utils.SimpleGraph
-
- size() - Method in class org.forester.archaeopteryx.tools.ProcessPool
-
- size() - Method in class org.forester.phylogeny.data.PropertiesMap
-
- SIZE_REF - Static variable in class org.forester.phylogeny.data.NodeVisualization
-
- SIZE_TYPE - Static variable in class org.forester.phylogeny.data.NodeVisualization
-
- skip(long) - Method in class org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
-
Skips characters.
- skip(long) - Method in class org.biojava.nbio.core.util.UncompressInputStream
-
- skip(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
-
Method skips n nucleotides in sequence stream.
- sleepAmount - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- slider - Variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- SLIDER_STEPS - Static variable in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- small - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- SmallAnnotation - Class in org.biojava.nbio.ontology.utils
-
Annotation that is optimized for memory usage.
- SmallAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation
-
Return a new SmallAnnotation optimised for small sets of properties.
- SmallAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation
-
Return a new SmallAnnotation that copies all values from another annoation.
- SmallAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation
-
Return a new SmallAnnotation that copies all values from a Map.
- SmallMap - Class in org.biojava.nbio.ontology.utils
-
Lightweight implementation of Map which uses little memory to store a
small number of mappings, at the expense of scalability.
- SmallMap() - Constructor for class org.biojava.nbio.ontology.utils.SmallMap
-
- SmallMap(int) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap
-
- SmallMap(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap
-
- SMART - Static variable in class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- smartAdapter - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
-
- smartAdapter - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- SmithWaterman<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
Sequence).
- SmithWaterman() - Constructor for class org.biojava.nbio.alignment.SmithWaterman
-
- SmithWaterman(S, S, GapPenalty, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SmithWaterman
-
Prepares for a pairwise local sequence alignment.
- SmithWaterman3Daligner - Class in org.biojava.nbio.structure.align.seq
-
provides a 3D superimposition based on the sequence alignment
- SmithWaterman3Daligner() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
-
- SmithWaterman3DParameters - Class in org.biojava.nbio.structure.align.seq
-
- SmithWaterman3DParameters() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
-
- SmithWatermanUserArgumentProcessor - Class in org.biojava.nbio.structure.align.seq
-
- SmithWatermanUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
-
- SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams - Class in org.biojava.nbio.structure.align.seq
-
- SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
-
- SoftHashMap<K,V> - Class in org.biojava.nbio.core.util
-
A in memory cache using soft references.
- SoftHashMap() - Constructor for class org.biojava.nbio.core.util.SoftHashMap
-
- SoftHashMap(int) - Constructor for class org.biojava.nbio.core.util.SoftHashMap
-
- SolexaFastqReader - Class in org.biojava.nbio.sequencing.io.fastq
-
- SolexaFastqReader() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader
-
- SolexaFastqWriter - Class in org.biojava.nbio.sequencing.io.fastq
-
- SolexaFastqWriter() - Constructor for class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter
-
- solve(Matrix) - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition
-
Solve A*X = B
- solve(Matrix) - Method in class org.biojava.nbio.structure.jama.LUDecomposition
-
Solve A*X = B
- solve(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Solve A*X = B
- solve(Matrix) - Method in class org.biojava.nbio.structure.jama.QRDecomposition
-
Least squares solution of A*X = B
- solveTranspose(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix
-
Solve X*A = B, which is also A'*X' = B'
- sort() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
-
Sorts the interface list and reassigns ids based on new sorting
- sortAfps(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
-
- sortByFoldDecending() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
-
- sortByStart() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Create a new list that is ordered by the starting index of the features' locations.
- sortDomainsWithAscendingConfidenceValues(Protein) - Static method in class org.forester.surfacing.SurfacingUtil
-
- sortNodeDescendents(PhylogenyNode, PhylogenyMethods.DESCENDANT_SORT_PRIORITY) - Static method in class org.forester.phylogeny.PhylogenyMethods
-
- sortSequenceClustersBySize(List<SequenceAlignmentCluster>) - Static method in class org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
-
- source() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
-
Get source (aka method).
- SOURCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- SpaceGroup - Class in org.biojava.nbio.structure.xtal
-
A crystallographic space group.
- SpaceGroup(int, int, int, String, String, BravaisLattice) - Constructor for class org.biojava.nbio.structure.xtal.SpaceGroup
-
- SpaceGroupMapElements - Class in org.biojava.nbio.structure.xtal.io
-
- SpaceGroupMapElements(Integer, SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
-
- SpaceGroupMapRoot - Class in org.biojava.nbio.structure.xtal.io
-
- SpaceGroupMapRoot() - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
-
- SparseSquareMatrix - Class in org.biojava.nbio.structure.math
-
A sparse, square matrix, implementing using two arrays of sparse
vectors, one representation for the rows and one for the columns.
- SparseSquareMatrix(int) - Constructor for class org.biojava.nbio.structure.math.SparseSquareMatrix
-
initialize an N-by-N matrix of all 0s
- SparseVector - Class in org.biojava.nbio.structure.math
-
A sparse vector, implemented using a symbol table.
- SparseVector(int) - Constructor for class org.biojava.nbio.structure.math.SparseVector
-
Constructor.
- SPECIATION - Static variable in class org.forester.archaeopteryx.TreeColorSet
-
- Species - Interface in org.forester.species
-
- SPECIES_NAME - Static variable in class org.forester.io.parsers.nhx.NHXtags
-
- SPECIES_SEPARATOR - Static variable in class org.forester.surfacing.PrintableDomainSimilarity
-
- SphereSampler - Class in org.biojava.nbio.structure.symmetry.geometry
-
- splice(DNASequence) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList
-
Concatenate successive portions of the specified sequence
using the feature locations in the list.
- splitBlocksByTopology(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools
-
- SplitFasta - Class in org.biojava.nbio.genome.util
-
Utility to write each Fasta entry to a unique file
- SplitFasta() - Constructor for class org.biojava.nbio.genome.util.SplitFasta
-
- sqrt(BigInteger) - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
Get square root
- sqrt(BigDecimal) - Method in class org.biojava.nbio.structure.secstruc.BigSqrt
-
Get square root
- sqrt(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- sqrt(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- SqrtColorMapper - Class in org.biojava.nbio.structure.gui.util.color
-
Performs a sqrt transform on input before passing the values off to another
colorMapper.
- SqrtColorMapper(ContinuousColorMapper) - Constructor for class org.biojava.nbio.structure.gui.util.color.SqrtColorMapper
-
Creates a new SqrtColorMapper.
- SSBond - Class in org.biojava.nbio.structure
-
A simple bean to store disulfid bridge information, the SSBOND records in the PDB files.
- SSBond() - Constructor for class org.biojava.nbio.structure.SSBond
-
- ssHash - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- StainType - Enum in org.biojava.nbio.genome.parsers.cytoband
-
- STANDARD - Static variable in class org.forester.io.parsers.nexus.NexusConstants
-
- standardAASet - Static variable in class org.biojava.nbio.aaproperties.PeptideProperties
-
Contains the 20 standard AA code in a set
- StandardAminoAcid - Class in org.biojava.nbio.structure
-
A class that provides a set of standard amino acids.
- standardErrorOfMean() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- standardErrorOfMean() - Method in interface org.forester.util.DescriptiveStatistics
-
- StandardRescoreRefiner<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
- StandardRescoreRefiner(Alignments.PairInProfileScorerType, Alignments.ProfileProfileAlignerType) - Constructor for class org.biojava.nbio.alignment.StandardRescoreRefiner
-
- start() - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Get starting index (origin 0).
- start() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- start() - Method in class org.forester.archaeopteryx.ArchaeopteryxA
-
- start() - Method in class org.forester.archaeopteryx.ArchaeopteryxE
-
- start(MainFrame, String) - Method in class org.forester.archaeopteryx.tools.RunnableProcess
-
- START_SEQUENCE_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- StartCodonSequence - Class in org.biojava.nbio.core.sequence
-
Used to map the start codon feature on a gene
- StartCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StartCodonSequence
-
- startDocument() - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
-
- startDocument() - Method in class org.forester.io.parsers.tol.TolXmlHandler
-
- startElement(String, String, String, Attributes) - Method in class org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
-
- startElement(String, String, String, Attributes) - Method in class org.forester.io.parsers.phyloxml.PhyloXmlHandler
-
- startElement(String, String, String, Attributes) - Method in class org.forester.io.parsers.tol.TolXmlHandler
-
- startingAlignment(String, Atom[], String, Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
-
- startingColor - Variable in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Starting color, set by setColor, and the color we return
to on a reset.
- startingColorBrewer - Variable in class org.jcolorbrewer.ui.ColorPaletteChooserDialog
-
Starting color, set by setColor, and the color we return
to on a reset.
- startsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location starts after the other location starts.
- startsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
Check if this location starts before other location starts.
- StartupParameters - Class in org.biojava.nbio.structure.align.ce
-
a simple bean that contains the parameters that can get set at startup
- StartupParameters() - Constructor for class org.biojava.nbio.structure.align.ce.StartupParameters
-
- stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.ScaleableMatrixPanel
-
- stateChanged(ChangeEvent) - Method in class org.biojava.nbio.structure.gui.SequenceDisplay
-
- stateChanged(ChangeEvent) - Method in class org.jcolorbrewer.ui.DivergingColorPalettePanel
-
- stateChanged(ChangeEvent) - Method in class org.jcolorbrewer.ui.QualitativeColorPalettePanel
-
- stateChanged(ChangeEvent) - Method in class org.jcolorbrewer.ui.SequentialColorPalettePanel
-
- StaticMemberPlaceHolder - Class in org.biojava.nbio.ontology.utils
-
- StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder
-
- StaticMemberPlaceHolder() - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder
-
- StatusDisplay - Class in org.biojava.nbio.structure.align.gui.aligpanel
-
- StatusDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay
-
- StdArrayIO - Class in org.biojava.nbio.survival.cox.matrix
-
Standard array IO.
- StdArrayIO() - Constructor for class org.biojava.nbio.survival.cox.matrix.StdArrayIO
-
- stdev - Variable in class org.biojava.nbio.structure.validation.AngleOutlier
-
- stdev - Variable in class org.biojava.nbio.structure.validation.BondOutlier
-
- stdev - Variable in class org.biojava.nbio.structure.validation.MogAngleOutlier
-
- stdev - Variable in class org.biojava.nbio.structure.validation.MogBondOutlier
-
- StockholmFileAnnotation - Class in org.biojava.nbio.alignment.io
-
Stores all the content parsed from the #=GF lines
- StockholmFileAnnotation() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- StockholmFileAnnotation.StockholmFileAnnotationReference - Class in org.biojava.nbio.alignment.io
-
- StockholmFileAnnotation.StockholmFileAnnotationReference() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
-
- StockholmFileParser - Class in org.biojava.nbio.alignment.io
-
- StockholmFileParser() - Constructor for class org.biojava.nbio.alignment.io.StockholmFileParser
-
- StockholmStructure - Class in org.biojava.nbio.alignment.io
-
Stores all the content of a Stockholm file.
- StockholmStructure() - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure
-
- StockholmStructure.DatabaseReference - Class in org.biojava.nbio.alignment.io
-
- StockholmStructure.DatabaseReference(String, String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- StockholmStructure.DatabaseReference(String) - Constructor for class org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
-
- STOP - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- stop() - Method in interface org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
-
Interrupt searching for suggestions
- stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider
-
- stop() - Method in class org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider
-
- stop() - Method in class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface
-
- stopAtStopCodons(boolean) - Method in class org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
-
If set, then the last codon translated in the resulting peptide
sequence will be the stop codon
- StopCodonSequence - Class in org.biojava.nbio.core.sequence
-
Used to map the stop codon sequence on a gene
- StopCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava.nbio.core.sequence.StopCodonSequence
-
- storeParameters() - Method in class org.biojava.nbio.structure.align.gui.ParameterGUI
-
- str - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair
-
- Strand - Enum in org.biojava.nbio.core.sequence
-
Provides a way of representing the strand of a sequence, location
hit or feature.
- strand - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- STRAND - Static variable in class org.biojava.nbio.structure.io.PDBFileParser
-
Strand secondary structure assignment.
- strandmax - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- strandmin - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- StrataInfo - Class in org.biojava.nbio.survival.cox
-
Information needed to represent a survival curve
- StrataInfo() - Constructor for class org.biojava.nbio.survival.cox.StrataInfo
-
- StrCompAlignment - Class in org.biojava.nbio.structure.align.pairwise
-
- StrCompAlignment(int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.StrCompAlignment
-
- stream(Readable, StreamListener) - Method in interface org.biojava.nbio.sequencing.io.fastq.FastqReader
-
Stream the specified readable.
- StreamListener - Interface in org.biojava.nbio.sequencing.io.fastq
-
Event based parser callback.
- STRING_LIMIT - Static variable in class org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser
-
- stringArrayToString(String[]) - Static method in class org.forester.util.ForesterUtil
-
- stringArrayToString(String[], String) - Static method in class org.forester.util.ForesterUtil
-
- stringListToArray(List<String>) - Static method in class org.forester.util.ForesterUtil
-
- stringListToString(List<String>, String) - Static method in class org.forester.util.ForesterUtil
-
- StringManipulationHelper - Class in org.biojava.nbio.core.util
-
A utility class for common String manipulation tasks.
- StringProxySequenceReader<C extends Compound> - Class in org.biojava.nbio.core.sequence.loader
-
An example of a ProxySequenceReader that is created from a String.
- StringProxySequenceReader() - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- StringProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader
-
- stringSetToArray(Set<String>) - Static method in class org.forester.util.ForesterUtil
-
- stringToFloats(String) - Method in class org.biojava.nbio.alignment.io.StockholmFileAnnotation
-
- strip - Class in org.forester.application
-
- strip() - Constructor for class org.forester.application.strip
-
- StrucAligParameters - Class in org.biojava.nbio.structure.align
-
A class that contains all the parameters of the structure alignment algorithm.
- StrucAligParameters() - Constructor for class org.biojava.nbio.structure.align.StrucAligParameters
-
- Struct - Class in org.biojava.nbio.structure.io.mmcif.model
-
a bean to contain the data of the _struct lines
- Struct() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Struct
-
- StructAsym - Class in org.biojava.nbio.structure.io.mmcif.model
-
Contains the data for _struct_asym
- StructAsym() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructAsym
-
- StructConn - Class in org.biojava.nbio.structure.io.mmcif.model
-
A bean that stores data from the mmcif category _struct_conn
- StructConn() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructConn
-
- StructKeywords - Class in org.biojava.nbio.structure.io.mmcif.model
-
- StructKeywords() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructKeywords
-
- StructNcsOper - Class in org.biojava.nbio.structure.io.mmcif.model
-
A class containing the _struct_ncs_oper data
- StructNcsOper() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
-
- StructRef - Class in org.biojava.nbio.structure.io.mmcif.model
-
A class to containt the _struct_ref field data
- StructRef() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRef
-
- StructRefSeq - Class in org.biojava.nbio.structure.io.mmcif.model
-
- StructRefSeq() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
-
- Structure - Interface in org.biojava.nbio.structure
-
Interface for a structure object.
- StructureAlignment - Interface in org.biojava.nbio.structure.align
-
- StructureAlignmentDisplay - Class in org.biojava.nbio.structure.align.gui
-
- StructureAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
-
- StructureAlignmentFactory - Class in org.biojava.nbio.structure.align
-
- StructureAlignmentFactory() - Constructor for class org.biojava.nbio.structure.align.StructureAlignmentFactory
-
- StructureAlignmentJmol - Class in org.biojava.nbio.structure.align.gui.jmol
-
A class that provides a simple GUI for Jmol
- StructureAlignmentJmol() - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- StructureAlignmentJmol(AFPChain, Atom[], Atom[]) - Constructor for class org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
-
- StructureAlignmentOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc
-
- StructureAlignmentOptimizer(int, int, Atom[], int, int, Atom[], int, int[][]) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
-
optimize the structural alignment by update the equivalent residues
and then run dynamic programming
input: len1 the length of structure 1; c1: the structure information of 1
len2 the length of structure 2; c2: the structure information of 2
iniLen and iniSet is the length and list of initial equivalent residues
- StructureAtom - Class in org.biojava.nbio.protmod.structure
-
Everything that is needed to uniquely describe a atom.
- StructureAtom(StructureGroup, String) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtom
-
- StructureAtomLinkage - Class in org.biojava.nbio.protmod.structure
-
- StructureAtomLinkage(StructureAtom, StructureAtom, double) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtomLinkage
-
- StructureAtomXMLConverter - Class in org.biojava.nbio.protmod.io
-
- StructureAtomXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureAtomXMLConverter
-
- StructureException - Exception in org.biojava.nbio.structure
-
An exception during the parsing of a PDB file.
- StructureException(String) - Constructor for exception org.biojava.nbio.structure.StructureException
-
Constructs a StructureException object.
- StructureException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException
-
Constructs a StructureException object.
- StructureException(Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException
-
Constructs a StructureException object.
- StructureGroup - Class in org.biojava.nbio.protmod.structure
-
Information of a group (residue or ligand) involved in a modification.
- StructureGroup() - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup
-
- StructureGroup(ResidueNumber, String, boolean) - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup
-
- StructureGroupXMLConverter - Class in org.biojava.nbio.protmod.io
-
- StructureGroupXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureGroupXMLConverter
-
- StructureIdentifier - Interface in org.biojava.nbio.structure
-
- StructureImpl - Class in org.biojava.nbio.structure
-
Implementation of a PDB Structure.
- StructureImpl() - Constructor for class org.biojava.nbio.structure.StructureImpl
-
Constructs a StructureImpl object.
- StructureImpl(Group) - Constructor for class org.biojava.nbio.structure.StructureImpl
-
construct a Structure object that only contains a single group
- StructureImpl(Chain) - Constructor for class org.biojava.nbio.structure.StructureImpl
-
construct a Structure object that contains a particular chain
- StructureInterface - Class in org.biojava.nbio.structure.contact
-
An interface between 2 molecules (2 sets of atoms).
- StructureInterface(Atom[], Atom[], String, String, AtomContactSet, CrystalTransform, CrystalTransform) - Constructor for class org.biojava.nbio.structure.contact.StructureInterface
-
Constructs a StructureInterface
- StructureInterface() - Constructor for class org.biojava.nbio.structure.contact.StructureInterface
-
Constructs an empty StructureInterface
- StructureInterfaceCluster - Class in org.biojava.nbio.structure.contact
-
- StructureInterfaceCluster() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceCluster
-
- StructureInterfaceList - Class in org.biojava.nbio.structure.contact
-
A list of interfaces between 2 molecules (2 sets of atoms)
- StructureInterfaceList() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceList
-
- StructureIO - Class in org.biojava.nbio.structure
-
A class that provides static access methods for easy lookup of protein structure related components
- StructureIO() - Constructor for class org.biojava.nbio.structure.StructureIO
-
- StructureIOFile - Interface in org.biojava.nbio.structure.io
-
StructureIOFile extends StructureProvider with methods specific to
parsing files from the filesystem.
- StructureLoaderThread - Class in org.biojava.nbio.structure.align.gui
-
- StructureName - Class in org.biojava.nbio.structure.align.client
-
A utility class that makes working with names of structures, domains and ranges easier.
- StructureName(String) - Constructor for class org.biojava.nbio.structure.align.client.StructureName
-
- StructurePairAligner - Class in org.biojava.nbio.structure.align
-
Perform a pairwise protein structure superimposition.
- StructurePairAligner() - Constructor for class org.biojava.nbio.structure.align.StructurePairAligner
-
- StructurePairSelector - Interface in org.biojava.nbio.structure.gui.util
-
To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
- StructureProvider - Interface in org.biojava.nbio.structure.io
-
A class that can provide a protein structure object from somewhere.
- StructureSequenceMatcher - Class in org.biojava.nbio.structure.io
-
A utility class with methods for matching ProteinSequences with
Structures.
- StructureSequenceMatcher() - Constructor for class org.biojava.nbio.structure.io.StructureSequenceMatcher
-
- StructureTools - Class in org.biojava.nbio.structure
-
A class that provides some tool methods.
- StructureTools() - Constructor for class org.biojava.nbio.structure.StructureTools
-
- StructureUtil - Class in org.biojava.nbio.protmod.structure
-
- StructureViewer - Interface in org.biojava.nbio.structure.gui
-
- submit(Callable<T>, String) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Queues up a task and adds a log entry.
- submit(Callable<T>) - Static method in class org.biojava.nbio.core.util.ConcurrencyTools
-
Queues up a task and adds a default log entry.
- subSequence(int, int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
-
- SUBSET - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- SubstitutionMatrix<C extends Compound> - Interface in org.biojava.nbio.alignment.template
-
Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one
Compound in a sequence for another.
- substitutionMatrix - Variable in class org.biojava.nbio.structure.align.ce.CeParameters
-
- SubstitutionMatrixHelper - Class in org.biojava.nbio.alignment
-
Static utility to access substitution matrices that come bundled with BioJava.
- SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound> - Class in org.biojava.nbio.alignment
-
Scores using a substitution matrix.
- SubstitutionMatrixScorer(SequencePair<S, C>, SubstitutionMatrix<C>) - Constructor for class org.biojava.nbio.alignment.SubstitutionMatrixScorer
-
- SubstructureIdentifier - Class in org.biojava.nbio.structure
-
An arbitrary collection of residues in a
Structure.
- SubstructureIdentifier(String, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier
-
- SubstructureIdentifier(String, AtomCache) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier
-
- subtract(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
subtract two atoms ( a - b).
- subtract(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
-
- SUBTREE_NEIGHBORS - Static variable in class org.forester.io.parsers.nhx.NHXtags
-
- SubunitGraph - Class in org.biojava.nbio.structure.symmetry.core
-
- SubunitGraph(List<Point3d[]>) - Constructor for class org.biojava.nbio.structure.symmetry.core.SubunitGraph
-
- Subunits - Class in org.biojava.nbio.structure.symmetry.core
-
- Subunits(List<Point3d[]>, List<Integer>, List<Boolean>, List<Double>, List<Double>, List<Integer>, List<String>, List<Integer>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Subunits
-
- suffix(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
The part of this location after the specified position.
- suffix(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location
-
The part of this location after the other location (not inclusive).
- suggestDomains(Structure) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser
-
Suggest domains for a protein structure
- suggestDomains(Atom[]) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser
-
Suggest domains for a set of Calpha atoms
- SULFUR_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator
-
- sumDeviations() - Method in class org.forester.util.BasicDescriptiveStatistics
-
- sumDeviations() - Method in interface org.forester.util.DescriptiveStatistics
-
- SUMMARY_POS - Static variable in class org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
-
Position at which the alignment summary is printed
- SUMOYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset
-
- SUPER_ORTHOLOGOUS - Static variable in class org.forester.io.parsers.nhx.NHXtags
-
- superpose(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
-
- superposeAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
-
- superposeAtOrigin(Point3d[], Point3d[], AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
-
- superposeWithTranslation(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
-
- SuperPosition - Class in org.biojava.nbio.structure.symmetry.geometry
-
- SuperPosition() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.SuperPosition
-
- SuperPositionQCP - Class in org.biojava.nbio.structure.symmetry.geometry
-
- SuperPositionQCP() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
-
- SUPPORT - Static variable in class org.forester.io.parsers.nhx.NHXtags
-
- support_statistics - Class in org.forester.application
-
- support_statistics() - Constructor for class org.forester.application.support_statistics
-
- support_transfer - Class in org.forester.application
-
- support_transfer() - Constructor for class org.forester.application.support_transfer
-
- SupportCount - Class in org.forester.tools
-
- surf - Variable in class org.biojava.nbio.structure.align.gui.MemoryMonitor
-
- surf_paup - Class in org.forester.application
-
- surf_paup() - Constructor for class org.forester.application.surf_paup
-
- surfacing - Class in org.forester.application
-
- surfacing() - Constructor for class org.forester.application.surfacing
-
- SurfacingConstants - Class in org.forester.surfacing
-
- SurfacingConstants() - Constructor for class org.forester.surfacing.SurfacingConstants
-
- SurfacingUtil - Class in org.forester.surfacing
-
- SurvFitInfo - Class in org.biojava.nbio.survival.cox
-
Contains info for graphing km figures
- SurvFitInfo() - Constructor for class org.biojava.nbio.survival.cox.SurvFitInfo
-
- SurvFitKM - Class in org.biojava.nbio.survival.kaplanmeier.figure
-
Ported from survfitKM.S When combining multiple entries with same time not
sure how the weighting adds up
- SurvFitKM() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
-
- SurvFitKM.ConfLower - Enum in org.biojava.nbio.survival.kaplanmeier.figure
-
- SurvFitKM.ConfType - Enum in org.biojava.nbio.survival.kaplanmeier.figure
-
- SurvFitKM.Error - Enum in org.biojava.nbio.survival.kaplanmeier.figure
-
- SurvFitKM.Method - Enum in org.biojava.nbio.survival.kaplanmeier.figure
-
- SurvivalInfo - Class in org.biojava.nbio.survival.cox
-
Data class to represent a single sample where time and event/censor status is required
Additionally each variable and data associated with that variable.
- SurvivalInfo(double, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
-
- SurvivalInfo(double, int, LinkedHashMap<String, Double>) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
-
- SurvivalInfo(double, int, String, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
-
- SurvivalInfoComparator - Class in org.biojava.nbio.survival.cox.comparators
-
- SurvivalInfoComparator() - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
-
- SurvivalInfoHelper - Class in org.biojava.nbio.survival.cox
-
Used to work with SurvivalInfo
- SurvivalInfoHelper() - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoHelper
-
- SurvivalInfoIndex - Class in org.biojava.nbio.survival.cox
-
Not used and probably should be deleted
- SurvivalInfoIndex(double, int, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
-
- SurvivalInfoIndex(double, int, int, double[]) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
-
- SurvivalInfoIndex(double, int, int, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
-
- SurvivalInfoValueComparator - Class in org.biojava.nbio.survival.cox.comparators
-
- SurvivalInfoValueComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
-
- svd() - Method in class org.biojava.nbio.structure.jama.Matrix
-
Singular Value Decomposition
- SVDSuperimposer - Class in org.biojava.nbio.structure
-
A class that calculates the superimposition between two sets of atoms
inspired by the biopython SVDSuperimposer class...
- SVDSuperimposer(Atom[], Atom[]) - Constructor for class org.biojava.nbio.structure.SVDSuperimposer
-
Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.
- swapChildren() - Method in class org.forester.phylogeny.PhylogenyNode
-
Swaps the the two childern of a PhylogenyNode node of this Phylogeny.
- swapRowAndColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
-
Swap the row and columns returning a new worksheet
- SYMBOLS - Static variable in class org.forester.io.parsers.nexus.NexusConstants
-
- SymbolTable<Key extends java.lang.Comparable<Key>,Value> - Class in org.biojava.nbio.structure.math
-
Sorted symbol table implementation using a java.util.TreeMap.
- SymbolTable() - Constructor for class org.biojava.nbio.structure.math.SymbolTable
-
Create an empty symbol table.
- symmClash - Variable in class org.biojava.nbio.structure.validation.ModelledSubgroup
-
- SymmClash - Class in org.biojava.nbio.structure.validation
-
Java class for anonymous complex type.
- SymmClash() - Constructor for class org.biojava.nbio.structure.validation.SymmClash
-
- SYMMETRIC - Static variable in class org.biojava.nbio.ontology.OntoTools
-
- SymmetricalDistanceMatrixParser - Class in org.forester.io.parsers
-
- SymmetricalDistanceMatrixParser.InputMatrixType - Enum in org.forester.io.parsers
-
- Symmetry - Class in org.biojava.nbio.structure.io.mmcif.model
-
- Symmetry() - Constructor for class org.biojava.nbio.structure.io.mmcif.model.Symmetry
-
- symmetryCoefficient() - Method in class org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
-
- symop - Variable in class org.biojava.nbio.structure.validation.SymmClash
-
- SymoplibParser - Class in org.biojava.nbio.structure.xtal
-
A class containing static methods to parse the symop.lib file from the
CCP4 package.
- SymoplibParser() - Constructor for class org.biojava.nbio.structure.xtal.SymoplibParser
-
- SynchronizedOutFile - Class in org.biojava.nbio.structure.align.util
-
- SynchronizedOutFile(File, boolean) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile
-
Create a thread safe wrapper for writing to this file, the file will be gzip compressed.
- SynchronizedOutFile(File) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile
-
create a thread safe wrapper for working with this file
- SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler
-
- Synonym - Class in org.biojava.nbio.ontology
-
- Synonym() - Constructor for class org.biojava.nbio.ontology.Synonym
-
- SystematicSolver - Class in org.biojava.nbio.structure.symmetry.core
-
- SystematicSolver(Subunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SystematicSolver
-
- SystemCommandExecutor - Class in org.forester.util
-
- SystemCommandExecutor(List<String>) - Constructor for class org.forester.util.SystemCommandExecutor
-
Pass in the system command you want to run as a List of Strings, as shown here:
List commands = new ArrayList();
commands.add("/sbin/ping");
commands.add("-c");
commands.add("5");
commands.add("www.google.com");
SystemCommandExecutor commandExecutor = new SystemCommandExecutor(commands);
commandExecutor.executeCommand();
Note: I've removed the other constructor that was here to support executing
the sudo command.
- SystemInfo - Class in org.biojava.nbio.structure.align.gui
-
- SystemInfo() - Constructor for class org.biojava.nbio.structure.align.gui.SystemInfo
-
- V - Static variable in class org.biojava.nbio.aaproperties.Constraints
-
- Val - Static variable in class org.biojava.nbio.phylo.ResidueProperties
-
- validate(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter
-
- validate(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter
-
- validate(Fastq) - Method in class org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter
-
- validateAllowedOptions(List<String>) - Method in class org.forester.util.CommandLineArguments
-
- validateAllowedOptionsAsString(List<String>) - Method in class org.forester.util.CommandLineArguments
-
- validateMandatoryOptions(List<String>) - Method in class org.forester.util.CommandLineArguments
-
- validateMandatoryOptionsAsString(List<String>) - Method in class org.forester.util.CommandLineArguments
-
- value - Variable in class org.biojava.nbio.structure.align.helper.GapArray
-
- value - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
-
- value - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
-
- valueChanged(ListSelectionEvent) - Method in class org.forester.archaeopteryx.FontChooser
-
- valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.template.AlignedSequence.Step
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.alignment.template.Profile.StringFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DataSource
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.Strand
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeConstructionAlgorithm
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.BondType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.Element
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.ElementType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.GroupType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.RenderStyle
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.TransformType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.CoxMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.archaeopteryx.AptxUtil.GraphicsExportType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.archaeopteryx.Configuration.UI
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.archaeopteryx.Options.CLADOGRAM_TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.Format
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.evoinference.matrix.distance.DistanceMatrix.Format
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.go.etc.OntologizerResult.TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.go.GoNameSpace.GoNamespaceType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.go.GoRelationship.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.go.GoSubset.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.go.GoXRef.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.go.OBOparser.ReturnType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.FilterType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.ReturnType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.parsers.SymmetricalDistanceMatrixParser.InputMatrixType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.writers.PhylogenyWriter.FORMAT
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.io.writers.SequenceWriter.SEQ_FORMAT
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.data.Event.EventType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.data.NodeVisualization.NodeFill
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.data.NodeVisualization.NodeShape
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.data.Property.AppliesTo
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.PhylogenyMethods.TAXONOMY_EXTRACTION
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.protein.BinaryDomainCombination.DomainCombinationType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.protein.BinaryDomainCombination.OutputFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.sdi.SDI.TaxonomyComparisonBase
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.sequence.Sequence.TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.Detailedness
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.tools.PhylogenyDecorator.FIELD
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.util.ForesterConstants.PhylogeneticTreeFormats
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.ws.seqdb.SequenceDbWsTools.Db
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.ws.uniprot.SequenceDbWsTools.Db
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.ws.wabi.TxSearch.RANKS
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.forester.ws.wabi.TxSearch.TAX_RANK
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jcolorbrewer.ColorBrewer
-
Returns the enum constant of this type with the specified name.
- valueOfIgnoreCase(String) - Static method in enum org.biojava.nbio.structure.Element
-
Returns the Element that corresponds to the specified element symbol.
- values() - Static method in enum org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.Alignments.RefinerType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.routines.AlignerHelper.Last
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.template.AlignedSequence.Step
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.template.GapPenalty.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.alignment.template.Profile.StringFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.DataSource
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.DNASequence.DNAType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.Strand
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.core.sequence.transcription.Frame
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.phylo.TreeConstructionAlgorithm
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.phylo.TreeType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.protmod.ModificationCategory
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.sequencing.io.fastq.FastqVariant
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.BondType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.cath.CathCategory
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.Element
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.ElementType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.GroupType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.gui.RenderStyle
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Method in class org.biojava.nbio.structure.gui.util.color.GradientMapper
-
- values() - Static method in enum org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.PolymerType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.io.mmcif.chem.ResidueType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
-
- values() - Static method in enum org.biojava.nbio.structure.PDBStatus.Status
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.scop.ScopCategory
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.structure.xtal.TransformType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.survival.cox.CoxMethod
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.archaeopteryx.AptxUtil.GraphicsExportType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.archaeopteryx.Configuration.UI
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.archaeopteryx.Options.CLADOGRAM_TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.Format
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.evoinference.matrix.distance.DistanceMatrix.Format
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.go.etc.OntologizerResult.TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.go.GoNameSpace.GoNamespaceType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.go.GoRelationship.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.go.GoSubset.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.go.GoXRef.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.go.OBOparser.ReturnType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.FilterType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.parsers.HmmPfamOutputParser.ReturnType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.parsers.SymmetricalDistanceMatrixParser.InputMatrixType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.writers.PhylogenyWriter.FORMAT
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.io.writers.SequenceWriter.SEQ_FORMAT
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.data.Event.EventType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.data.NodeVisualization.NodeFill
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.data.NodeVisualization.NodeShape
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.data.Property.AppliesTo
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.PhylogenyMethods.TAXONOMY_EXTRACTION
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.protein.BinaryDomainCombination.DomainCombinationType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.protein.BinaryDomainCombination.OutputFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.sdi.SDI.TaxonomyComparisonBase
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.sequence.Sequence.TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.Detailedness
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.tools.PhylogenyDecorator.FIELD
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.util.ForesterConstants.PhylogeneticTreeFormats
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.ws.seqdb.SequenceDbWsTools.Db
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.ws.uniprot.SequenceDbWsTools.Db
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.ws.wabi.TxSearch.RANKS
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.forester.ws.wabi.TxSearch.TAX_RANK
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jcolorbrewer.ColorBrewer
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- Variable - Interface in org.biojava.nbio.ontology
-
- Variable.Impl - Class in org.biojava.nbio.ontology
-
- Variable.Impl(Ontology, String, String) - Constructor for class org.biojava.nbio.ontology.Variable.Impl
-
- Variable.Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Variable.Impl
-
- VECTOR_PROPERTY_REF - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
-
- VECTOR_PROPERTY_TYPE - Static variable in class org.forester.io.parsers.phyloxml.PhyloXmlUtil
-
- vectorProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc
-
Vector product (cross product).
- verbose - Static variable in class org.biojava.nbio.structure.domain.pdp.CutDomain
-
- VERBOSE - Static variable in class org.forester.tools.PhylogenyDecorator
-
- version - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain
-
version history:
1.5 - Added more parameters to the command line, including -maxOptRMSD
1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
1.3 - Short CPs are now discarded
1.2 - now supports check AlignmentTools.isSequentialAlignment.
- version - Static variable in class org.biojava.nbio.structure.align.ce.CeMain
-
version history:
1.2 - Added more parameters to the command line, including -maxOptRMSD
1.1 - Additional parameters
1.0 - Initial port from C code
- version - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
-
version history:
1.0 - Initial version
- VERSION - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
-
version history:
1.1 - Added more parameters to the command line
1.0 - Initial version
- version - Static variable in class org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
-
- version - Variable in class org.biojava.nbio.structure.validation.Program
-
- VERSION_1_55 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_57 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_59 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_61 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_63 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_65 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_67 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_69 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_71 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_73 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_75 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_75A - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_75B - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_1_75C - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_2_0_1 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_2_0_2 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_2_0_3 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_2_0_4 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory
-
- VERSION_3_5_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory
-
- VERSION_TAG - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-
- viewer - Static variable in class org.biojava.nbio.structure.gui.BiojavaJmol
-
- viewer - Static variable in class org.biojava.nbio.structure.gui.JmolViewerImpl
-
- VIRUSES - Static variable in class org.forester.ws.seqdb.UniProtTaxonomy
-
- VIRUSES - Static variable in class org.forester.ws.uniprot.UniProtTaxonomy
-
- vp - Static variable in class org.biojava.nbio.core.sequence.io.GenbankSequenceParser
-