Constant Field Values
Contents
org.biojava.*
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org.biojava.nbio.aaproperties.profeat.convertor.Convertor Modifier and Type Constant Field Value public static final char
group1
49
public static final char
group2
50
public static final char
group3
51
public static final char
unknownGroup
48
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org.biojava.nbio.alignment.io.StockholmFileParser Modifier and Type Constant Field Value public static final int
INFINITY
-1
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org.biojava.nbio.alignment.io.StockholmStructure Modifier and Type Constant Field Value public static final java.lang.String
PFAM
"PFAM"
public static final java.lang.String
RFAM
"RFAM"
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org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference Modifier and Type Constant Field Value public static final java.lang.String
EXPERT
"EXPERT"
public static final java.lang.String
HOMSTRAD
"HOMSTRAD"
public static final java.lang.String
INTERPRO
"INTERPRO"
public static final java.lang.String
LOAD
"LOAD"
public static final java.lang.String
MIM
"MIM"
public static final java.lang.String
PDB
"PDB"
public static final java.lang.String
PFAMB
"PFAMB"
public static final java.lang.String
PRINTS
"PRINTS"
public static final java.lang.String
PROSITE
"PROSITE"
public static final java.lang.String
PROSITE_PROFILE
"PROSITE_PROFILE"
public static final java.lang.String
SCOP
"SCOP"
public static final java.lang.String
SMART
"SMART"
public static final java.lang.String
URL
"URL"
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org.biojava.nbio.core.exceptions.Messages Modifier and Type Constant Field Value public static final java.lang.String
ENDOFFILE
"end of file"
public static final java.lang.String
SECTIONKEYNULL
"section key is null"
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org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound> Modifier and Type Constant Field Value protected static final java.lang.String
ACCESSION_TAG
"ACCESSION"
protected static final java.lang.String
AUTHORS_TAG
"AUTHORS"
protected static final java.lang.String
BASE_COUNT_TAG
"BASE"
protected static final java.lang.String
BASE_COUNT_TAG_FULL
"BASE COUNT"
protected static final java.lang.String
COMMENT_TAG
"COMMENT"
protected static final java.lang.String
CONSORTIUM_TAG
"CONSRTM"
protected static final java.lang.String
DEFINITION_TAG
"DEFINITION"
protected static final java.lang.String
END_SEQUENCE_TAG
"//"
protected static final java.lang.String
FEATURE_TAG
"FEATURES"
public static final java.lang.String
GENBANK_FORMAT
"GENBANK"
protected static final java.lang.String
JOURNAL_TAG
"JOURNAL"
protected static final java.lang.String
KEYWORDS_TAG
"KEYWORDS"
protected static final java.lang.String
LOCUS_TAG
"LOCUS"
protected static final java.lang.String
MEDLINE_TAG
"MEDLINE"
protected static final java.lang.String
ORGANISM_TAG
"ORGANISM"
protected static final java.lang.String
PUBMED_TAG
"PUBMED"
protected static final java.lang.String
REFERENCE_TAG
"REFERENCE"
protected static final java.lang.String
REMARK_TAG
"REMARK"
protected static final java.lang.String
SOURCE_TAG
"SOURCE"
protected static final java.lang.String
START_SEQUENCE_TAG
"ORIGIN"
protected static final java.lang.String
TITLE_TAG
"TITLE"
protected static final java.lang.String
VERSION_TAG
"VERSION"
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org.biojava.nbio.core.sequence.io.GenbankWriterHelper Modifier and Type Constant Field Value public static final java.lang.String
CIRCULAR_DNA
"circular"
public static final java.lang.String
LINEAR_DNA
"linear"
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org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound> Modifier and Type Constant Field Value protected static final int
MAX_WIDTH
80
protected static final int
QUALIFIER_INDENT
21
protected static final java.lang.String
QUALIFIER_INDENT_STR
" "
protected static final java.lang.String
QUALIFIER_INDENT_TMP
" %s "
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org.biojava.nbio.core.sequence.io.IUPACParser Modifier and Type Constant Field Value public static final java.lang.String
IUPAC_LOCATION
"org/biojava/nbio/core/sequence/iupac.txt"
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org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound> Modifier and Type Constant Field Value public static final java.lang.String
UNKNOWN_DNA
"UNK"
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org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader<C extends Compound> Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_UNIPROT_BASE_URL
"https://www.uniprot.org"
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org.biojava.nbio.core.sequence.location.InsdcParser<S extends AbstractSequence<C>,C extends Compound> Modifier and Type Constant Field Value protected static final java.lang.String
locationSplitPattern
",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)"
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org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C extends Compound> Modifier and Type Constant Field Value public static final int
BYTES_PER_INT
32
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org.biojava.nbio.core.util.Hashcoder Modifier and Type Constant Field Value public static final int
PRIME
79
public static final int
SEED
9
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org.biojava.nbio.core.util.InputStreamProvider Modifier and Type Constant Field Value public static final java.lang.String
CACHE_PROPERTY
"biojava.cache.files"
public static final int
GZIP_MAGIC
8075
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org.biojava.nbio.core.util.SequenceTools Modifier and Type Constant Field Value protected static final java.lang.String
NUCLEOTIDE_LETTERS
"GCTAUXN"
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org.biojava.nbio.core.util.SoftHashMap<K,V> Modifier and Type Constant Field Value public static final int
DEFAULT_LIMIT
1
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org.biojava.nbio.genome.parsers.cytoband.CytobandParser Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_LOCATION
"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz"
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org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_MAPPING_URL
"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz"
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org.biojava.nbio.genome.parsers.genename.GeneNamesParser Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_GENENAMES_URL
"https://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag"
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org.biojava.nbio.genome.util.ChromosomeMappingTools Modifier and Type Constant Field Value public static final java.lang.String
CDS
"CDS"
public static final java.lang.String
CHROMOSOME
"CHROMOSOME"
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org.biojava.nbio.ontology.Synonym Modifier and Type Constant Field Value public static final int
BROAD_SYNONYM
3
public static final int
EXACT_SYNONYM
1
public static final int
NARROW_SYNONYM
2
public static final int
RELATED_SYNONYM
0
public static final int
UNKNOWN_SCOPE
-1
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org.biojava.nbio.ontology.obo.OboFileHandler Modifier and Type Constant Field Value public static final java.lang.String
ALT_ID
"alt_id"
public static final java.lang.String
BROAD_SYNONYM
"broad_synonym"
public static final java.lang.String
COMMENT
"comment"
public static final java.lang.String
DEF
"def"
public static final java.lang.String
DISJOINT_FROM
"disjoint_from"
public static final java.lang.String
EXACT_SYNONYM
"exact_synonym"
public static final java.lang.String
ID_KEY
"id"
public static final java.lang.String
INTERSECTION_OF
"intersection_of"
public static final java.lang.String
IS_A
"is_a"
public static final java.lang.String
IS_OBSOLETE
"is_obsolete"
public static final java.lang.String
NAME
"name"
public static final java.lang.String
NAMESPACE
"namespace"
public static final java.lang.String
NARROW_SYNONYM
"narrow_synonym"
public static final java.lang.String
ONTOLOGY
"ontologys"
public static final java.lang.String
REL_SYNONYM
"related_synonym"
public static final java.lang.String
RELATIONSHIP
"relationship"
public static final java.lang.String
REPLACED_BY
"replaced_by"
public static final java.lang.String
SUBSET
"subset"
public static final java.lang.String
SYNONYM
"synonym"
public static final java.lang.String
TERM
"Term"
public static final java.lang.String
TYPEDEF
"Typedef"
public static final java.lang.String
XREF_ANALOG
"xref_analog"
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org.biojava.nbio.phosphosite.Dataset Modifier and Type Constant Field Value public static final java.lang.String
ACETYLATION
"https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz"
public static final java.lang.String
DISEASE_ASSOC
"https://www.phosphosite.org/downloads/Disease-associated_sites.gz"
public static final java.lang.String
METHYLATION
"https://www.phosphosite.org/downloads/Methylation_site_dataset.gz"
public static final java.lang.String
PHOSPHORYLATION
"https://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz"
public static final java.lang.String
REGULATORY
"https://www.phosphosite.org/downloads/Regulatory_sites.gz"
public static final java.lang.String
SUMOYLATION
"https://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz"
public static final java.lang.String
UBIQUITINATION
"https://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz"
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org.biojava.nbio.ronn.RonnConstraint Modifier and Type Constant Field Value public static final float
DEFAULT_DISORDER
0.5299999713897705f
public static final float
DEFAULT_ORDER
0.4699999988079071f
public static final float
DEFAULT_RANGE_PROBABILITY_THRESHOLD
0.5f
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org.biojava.nbio.structure.AminoAcid Modifier and Type Constant Field Value public static final java.lang.String
ATOMRECORD
"ATOM"
public static final java.lang.String
SEQRESRECORD
"SEQRES"
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org.biojava.nbio.structure.AtomImpl Modifier and Type Constant Field Value public static final int
BONDS_INITIAL_CAPACITY
3
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org.biojava.nbio.structure.Group Modifier and Type Constant Field Value public static final java.lang.String
SEC_STRUC
"secstruc"
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org.biojava.nbio.structure.PDBHeader Modifier and Type Constant Field Value public static final float
DEFAULT_RESOLUTION
99.0f
public static final float
DEFAULT_RFREE
1.0f
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org.biojava.nbio.structure.PDBStatus Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_PDB_SERVER
"www.rcsb.org"
public static final java.lang.String
PDB_SERVER_PROPERTY
"PDB.SERVER"
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org.biojava.nbio.structure.StructureException Modifier and Type Constant Field Value public static final long
serialVersionUID
62946250941673093L
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org.biojava.nbio.structure.StructureTools Modifier and Type Constant Field Value public static final java.lang.String
C_ATOM_NAME
"C"
public static final java.lang.String
C1_ATOM_NAME
"C1\'"
public static final java.lang.String
C2_ATOM_NAME
"C2\'"
public static final java.lang.String
C3_ATOM_NAME
"C3\'"
public static final java.lang.String
C4_ATOM_NAME
"C4\'"
public static final java.lang.String
CA_ATOM_NAME
"CA"
public static final java.lang.String
CB_ATOM_NAME
"CB"
public static final double
DEFAULT_LIGAND_PROXIMITY_CUTOFF
5.0
public static final java.lang.String
N_ATOM_NAME
"N"
public static final java.lang.String
NUCLEOTIDE_REPRESENTATIVE
"P"
public static final java.lang.String
O_ATOM_NAME
"O"
public static final java.lang.String
O2_ATOM_NAME
"O2\'"
public static final java.lang.String
O3_ATOM_NAME
"O3\'"
public static final java.lang.String
O4_ATOM_NAME
"O4\'"
public static final java.lang.String
O5_ATOM_NAME
"O5\'"
public static final java.lang.String
OP1_ATOM_NAME
"OP1"
public static final java.lang.String
OP2_ATOM_NAME
"OP2"
public static final java.lang.String
P_ATOM_NAME
"P"
public static final double
RATIO_RESIDUES_TO_TOTAL
0.95
public static final char
UNKNOWN_GROUP_LABEL
88
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org.biojava.nbio.structure.URLIdentifier Modifier and Type Constant Field Value public static final java.lang.String
CHAINID_PARAM
"chainid"
public static final java.lang.String
FORMAT_PARAM
"format"
public static final java.lang.String
PDBID_PARAM
"pdbid"
public static final java.lang.String
RESIDUES_PARAM
"residues"
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org.biojava.nbio.structure.align.BioJavaStructureAlignment Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"BioJava_structure"
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org.biojava.nbio.structure.align.ClusterAltAligs Modifier and Type Constant Field Value public static final int
DEFAULT_CLUSTER_CUTOFF
95
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org.biojava.nbio.structure.align.ce.CECalculator Modifier and Type Constant Field Value protected static final boolean
isPrint
false
protected static final int
nIter
1
protected static final double
zThr
-0.1
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org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced Modifier and Type Constant Field Value public static final boolean
GLOBAL_ALIGN1
false
public static final boolean
GLOBAL_ALIGN2
false
protected static final boolean
isPrint
true
protected static final int
nIter
1
protected static final double
zThr
-0.1
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org.biojava.nbio.structure.align.ce.CeCPMain Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jCE Circular Permutation"
public static final java.lang.String
version
"1.5"
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org.biojava.nbio.structure.align.ce.CECPParameters Modifier and Type Constant Field Value public static final int
DEFAULT_MIN_CP_LENGTH
5
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org.biojava.nbio.structure.align.ce.CeMain Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jCE"
public static final java.lang.String
version
"1.2"
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org.biojava.nbio.structure.align.ce.CeParameters Modifier and Type Constant Field Value protected static final double
DEFAULT_GAP_EXTENSION
0.5
protected static final double
DEFAULT_GAP_OPEN
5.0
protected static final double
DEFAULT_oRmsdThr
2.0
protected static final java.lang.String
DEFAULT_SUBSTITUTION_MATRIX
"PRLA000101"
protected static final double
DISTANCE_INCREMENT
0.5
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org.biojava.nbio.structure.align.ce.CeSideChainMain Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jCE-sidechain"
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org.biojava.nbio.structure.align.ce.OptimalCECPMain Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jCE Optimal Circular Permutation"
public static final java.lang.String
version
"1.0"
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org.biojava.nbio.structure.align.client.FarmJobParameters Modifier and Type Constant Field Value public static final int
DEFAULT_BATCH_SIZE
100
public static final int
DEFAULT_JOB_TIME
-1
public static final int
DEFAULT_NR_ALIGNMENTS
-1
public static final int
DEFAULT_NR_THREADS
1
public static final java.lang.String
DEFAULT_PDB_PATH
"/tmp/"
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org.biojava.nbio.structure.align.fatcat.FatCat Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jFatCat"
public static final java.lang.String
VERSION
"1.1"
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org.biojava.nbio.structure.align.fatcat.FatCatFlexible Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jFatCat_flexible"
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org.biojava.nbio.structure.align.fatcat.FatCatRigid Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jFatCat_rigid"
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org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator Modifier and Type Constant Field Value public static final boolean
debug
false
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org.biojava.nbio.structure.align.fatcat.calc.AFPChainer Modifier and Type Constant Field Value public static final boolean
debug
false
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org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer Modifier and Type Constant Field Value public static final boolean
debug
false
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org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor Modifier and Type Constant Field Value public static final boolean
debug
false
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org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner Modifier and Type Constant Field Value public static final boolean
debug
false
public static final boolean
printTimeStamps
false
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org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters Modifier and Type Constant Field Value public static final int
DEFAULT_FRAGLEN
8
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org.biojava.nbio.structure.align.gui.ChooseDirAction Modifier and Type Constant Field Value public static final long
serialVersionUID
0L
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org.biojava.nbio.structure.align.gui.MemoryMonitor Modifier and Type Constant Field Value public static final long
serialVersionUID
56289234782130L
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org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface Modifier and Type Constant Field Value public static final long
serialVersionUID
2387409854370432908L
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org.biojava.nbio.structure.align.gui.MenuCreator Modifier and Type Constant Field Value public static final java.lang.String
ALIGNMENT_PANEL
"Alignment Panel"
public static final java.lang.String
DIST_MATRICES
"Show Distance Matrices"
public static final java.lang.String
DOT_PLOT
"Show Dot Plot"
public static final java.lang.String
EQR_COLOR
"Color By EQR"
public static final java.lang.String
FASTA_FORMAT
"View FASTA Alignment"
public static final java.lang.String
FATCAT_BLOCK
"Color By Alignment Block"
public static final java.lang.String
FATCAT_TEXT
"View as FATCAT result"
public static final java.lang.String
LOAD_ALIGNMENT_XML
"Load Alignment XML"
public static final java.lang.String
LOAD_DB_RESULTS
"Load DB search results"
public static final java.lang.String
MULTIPLE_ALIGN
"New Multiple Alignment"
public static final java.lang.String
PAIRS_ONLY
"View Aligned Pairs"
public static final java.lang.String
PAIRWISE_ALIGN
"New Pairwise Alignment"
public static final java.lang.String
PHYLOGENETIC_TREE
"Phylogenetic Tree"
public static final java.lang.String
PRINT
"Print"
public static final java.lang.String
SAVE_ALIGNMENT_XML
"Save Alignment XML"
public static final java.lang.String
SELECT_EQR
"Select Equivalent Positions"
public static final java.lang.String
SIMILARITY_COLOR
"Color By Similarity"
public static final java.lang.String
TEXT_ONLY
"View Text Only"
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org.biojava.nbio.structure.align.gui.SystemInfo Modifier and Type Constant Field Value public static final java.lang.String
defaultProperties
"browser file.separator java.class.version java.vendor java.vendor.url java.version line.separator os.arch os.name os.version path.separator "
public static final java.lang.String
hexPropertyNames
" file.separator line.separator path.separator "
public static final java.lang.String
urlPropertyNames
" browser.vendor.url java.class.path java.home user.dir user.home user.name "
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org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager Modifier and Type Constant Field Value public static final int
DEFAULT_CHAR_SIZE
12
public static final int
DEFAULT_LINE_LENGTH
70
public static final int
DEFAULT_LINE_SEPARATION
20
public static final int
DEFAULT_RIGHT_SPACER
10
public static final int
DEFAULT_X_SPACE
20
public static final int
DEFAULT_Y_SPACE
40
public static final int
DEFAULT_Y_STEP
60
public static final int
SUMMARY_POS
20
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org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager Modifier and Type Constant Field Value public static final int
DEFAULT_CHAR_SIZE
12
public static final int
DEFAULT_LINE_LENGTH
70
public static final int
DEFAULT_LINE_SEPARATION
20
public static final int
DEFAULT_RIGHT_SPACER
10
public static final int
DEFAULT_X_SPACE
20
public static final int
DEFAULT_Y_SPACE
40
public static final int
SUMMARY_POS
20
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org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol Modifier and Type Constant Field Value protected static final java.lang.String
COMMAND_LINE_HELP
"enter Jmol scripting command..."
protected static final int
DEFAULT_HEIGHT
500
protected static final int
DEFAULT_WIDTH
500
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org.biojava.nbio.structure.align.model.AFPChain Modifier and Type Constant Field Value public static final java.lang.String
UNKNOWN_ALGORITHM
"unknown"
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org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jMultipleMC"
public static final java.lang.String
version
"1.1"
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org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer Modifier and Type Constant Field Value public static final java.lang.String
AVGTM_SCORE
"AvgTM-score"
public static final java.lang.String
CE_SCORE
"CE-score"
public static final java.lang.String
MC_SCORE
"MC-score"
public static final java.lang.String
PROBABILITY
"Probability"
public static final java.lang.String
REF_RMSD
"Ref-RMSD"
public static final java.lang.String
REFTM_SCORE
"RefTM-score"
public static final java.lang.String
RMSD
"RMSD"
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org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"Smith-Waterman superposition"
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org.biojava.nbio.structure.align.util.AtomCache Modifier and Type Constant Field Value public static final java.lang.String
BIOL_ASSEMBLY_IDENTIFIER
"BIO:"
public static final java.lang.String
CHAIN_NR_SYMBOL
":"
public static final java.lang.String
CHAIN_SPLIT_SYMBOL
"."
public static final boolean
DEFAULT_BIOASSEMBLY_STYLE
false
public static final java.lang.String
PDP_DOMAIN_IDENTIFIER
"PDP:"
public static final java.lang.String
UNDERSCORE
"_"
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org.biojava.nbio.structure.align.util.URLConnectionTools Modifier and Type Constant Field Value public static final int
DEFAULT_CONNECTION_TIMEOUT
30000
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org.biojava.nbio.structure.align.util.UserConfiguration Modifier and Type Constant Field Value public static final java.lang.String
MMCIF_FORMAT
"mmCif"
public static final java.lang.String
MMTF_FORMAT
"mmtf"
public static final java.lang.String
PDB_CACHE_DIR
"PDB_CACHE_DIR"
public static final java.lang.String
PDB_DIR
"PDB_DIR"
public static final java.lang.String
PDB_FORMAT
"PDB"
public static final java.lang.String
TMP_DIR
"java.io.tmpdir"
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org.biojava.nbio.structure.align.xml.AFPChainXMLParser Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_ALGORITHM_NAME
"jFatCat_rigid"
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org.biojava.nbio.structure.align.xml.PdbPairXMLConverter Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_METHOD_NAME
"jFatCat_rigid"
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org.biojava.nbio.structure.asa.AsaCalculator Modifier and Type Constant Field Value public static final int
DEFAULT_N_SPHERE_POINTS
1000
public static final int
DEFAULT_NTHREADS
1
public static final double
DEFAULT_PROBE_SIZE
1.4
public static final double
NUC_CARBON_VDW
1.8
public static final double
NUC_NITROGEN_VDW
1.6
public static final double
OXIGEN_VDW
1.4
public static final double
PHOSPHOROUS_VDW
1.9
public static final double
SULFUR_VDW
1.85
public static final double
TETRAHEDRAL_CARBON_VDW
1.87
public static final double
TETRAHEDRAL_NITROGEN_VDW
1.5
public static final double
TRIGONAL_CARBON_VDW
1.76
public static final double
TRIGONAL_NITROGEN_VDW
1.65
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org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters Modifier and Type Constant Field Value public static final double
DEFAULT_MAX_PROPELLER
60.0
public static final double
DEFAULT_MAX_SHEAR
5.0
public static final double
DEFAULT_MAX_STAGGER
2.0
public static final double
DEFAULT_MAX_STRETCH
5.0
-
org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters Modifier and Type Constant Field Value public static final double
DEFAULT_MAX_PROPELLER
60.0
public static final double
DEFAULT_MAX_STAGGER
2.0
-
org.biojava.nbio.structure.cath.CathDomain Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
-
org.biojava.nbio.structure.cath.CathFactory Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_VERSION
"4_2_0"
public static final java.lang.String
LATEST_VERSION
"4_2_0"
public static final java.lang.String
VERSION_3_5_0
"3_5_0"
public static final java.lang.String
VERSION_4_0_0
"4_0_0"
public static final java.lang.String
VERSION_4_1_0
"4_1_0"
public static final java.lang.String
VERSION_4_2_0
"4_2_0"
-
org.biojava.nbio.structure.cath.CathFragment Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
-
org.biojava.nbio.structure.cath.CathInstallation Modifier and Type Constant Field Value public static final java.lang.String
CATH_DOWNLOAD_ALL_RELEASES_DIR
"all-releases"
public static final java.lang.String
CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR
"cath-classification-data"
public static final java.lang.String
CATH_DOWNLOAD_URL
"http://download.cathdb.info/cath/releases/"
public static final java.lang.String
DEFAULT_VERSION
"4_2_0"
public static final java.lang.String
domainDescriptionFileName
"cath-domain-description-file-v%s.txt"
public static final java.lang.String
domainListFileName
"cath-domain-list-v%s.txt"
public static final java.lang.String
domallFileName
"cath-domain-boundaries-v%s.txt"
public static final java.lang.String
nodeListFileName
"cath-names-v%s.txt"
-
org.biojava.nbio.structure.cath.CathNode Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
-
org.biojava.nbio.structure.cath.CathSegment Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
-
org.biojava.nbio.structure.contact.InterfaceFinder Modifier and Type Constant Field Value public static final double
DEFAULT_CONTACT_CUTOFF
6.0
-
org.biojava.nbio.structure.contact.StructureInterfaceList Modifier and Type Constant Field Value public static final int
DEFAULT_ASA_SPHERE_POINTS
3000
public static final double
DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF
0.2
public static final int
DEFAULT_MIN_COFACTOR_SIZE
40
public static final double
DEFAULT_MINIMUM_INTERFACE_AREA
35.0
-
org.biojava.nbio.structure.domain.PDBDomainProvider Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_PDB_API_URL
"http://www.rcsb.org/pdb/rest/"
public static final java.lang.String
DEFAULT_PDB_HOST
"http://www.rcsb.org"
-
org.biojava.nbio.structure.domain.RemotePDPProvider Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_SERVER
"http://source.rcsb.org/jfatcatserver/domains/"
-
org.biojava.nbio.structure.domain.pdp.PDPParameters Modifier and Type Constant Field Value public static final float
CUT_OFF_VALUE
0.5f
public static final float
CUT_OFF_VALUE1
0.28999999165534973f
public static final float
CUT_OFF_VALUE1M
0.20999999344348907f
public static final float
CUT_OFF_VALUE1S
0.1899999976158142f
public static final float
CUT_OFF_VALUE2
0.4399999976158142f
public static final float
DBL
0.05000000074505806f
public static final int
ENDS
12
public static final int
ENDSEND
9
public static final int
MAX_CUTS
80
public static final int
MAXCONT
900
public static final int
MAXDOM
30
public static final int
MAXLEN
3200
public static final int
MAXSIZE
350
public static final int
MIN_DOMAIN_LENGTH
35
public static final float
RG
0.0f
public static final float
RG1
1.0f
public static final float
TD
25.0f
public static final float
TD1
40.0f
-
org.biojava.nbio.structure.ecod.EcodFactory Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_VERSION
"latest"
-
org.biojava.nbio.structure.ecod.EcodInstallation Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_VERSION
"latest"
public static final java.lang.String
DOMAINS_PATH
"/ecod/distributions/"
public static final java.lang.String
ECOD_URL
"http://prodata.swmed.edu"
-
org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser Modifier and Type Constant Field Value public static final java.lang.String
F_UNCLASSIFIED
"F_UNCLASSIFIED"
public static final java.lang.String
IS_DOMAIN_ASSEMBLY
"IS_DOMAIN_ASSEMBLY"
public static final java.lang.String
IS_REPRESENTATIVE
"MANUAL_REP"
public static final java.lang.String
NOT_DOMAIN_ASSEMBLY
"NOT_DOMAIN_ASSEMBLY"
public static final java.lang.String
NOT_REPRESENTATIVE
"AUTO_NONREP"
-
org.biojava.nbio.structure.gui.BiojavaJmol Modifier and Type Constant Field Value public static final java.lang.String
adapter
"org.jmol.api.JmolAdapter"
public static final java.lang.String
smartAdapter
"org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final java.lang.String
viewer
"org.jmol.api.JmolSimpleViewer"
-
org.biojava.nbio.structure.gui.JmolViewerImpl Modifier and Type Constant Field Value public static final java.lang.String
adapter
"org.jmol.api.JmolAdapter"
public static final java.lang.String
smartAdapter
"org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final java.lang.String
viewer
"org.jmol.api.JmolSimpleViewer"
-
org.biojava.nbio.structure.gui.ScaleableMatrixPanel Modifier and Type Constant Field Value protected static final int
SLIDER_STEPS
8
-
org.biojava.nbio.structure.gui.SequenceDisplay Modifier and Type Constant Field Value public static final int
MAX_SCALE
10
-
org.biojava.nbio.structure.gui.util.AlignedPosition Modifier and Type Constant Field Value public static final int
EQUIVALENT
1
public static final int
NOT_ALIGNED
0
-
org.biojava.nbio.structure.gui.util.SequenceScalePanel Modifier and Type Constant Field Value public static final int
DEFAULT_X_RIGHT_BORDER
40
public static final int
DEFAULT_X_START
10
public static final int
DEFAULT_Y_BOTTOM
16
public static final int
DEFAULT_Y_HEIGHT
8
public static final int
DEFAULT_Y_START
0
public static final int
DEFAULT_Y_STEP
10
public static final int
LINE_HEIGHT
10
public static final int
MINIMUM_HEIGHT
20
public static final int
SIZE
20
-
org.biojava.nbio.structure.gui.util.color.GradientMapper Modifier and Type Constant Field Value public static final int
BLACK_WHITE_GRADIENT
1
public static final int
RAINBOW_GRADIENT
4
public static final int
RAINBOW_INTENSITY_GRADIENT
5
public static final int
RED_BLUE_GRADIENT
3
public static final int
WHITE_BLACK_GRADIENT
2
-
org.biojava.nbio.structure.gui.util.color.HSVColorSpace Modifier and Type Constant Field Value public static final int
CS_HSV
1007
-
org.biojava.nbio.structure.io.EntityFinder Modifier and Type Constant Field Value public static final double
GAP_COVERAGE_THRESHOLD
0.3
public static final double
IDENTITY_THRESHOLD
0.99999
public static final double
RATIO_GAPS_FOR_MISMATCH
0.5
-
org.biojava.nbio.structure.io.FileParsingParameters Modifier and Type Constant Field Value public static final int
ATOM_CA_THRESHOLD
500000
public static final int
MAX_ATOMS
2147483647
-
org.biojava.nbio.structure.io.LocalPDBDirectory Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_PDB_FILE_SERVER
"http://ftp.wwpdb.org"
public static final long
MIN_PDB_FILE_SIZE
40L
public static final java.lang.String
PDB_FILE_SERVER_PROPERTY
"PDB.FILE.SERVER"
-
org.biojava.nbio.structure.io.PDBParseException Modifier and Type Constant Field Value public static final long
serialVersionUID
219047230178423923L
-
org.biojava.nbio.structure.io.mmcif.AllChemCompProvider Modifier and Type Constant Field Value public static final java.lang.String
COMPONENTS_FILE_LOCATION
"pub/pdb/data/monomers/components.cif.gz"
-
org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider Modifier and Type Constant Field Value public static final java.lang.String
CHEM_COMP_CACHE_DIRECTORY
"chemcomp"
public static final java.lang.String
DEFAULT_SERVER_URL
"http://files.rcsb.org/ligands/download/"
-
org.biojava.nbio.structure.io.mmcif.MMCIFFileTools Modifier and Type Constant Field Value public static final java.lang.String
MMCIF_DEFAULT_VALUE
"."
public static final java.lang.String
MMCIF_MISSING_VALUE
"?"
-
org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser Modifier and Type Constant Field Value public static final java.lang.String
COMMENT_CHAR
"#"
public static final java.lang.String
FIELD_LINE
"_"
public static final java.lang.String
LOOP_START
"loop_"
public static final java.lang.String
MMCIF_TOP_HEADER
"data_"
public static final java.lang.String
STRING_LIMIT
";"
-
org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder Modifier and Type Constant Field Value public static final java.lang.String
COMPOSED_OPERATOR_SEPARATOR
"x"
public static final java.lang.String
SYM_CHAIN_ID_SEPARATOR
"_"
-
org.biojava.nbio.structure.rcsb.PdbIdLists Modifier and Type Constant Field Value public static final java.lang.String
SERVICELOCATION
"http://www.rcsb.org/pdb/rest/search"
-
org.biojava.nbio.structure.rcsb.RCSBUpdates Modifier and Type Constant Field Value public static final java.lang.String
baseURL
"http://ftp.rcsb.org/pub/pdb/data/status/latest/"
-
org.biojava.nbio.structure.scop.RemoteScopInstallation Modifier and Type Constant Field Value public static final java.lang.String
DEFAULT_SERVER
"http://source.rcsb.org/jfatcatserver/domains/"
-
org.biojava.nbio.structure.scop.ScopFactory Modifier and Type Constant Field Value public static final java.lang.String
LATEST_VERSION
"2.07"
public static final java.lang.String
VERSION_1_55
"1.55"
public static final java.lang.String
VERSION_1_57
"1.57"
public static final java.lang.String
VERSION_1_59
"1.59"
public static final java.lang.String
VERSION_1_61
"1.61"
public static final java.lang.String
VERSION_1_63
"1.63"
public static final java.lang.String
VERSION_1_65
"1.65"
public static final java.lang.String
VERSION_1_67
"1.67"
public static final java.lang.String
VERSION_1_69
"1.69"
public static final java.lang.String
VERSION_1_71
"1.71"
public static final java.lang.String
VERSION_1_73
"1.73"
public static final java.lang.String
VERSION_1_75
"1.75"
public static final java.lang.String
VERSION_1_75A
"2.01"
public static final java.lang.String
VERSION_1_75B
"2.02"
public static final java.lang.String
VERSION_1_75C
"2.03"
public static final java.lang.String
VERSION_2_0_1
"2.01"
public static final java.lang.String
VERSION_2_0_2
"2.02"
public static final java.lang.String
VERSION_2_0_3
"2.03"
public static final java.lang.String
VERSION_2_0_4
"2.04"
public static final java.lang.String
VERSION_2_0_5
"2.05"
public static final java.lang.String
VERSION_2_0_6
"2.06"
public static final java.lang.String
VERSION_2_0_7
"2.07"
-
org.biojava.nbio.structure.scop.ScopInstallation Modifier and Type Constant Field Value public static final java.lang.String
claFileName
"dir.cla.scop.txt_"
public static final java.lang.String
comFileName
"dir.com.scop.txt_"
public static final java.lang.String
DEFAULT_VERSION
"1.75"
public static final java.lang.String
desFileName
"dir.des.scop.txt_"
public static final java.lang.String
hieFileName
"dir.hie.scop.txt_"
public static final java.lang.String
SCOP_DOWNLOAD
"http://scop.berkeley.edu/downloads/parse/"
public static final java.lang.String
SCOP_DOWNLOAD_ALTERNATE
"http://scop.berkeley.edu/downloads/parse/"
-
org.biojava.nbio.structure.secstruc.SecStrucCalc Modifier and Type Constant Field Value public static final double
CA_MIN_DIST
9.0
public static final double
HBONDHIGHENERGY
-500.0
public static final int
HBONDLOWENERGY
-9900
public static final double
MAX_PEPTIDE_BOND_LENGTH
2.5
public static final double
MINDIST
0.5
public static final double
Q
-27888.0
-
org.biojava.nbio.structure.secstruc.SecStrucInfo Modifier and Type Constant Field Value public static final java.lang.String
BIOJAVA_ASSIGNMENT
"BIOJAVA_ASSIGNMENT"
public static final java.lang.String
DSSP_ASSIGNMENT
"DSSP_ASSIGNMENT"
public static final java.lang.String
PDB_AUTHOR_ASSIGNMENT
"PDB_AUTHOR_ASSIGNMENT"
-
org.biojava.nbio.structure.symmetry.internal.CeSymm Modifier and Type Constant Field Value public static final java.lang.String
algorithmName
"jCE-symm"
public static final java.lang.String
version
"2.2"
-
org.biojava.nbio.structure.symmetry.internal.CESymmParameters Modifier and Type Constant Field Value public static final double
DEFAULT_SYMMETRY_THRESHOLD
0.4
-
org.biojava.nbio.structure.xtal.CrystalBuilder Modifier and Type Constant Field Value public static final int
DEF_NUM_CELLS
20
public static final double
DEFAULT_INTERFACE_DISTANCE_CUTOFF
5.5
public static final java.lang.String
NCS_CHAINID_SUFFIX_CHAR
"n"
-
org.biojava.nbio.structure.xtal.CrystalCell Modifier and Type Constant Field Value public static final double
MIN_VALID_CELL_SIZE
10.0
-
org.biojava.nbio.structure.xtal.SpaceGroup Modifier and Type Constant Field Value protected static final double
DELTA
1.0E-7
-
org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
-
org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties Modifier and Type Constant Field Value public static final long
serialVersionUID
1L
-
org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService Modifier and Type Constant Field Value public static final long
WAIT_INCREMENT
3000L
-
org.biojava.nbio.ws.hmmer.RemoteHmmerScan Modifier and Type Constant Field Value public static final java.lang.String
HMMER_SERVICE
"https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan"
org.forester.*
-
org.forester.application.gsdi Modifier and Type Constant Field Value public static final boolean
REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE
true
-
org.forester.application.surfacing Modifier and Type Constant Field Value public static final java.lang.String
ALL_PFAMS_ENCOUNTERED_SUFFIX
"_all_encountered_pfams"
public static final java.lang.String
ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
"_all_encountered_pfams_with_go_annotation"
public static final java.lang.String
ALL_PFAMS_GAINED_AS_DC_SUFFIX
"_all_pfams_gained_as_dc"
public static final java.lang.String
ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
"_all_pfams_gained_as_domains"
public static final java.lang.String
ALL_PFAMS_LOST_AS_DC_SUFFIX
"_all_pfams_lost_as_dc"
public static final java.lang.String
ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
"_all_pfams_lost_as_domains"
public static final java.lang.String
BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
"PER_NODE_EVENTS"
public static final java.lang.String
BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
"PER_SUBTREE_EVENTS"
public static final java.lang.String
BDC_PRESENT_NEXUS
"_dc.nex"
public static final java.lang.String
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
"_dc_dollo.xml"
public static final java.lang.String
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
"_dc_fitch.xml"
public static final java.lang.String
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED
"_dc_MAPPED_secondary_features_fitch.xml"
public static final java.lang.String
D_PROMISCUITY_FILE_SUFFIX
"_domain_promiscuities"
public static final java.lang.String
DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
".dcc"
public static final java.lang.String
DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION
"dcc"
public static final java.lang.String
DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
"graph_analysis_out"
public static final java.lang.String
DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
"_dc.dot"
public static final java.lang.String
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
"_d_dollo.xml"
public static final java.lang.String
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
"_d_fitch.xml"
public static final java.lang.String
DOMAINS_PRESENT_NEXUS
"_dom.nex"
public static final java.lang.String
ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
"_encountered_pfams_summary"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX
"_indep_dc_gains_fitch_counts_MAPPED.txt"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX
"_indep_dc_gains_fitch_counts.txt"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX
"_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX
"_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX
"_indep_dc_gains_fitch_lists_for_go_mapping.txt"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX
"_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX
"_indep_dc_gains_fitch_lists_MAPPED.txt"
public static final java.lang.String
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX
"_indep_dc_gains_fitch_lists.txt"
public static final int
MAX_ALLOWED_OVERLAP_DEFAULT
-1
public static final java.lang.String
NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
"_dc.nex"
public static final java.lang.String
NEXUS_EXTERNAL_DOMAINS
"_dom.nex"
public static final java.lang.String
NEXUS_SECONDARY_FEATURES
"_secondary_features.nex"
public static final java.lang.String
PAIRWISE_DOMAIN_COMPARISONS_PREFIX
"pwc_"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
"_dollo_goid_d"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_GAINS_D
"_dollo_gains_d"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
"_dollo_gains_d.html"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
"_dollo_gains_secondary_features"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_LOSSES_D
"_dollo_losses_d"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
"_dollo_losses_d.html"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
"_dollo_losses_secondary_features"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_PRESENT_D
"_dollo_present_d"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
"_dollo_present_d.html"
public static final java.lang.String
PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
"_dollo_present_secondary_features"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
"_fitch_goid_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_GAINS_BC
"_fitch_gains_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
"_fitch_gains_dc.html"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_LOSSES_BC
"_fitch_losses_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
"_fitch_losses_dc.html"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_PRESENT_BC
"_fitch_present_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
"_fitch_present_dc.dot"
public static final java.lang.String
PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
"_fitch_present_dc.html"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
"_dollo_glc_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
"_dollo_glc_d"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
"_dollo_glc_secondary_features"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
"_fitch_glc_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
"_fitch_glc_d"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
"_dollo_gl_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
"_dollo_gl_d"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
"_dollo_gl_secondary_features"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
"_fitch_gl_dc"
public static final java.lang.String
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
"_fitch_gl_d"
public static final java.lang.String
PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX
"_plus_minus_go_ids_all.txt"
public static final double
PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT
1.0
public static final int
PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT
0
public static final java.lang.String
PLUS_MINUS_ANALYSIS_OPTION
"plus_minus"
public static final java.lang.String
PLUS_MINUS_DC_SUFFIX_HTML
"_plus_minus_dc.html"
public static final java.lang.String
PLUS_MINUS_DOM_SUFFIX
"_plus_minus_dom.txt"
public static final java.lang.String
PLUS_MINUS_DOM_SUFFIX_HTML
"_plus_minus_dom.html"
public static final java.lang.String
PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX
"_plus_minus_go_ids_passing.txt"
public static final java.lang.String
PRG_NAME
"surfacing"
public static final java.lang.String
SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
"_secondary_features_dollo.xml"
public static final java.lang.String
SEQ_EXTRACT_SUFFIX
".prot"
public static final boolean
VERBOSE
false
-
org.forester.applications.aaa Modifier and Type Constant Field Value public static final int
MIN_LENGTH
85
-
org.forester.applications.get_shared_chars Modifier and Type Constant Field Value public static final boolean
DEBUG
true
-
org.forester.archaeopteryx.ArchaeopteryxA Modifier and Type Constant Field Value public static final java.lang.String
NAME
"ArchaeopteryxA"
-
org.forester.archaeopteryx.Constants Modifier and Type Constant Field Value public static final boolean
__RELEASE
false
public static final boolean
__SNAPSHOT_RELEASE
false
public static final boolean
__SYNTH_LF
false
public static final boolean
ALLOW_DDBJ_BLAST
false
public static final boolean
NH_PARSING_IGNORE_QUOTES_DEFAULT
false
public static final java.lang.String
PRG_NAME
"Archaeopteryx"
-
org.forester.archaeopteryx.FontChooser Modifier and Type Constant Field Value public static final long
serialVersionUID
62256323L
-
org.forester.archaeopteryx.TreeColorSet Modifier and Type Constant Field Value public static final java.lang.String
ANNOTATION
"Annotation"
public static final java.lang.String
BACKGROUND
"Background"
public static final java.lang.String
BACKGROUND_GRADIENT_BOTTOM
"Background Gradient Bottom"
public static final java.lang.String
BINARY_DOMAIN_COMBINATIONS
"Binary Domain Combinations"
public static final java.lang.String
BRANCH
"Branch"
public static final java.lang.String
BRANCH_LENGTH
"Branch Length"
public static final java.lang.String
COLLAPSED
"Collapsed"
public static final java.lang.String
CONFIDENCE
"Confidence"
public static final java.lang.String
DOMAIN_BASE
"Domain Base"
public static final java.lang.String
DOMAIN_LABEL
"Domain Label"
public static final java.lang.String
DUPLICATION
"Duplication"
public static final java.lang.String
DUPLICATION_OR_SPECATION
"Duplication or Specation"
public static final java.lang.String
MATCHING_NODES_A
"Matching A"
public static final java.lang.String
MATCHING_NODES_A_AND_B
"Matching A and B"
public static final java.lang.String
MATCHING_NODES_B
"Matching B"
public static final java.lang.String
NODE_BOX
"Node Box"
public static final java.lang.String
OVERVIEW
"Overview"
public static final java.lang.String
SEQUENCE
"Sequence"
public static final java.lang.String
SPECIATION
"Speciation"
public static final java.lang.String
TAXONOMY
"Taxonomy"
-
org.forester.archaeopteryx.TreePanel Modifier and Type Constant Field Value public static final boolean
SPECIAL_DOMAIN_COLORING
true
-
org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence Modifier and Type Constant Field Value public static final int
DEFAULT_WIDTH
400
-
org.forester.archaeopteryx.phylogeny.data.RenderableVector Modifier and Type Constant Field Value public static final int
VECTOR_DEFAULT_WIDTH
120
-
org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions Modifier and Type Constant Field Value public static final long
RANDOM_NUMBER_SEED_DEFAULT
42L
-
org.forester.archaeopteryx.tools.PhylogeneticInferrer Modifier and Type Constant Field Value public static final java.lang.String
MSA_FILE_SUFFIX
".aln"
public static final java.lang.String
PWD_FILE_SUFFIX
".pwd"
-
org.forester.archaeopteryx.tools.SequenceDataRetriver Modifier and Type Constant Field Value public static final boolean
DEBUG
false
-
org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient Modifier and Type Constant Field Value public static final java.lang.String
QUERY_PLACEHOLDER
"__query__"
-
org.forester.archaeopteryx.webservices.WebserviceUtil Modifier and Type Constant Field Value public static final java.lang.String
PFAM_INST
"pfam"
public static final java.lang.String
PFAM_NAME
"Pfam"
public static final java.lang.String
PFAM_SERVER
"http://pfam.xfam.org"
public static final java.lang.String
TOL_NAME
"Tree of Life (ToL)"
public static final java.lang.String
TOL_URL_BASE
"http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id="
public static final java.lang.String
TOL_WEBSERVER
"http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=__query__"
public static final java.lang.String
TREE_BASE_DESC
"This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment."
public static final java.lang.String
TREE_BASE_INST
"treebase"
public static final java.lang.String
TREE_BASE_NAME
"TreeBASE"
public static final java.lang.String
TREE_FAM_INST
"tree_fam"
public static final java.lang.String
TREE_FAM_NAME
"TreeFam"
public static final java.lang.String
TREE_FAM_URL_BASE
"http://www.treefam.org/family/TF"
public static final java.lang.String
TREEBASE_PHYLOWS_STUDY_URL_BASE
"http://purl.org/phylo/treebase/phylows/study/TB2:S"
public static final java.lang.String
TREEBASE_PHYLOWS_TREE_URL_BASE
"http://purl.org/phylo/treebase/phylows/tree/TB2:Tr"
-
org.forester.evoinference.distance.PairwiseDistanceCalculator Modifier and Type Constant Field Value public static final double
DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA
10.0
-
org.forester.evoinference.distance.Sarray Modifier and Type Constant Field Value public static final int
FACTOR
1000000
-
org.forester.evoinference.distance.Sset Modifier and Type Constant Field Value public static final int
FACTOR
1000000
-
org.forester.go.GoNameSpace Modifier and Type Constant Field Value public static final java.lang.String
BIOLOGICAL_PROCESS_STR
"biological_process"
public static final java.lang.String
CELLULAR_COMPONENT_STR
"cellular_component"
public static final java.lang.String
MOLECULAR_FUNCTION_STR
"molecular_function"
public static final java.lang.String
UNASSIGNED_STR
"unassigned"
-
org.forester.go.GoRelationship Modifier and Type Constant Field Value public static final java.lang.String
HAS_PART_STR
"has_part"
public static final java.lang.String
NEGATIVELY_REGULATES_STR
"negatively_regulates"
public static final java.lang.String
OCCURS_IN_STR
"occurs_in"
public static final java.lang.String
PART_OF_STR
"part_of"
public static final java.lang.String
POSITIVELY_REGULATES_STR
"positively_regulates"
public static final java.lang.String
REGULATES_STR
"regulates"
-
org.forester.go.GoSubset Modifier and Type Constant Field Value public static final java.lang.String
GOSLIM_ASPERGILLUS_STR
"goslim_aspergillus"
public static final java.lang.String
GOSLIM_CANDIDA_STR
"goslim_candida"
public static final java.lang.String
GOSLIM_GENERIC_STR
"goslim_generic"
public static final java.lang.String
GOSLIM_GOA_STR
"goslim_goa"
public static final java.lang.String
GOSLIM_PIR_STR
"goslim_pir"
public static final java.lang.String
GOSLIM_PLANT_STR
"goslim_plant"
public static final java.lang.String
GOSLIM_POMBE_STR
"goslim_pombe"
public static final java.lang.String
GOSLIM_YEAST_STR
"goslim_yeast"
public static final java.lang.String
GOSUBSET_PROK_STR
"gosubset_prok"
-
org.forester.go.GoXRef Modifier and Type Constant Field Value public static final java.lang.String
ARACYC_STR
"AraCyc"
public static final java.lang.String
CORUM_STR
"CORUM"
public static final java.lang.String
EC_STR
"EC"
public static final java.lang.String
GOC_STR
"GOC"
public static final java.lang.String
IMG_STR
"IMG"
public static final java.lang.String
KEGG_STR
"KEGG"
public static final java.lang.String
META_CYC_STR
"MetaCyc"
public static final java.lang.String
NIF_SUBCELLULAR_STR
"NIF_Subcellular"
public static final java.lang.String
PMID_STR
"PMID"
public static final java.lang.String
PO_STR
"PO"
public static final java.lang.String
REACTOME_STR
"Reactome"
public static final java.lang.String
RESID_STR
"RESID"
public static final java.lang.String
RHEA_STR
"RHEA"
public static final java.lang.String
SABIO_RK_STR
"SABIO-RK"
public static final java.lang.String
TC_STR
"TC"
public static final java.lang.String
UM_BBD_ENZYME_ID_STR
"UM-BBD_enzymeID"
public static final java.lang.String
UM_BBD_PATHWAY_ID_STR
"UM-BBD_pathwayID"
public static final java.lang.String
UM_BBD_REACTIONID_STR
"UM-BBD_reactionID"
public static final java.lang.String
UNIPATHWAY_STR
"UniPathway"
public static final java.lang.String
WIKIPEDIA_STR
"Wikipedia"
public static final java.lang.String
XX_STR
"XX"
-
org.forester.io.parsers.nexus.NexusConstants Modifier and Type Constant Field Value public static final java.lang.String
BEGIN_CHARACTERS
"Begin Characters;"
public static final java.lang.String
BEGIN_DATA
"Begin Data;"
public static final java.lang.String
BEGIN_TAXA
"Begin Taxa;"
public static final java.lang.String
BEGIN_TREES
"Begin Trees;"
public static final java.lang.String
CHARSTATELABELS
"CharStateLabels"
public static final java.lang.String
DATATYPE
"DataType"
public static final java.lang.String
DIMENSIONS
"Dimensions"
public static final java.lang.String
END
"End;"
public static final java.lang.String
FORMAT
"Format"
public static final java.lang.String
MATRIX
"Matrix"
public static final java.lang.String
NCHAR
"NChar"
public static final java.lang.String
NEXUS
"#NEXUS"
public static final java.lang.String
NTAX
"NTax"
public static final java.lang.String
STANDARD
"Standard"
public static final java.lang.String
SYMBOLS
"Symbols"
public static final java.lang.String
TAXLABELS
"TaxLabels"
public static final java.lang.String
TRANSLATE
"Translate"
public static final java.lang.String
TREE
"Tree"
public static final java.lang.String
UTREE
"UTREE"
-
org.forester.io.parsers.nhx.NHXParser Modifier and Type Constant Field Value public static final boolean
REPLACE_UNDERSCORES_DEFAULT
false
-
org.forester.io.parsers.nhx.NHXtags Modifier and Type Constant Field Value public static final java.lang.String
DOMAIN_STRUCTURE
"DS="
public static final java.lang.String
GENE_NAME
"GN="
public static final java.lang.String
IS_DUPLICATION
"D="
public static final java.lang.String
SEQUENCE_ACCESSION
"AC="
public static final java.lang.String
SPECIES_NAME
"S="
public static final java.lang.String
SUPPORT
"B="
public static final java.lang.String
TAXONOMY_ID
"T="
-
org.forester.io.parsers.phyloxml.PhyloXmlMapping Modifier and Type Constant Field Value public static final java.lang.String
ACCESSION
"accession"
public static final java.lang.String
ACCESSION_COMMENT_ATTR
"comment"
public static final java.lang.String
ACCESSION_SOURCE_ATTR
"source"
public static final java.lang.String
ANNOTATION
"annotation"
public static final java.lang.String
ANNOTATION_DESC
"desc"
public static final java.lang.String
ANNOTATION_EVIDENCE_ATTR
"evidence"
public static final java.lang.String
ANNOTATION_REF_ATTR
"ref"
public static final java.lang.String
ANNOTATION_SOURCE_ATTR
"source"
public static final java.lang.String
ANNOTATION_TYPE_ATTR
"type"
public static final java.lang.String
BINARY_CHARACTER
"bc"
public static final java.lang.String
BINARY_CHARACTERS
"binary_characters"
public static final java.lang.String
BINARY_CHARACTERS_GAINED
"gained"
public static final java.lang.String
BINARY_CHARACTERS_GAINED_COUNT_ATTR
"gained_count"
public static final java.lang.String
BINARY_CHARACTERS_LOST
"lost"
public static final java.lang.String
BINARY_CHARACTERS_LOST_COUNT_ATTR
"lost_count"
public static final java.lang.String
BINARY_CHARACTERS_PRESENT
"present"
public static final java.lang.String
BINARY_CHARACTERS_PRESENT_COUNT_ATTR
"present_count"
public static final java.lang.String
BINARY_CHARACTERS_TYPE_ATTR
"type"
public static final java.lang.String
BRANCH_LENGTH
"branch_length"
public static final java.lang.String
CLADE
"clade"
public static final java.lang.String
CLADE_DATE
"date"
public static final java.lang.String
CLADE_DATE_DESC
"desc"
public static final java.lang.String
CLADE_DATE_MAX
"maximum"
public static final java.lang.String
CLADE_DATE_MIN
"minimum"
public static final java.lang.String
CLADE_DATE_UNIT
"unit"
public static final java.lang.String
CLADE_DATE_VALUE
"value"
public static final java.lang.String
COLOR
"color"
public static final java.lang.String
COLOR_BLUE
"blue"
public static final java.lang.String
COLOR_GREEN
"green"
public static final java.lang.String
COLOR_RED
"red"
public static final java.lang.String
CONFIDENCE
"confidence"
public static final java.lang.String
CONFIDENCE_SD_ATTR
"stddev"
public static final java.lang.String
CONFIDENCE_TYPE_ATTR
"type"
public static final java.lang.String
DISTRIBUTION
"distribution"
public static final java.lang.String
DISTRIBUTION_DESC
"desc"
public static final java.lang.String
EVENT_DUPLICATIONS
"duplications"
public static final java.lang.String
EVENT_LOSSES
"losses"
public static final java.lang.String
EVENT_SPECIATIONS
"speciations"
public static final java.lang.String
EVENT_TYPE
"type"
public static final java.lang.String
EVENTS
"events"
public static final java.lang.String
ID_REF
"id_ref"
public static final java.lang.String
IDENTIFIER
"id"
public static final java.lang.String
IDENTIFIER_PROVIDER_ATTR
"provider"
public static final java.lang.String
NODE_COLLAPSE
"collapse"
public static final java.lang.String
NODE_NAME
"name"
public static final java.lang.String
PHYLOGENY
"phylogeny"
public static final java.lang.String
PHYLOGENY_BRANCHLENGTH_UNIT_ATTR
"branch_length_unit"
public static final java.lang.String
PHYLOGENY_DESCRIPTION
"description"
public static final java.lang.String
PHYLOGENY_IS_REROOTABLE_ATTR
"rerootable"
public static final java.lang.String
PHYLOGENY_IS_ROOTED_ATTR
"rooted"
public static final java.lang.String
PHYLOGENY_NAME
"name"
public static final java.lang.String
PHYLOGENY_TYPE_ATTR
"type"
public static final java.lang.String
POINT
"point"
public static final java.lang.String
POINT_ALTITUDE
"alt"
public static final java.lang.String
POINT_ALTITUDE_UNIT_ATTR
"alt_unit"
public static final java.lang.String
POINT_GEODETIC_DATUM
"geodetic_datum"
public static final java.lang.String
POINT_LATITUDE
"lat"
public static final java.lang.String
POINT_LONGITUDE
"long"
public static final java.lang.String
POLYGON
"polygon"
public static final java.lang.String
PROPERTY
"property"
public static final java.lang.String
PROPERTY_APPLIES_TO
"applies_to"
public static final java.lang.String
PROPERTY_DATATYPE
"datatype"
public static final java.lang.String
PROPERTY_REF
"ref"
public static final java.lang.String
PROPERTY_UNIT
"unit"
public static final java.lang.String
REFERENCE
"reference"
public static final java.lang.String
REFERENCE_DESC
"desc"
public static final java.lang.String
REFERENCE_DOI_ATTR
"doi"
public static final java.lang.String
SEQUENCE
"sequence"
public static final java.lang.String
SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN
"domain"
public static final java.lang.String
SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH
"length"
public static final java.lang.String
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE
"confidence"
public static final java.lang.String
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM
"from"
public static final java.lang.String
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO
"to"
public static final java.lang.String
SEQUENCE_DOMAIN_ARCHITECURE
"domain_architecture"
public static final java.lang.String
SEQUENCE_GENE_NAME
"gene_name"
public static final java.lang.String
SEQUENCE_LOCATION
"location"
public static final java.lang.String
SEQUENCE_MOL_SEQ
"mol_seq"
public static final java.lang.String
SEQUENCE_MOL_SEQ_ALIGNED_ATTR
"is_aligned"
public static final java.lang.String
SEQUENCE_NAME
"name"
public static final java.lang.String
SEQUENCE_RELATION
"sequence_relation"
public static final java.lang.String
SEQUENCE_RELATION_DISTANCE
"distance"
public static final java.lang.String
SEQUENCE_RELATION_ID_REF0
"id_ref_0"
public static final java.lang.String
SEQUENCE_RELATION_ID_REF1
"id_ref_1"
public static final java.lang.String
SEQUENCE_RELATION_TYPE
"type"
public static final java.lang.String
SEQUENCE_SOURCE_ID
"id_source"
public static final java.lang.String
SEQUENCE_SYMBOL
"symbol"
public static final java.lang.String
SEQUENCE_TYPE
"type"
public static final java.lang.String
SEQUENCE_X_REFS
"cross_references"
public static final java.lang.String
TAXONOMY
"taxonomy"
public static final java.lang.String
TAXONOMY_AUTHORITY
"authority"
public static final java.lang.String
TAXONOMY_CODE
"code"
public static final java.lang.String
TAXONOMY_COMMON_NAME
"common_name"
public static final java.lang.String
TAXONOMY_RANK
"rank"
public static final java.lang.String
TAXONOMY_SCIENTIFIC_NAME
"scientific_name"
public static final java.lang.String
TAXONOMY_SYNONYM
"synonym"
public static final java.lang.String
TYPE_ATTR
"type"
public static final java.lang.String
URI
"uri"
public static final java.lang.String
URI_DESC_ATTR
"desc"
public static final java.lang.String
WIDTH
"width"
-
org.forester.io.parsers.phyloxml.PhyloXmlParser Modifier and Type Constant Field Value public static final java.lang.String
APACHE_FEATURES_VALIDATION_SCHEMA
"http://apache.org/xml/features/validation/schema"
public static final java.lang.String
APACHE_FEATURES_VALIDATION_SCHEMA_FULL
"http://apache.org/xml/features/validation/schema-full-checking"
public static final java.lang.String
APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION
"http://apache.org/xml/properties/schema/external-schemaLocation"
public static final java.lang.String
JAXP_SCHEMA_LANGUAGE
"http://java.sun.com/xml/jaxp/properties/schemaLanguage"
public static final java.lang.String
JAXP_SCHEMA_SOURCE
"http://java.sun.com/xml/jaxp/properties/schemaSource"
public static final java.lang.String
SAX_FEATURES_VALIDATION
"http://xml.org/sax/features/validation"
public static final java.lang.String
W3C_XML_SCHEMA
"http://www.w3.org/2001/XMLSchema"
-
org.forester.io.parsers.phyloxml.PhyloXmlUtil Modifier and Type Constant Field Value public static final java.lang.String
OTHER
"other"
public static final int
ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT
9
public static final java.lang.String
SEQ_TYPE_DNA
"dna"
public static final java.lang.String
SEQ_TYPE_PROTEIN
"protein"
public static final java.lang.String
SEQ_TYPE_RNA
"rna"
public static final java.lang.String
UNIPROT_TAX_PROVIDER
"uniprot"
public static final java.lang.String
UNKNOWN
"unknown"
public static final java.lang.String
VECTOR_PROPERTY_REF
"vector:index="
public static final java.lang.String
VECTOR_PROPERTY_TYPE
"xsd:decimal"
-
org.forester.io.parsers.phyloxml.XmlElement Modifier and Type Constant Field Value public static final boolean
DEBUG
false
-
org.forester.io.parsers.tol.TolParser Modifier and Type Constant Field Value public static final java.lang.String
APACHE_FEATURES_VALIDATION_SCHEMA
"http://apache.org/xml/features/validation/schema"
public static final java.lang.String
APACHE_FEATURES_VALIDATION_SCHEMA_FULL
"http://apache.org/xml/features/validation/schema-full-checking"
public static final java.lang.String
APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION
"http://apache.org/xml/properties/schema/external-schemaLocation"
public static final java.lang.String
JAXP_SCHEMA_LANGUAGE
"http://java.sun.com/xml/jaxp/properties/schemaLanguage"
public static final java.lang.String
JAXP_SCHEMA_SOURCE
"http://java.sun.com/xml/jaxp/properties/schemaSource"
public static final java.lang.String
SAX_FEATURES_VALIDATION
"http://xml.org/sax/features/validation"
public static final java.lang.String
W3C_XML_SCHEMA
"http://www.w3.org/2001/XMLSchema"
-
org.forester.io.parsers.tol.TolXmlMapping Modifier and Type Constant Field Value public static final java.lang.String
AUTHDATE
"AUTHDATE"
public static final java.lang.String
AUTHORITY
"AUTHORITY"
public static final java.lang.String
CLADE
"NODE"
public static final java.lang.String
NODE_ID_ATTR
"ID"
public static final java.lang.String
NODE_ITALICIZENAME_ATTR
"ITALICIZENAME"
public static final java.lang.String
OTHERNAME
"OTHERNAME"
public static final java.lang.String
OTHERNAME_NAME
"NAME"
public static final java.lang.String
OTHERNAMES
"OTHERNAMES"
public static final java.lang.String
PHYLOGENY
"TREE"
public static final java.lang.String
TAXONOMY_NAME
"NAME"
public static final java.lang.String
TOL_TAXONOMY_ID_TYPE
"tol"
-
org.forester.io.parsers.util.ParserUtils Modifier and Type Constant Field Value public static final java.lang.String
TAX_CODE
"(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA"
public static final java.lang.String
TAX_CODE_LO
"(?:[A-Z]{5})|RAT|PIG|PEA"
-
org.forester.io.writers.PhylogenyWriter Modifier and Type Constant Field Value public static final boolean
INDENT_PHYLOXML_DEAFULT
true
public static final java.lang.String
PHYLO_XML_END
"</phyloxml>"
public static final java.lang.String
PHYLO_XML_INTENDATION_BASE
" "
public static final java.lang.String
PHYLO_XML_NAMESPACE_LINE
"<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd\" xmlns=\"http://www.phyloxml.org\">"
public static final java.lang.String
PHYLO_XML_VERSION_ENCODING_LINE
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
-
org.forester.pccx.BranchLengthBasedScoringMethod Modifier and Type Constant Field Value public static final double
MIN_ALLOWED_BL_VALUE
0.001
-
org.forester.pccx.LogBranchLengthBasedScoringMethod Modifier and Type Constant Field Value public static final double
MAX_ALLOWED_BL_VALUE
1.0
public static final double
MIN_ALLOWED_BL_VALUE
1.0E-4
-
org.forester.phylogeny.Phylogeny Modifier and Type Constant Field Value public static final boolean
ALLOW_MULTIPLE_PARENTS_DEFAULT
false
-
org.forester.phylogeny.data.BinaryCharacters Modifier and Type Constant Field Value public static final int
COUNT_DEFAULT
-1
-
org.forester.phylogeny.data.BranchWidth Modifier and Type Constant Field Value public static final double
BRANCH_WIDTH_DEFAULT_VALUE
1.0
-
org.forester.phylogeny.data.Confidence Modifier and Type Constant Field Value public static final int
CONFIDENCE_DEFAULT_VALUE
-9999
-
org.forester.phylogeny.data.DomainArchitecture Modifier and Type Constant Field Value public static final java.lang.String
NHX_SEPARATOR
">"
-
org.forester.phylogeny.data.Event Modifier and Type Constant Field Value public static final int
DEFAULT_VALUE
-1
-
org.forester.phylogeny.data.NodeVisualData Modifier and Type Constant Field Value public static final java.lang.String
APTX_VISUALIZATION_REF
"style:"
public static final int
DEFAULT_SIZE
-1
public static final java.lang.String
FONT_COLOR_REF
"style:font_color"
public static final java.lang.String
FONT_COLOR_TYPE
"xsd:token"
public static final java.lang.String
FONT_REF
"style:font"
public static final java.lang.String
FONT_SIZE_REF
"style:font_size"
public static final java.lang.String
FONT_SIZE_TYPE
"xsd:unsignedByte"
public static final java.lang.String
FONT_STYLE_BOLD
"bold"
public static final java.lang.String
FONT_STYLE_BOLD_ITALIC
"bold_italic"
public static final java.lang.String
FONT_STYLE_ITALIC
"italic"
public static final java.lang.String
FONT_STYLE_PLAIN
"plain"
public static final java.lang.String
FONT_STYLE_REF
"style:font_style"
public static final java.lang.String
FONT_STYLE_TYPE
"xsd:token"
public static final java.lang.String
FONT_TYPE
"xsd:token"
public static final java.lang.String
NODE_COLOR_REF
"style:node_color"
public static final java.lang.String
NODE_COLOR_TYPE
"xsd:token"
public static final java.lang.String
NODE_FILL_GRADIENT
"gradient"
public static final java.lang.String
NODE_FILL_NONE
"none"
public static final java.lang.String
NODE_FILL_SOLID
"solid"
public static final java.lang.String
NODE_FILL_TYPE_REF
"style:node_fill_type"
public static final java.lang.String
NODE_FILL_TYPE_TYPE
"xsd:token"
public static final java.lang.String
NODE_SHAPE_CIRCLE
"circle"
public static final java.lang.String
NODE_SHAPE_RECTANGLE
"rectangle"
public static final java.lang.String
NODE_SHAPE_REF
"style:node_shape"
public static final java.lang.String
NODE_SHAPE_TYPE
"xsd:token"
public static final java.lang.String
NODE_SIZE_REF
"style:node_size"
public static final java.lang.String
NODE_SIZE_TYPE
"xsd:float"
public static final java.lang.String
NODE_TRANSPARENCY_REF
"style:node_transparency"
public static final java.lang.String
NODE_TRANSPARENCY_TYPE
"xsd:float"
-
org.forester.phylogeny.data.PhylogenyDataUtil Modifier and Type Constant Field Value public static final double
BRANCH_LENGTH_DEFAULT
-1024.0
-
org.forester.phylogeny.data.Point Modifier and Type Constant Field Value public static final java.lang.String
UNKNOWN_GEODETIC_DATUM
"?"
-
org.forester.phylogeny.data.ProteinDomain Modifier and Type Constant Field Value public static final double
CONFIDENCE_DEFAULT
-1.0
public static final java.lang.String
IDENTIFIER_DEFAULT
""
-
org.forester.phylogeny.data.SequenceRelation Modifier and Type Constant Field Value public static final java.lang.String
SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY
"one_to_one_orthology"
public static final java.lang.String
SEQUENCE_RELATION_TYPE_ORTHOLOGY
"orthology"
public static final java.lang.String
SEQUENCE_RELATION_TYPE_OTHER
"other"
public static final java.lang.String
SEQUENCE_RELATION_TYPE_PARALOGY
"paralogy"
public static final java.lang.String
SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY
"super_orthology"
public static final java.lang.String
SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY
"ultra_paralogy"
public static final java.lang.String
SEQUENCE_RELATION_TYPE_UNKNOWN
"unknown"
public static final java.lang.String
SEQUENCE_RELATION_TYPE_XENOLOGY
"xenology"
-
org.forester.protein.BinaryDomainCombination Modifier and Type Constant Field Value public static final java.lang.String
SEPARATOR
"="
-
org.forester.rio.RIO Modifier and Type Constant Field Value public static final int
DEFAULT_RANGE
-1
-
org.forester.sequence.MolecularSequence Modifier and Type Constant Field Value public static final java.lang.String
AA_REGEXP
"[^ARNDBCQEZGHILKMFPSTWYVXUO\\-\\*]"
public static final java.lang.String
DNA_REGEXP
"[^ACGTRYMKWSN\\-\\*]"
public static final char
GAP
45
public static final java.lang.String
RNA_REGEXP
"[^ACGURYMKWSN\\-\\*]"
public static final char
TERMINATE
42
public static final char
UNSPECIFIED_AA
88
public static final char
UNSPECIFIED_NUC
78
-
org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator Modifier and Type Constant Field Value public static final double
MAX_SIMILARITY_SCORE
1.0
public static final double
MIN_SIMILARITY_SCORE
0.0
-
org.forester.surfacing.DomainSimilarity Modifier and Type Constant Field Value public static final java.lang.String
SPECIES_SEPARATOR
" "
-
org.forester.surfacing.SurfacingConstants Modifier and Type Constant Field Value public static final java.lang.String
AMIGO_LINK
"http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query="
public static final java.lang.String
EOL_LINK
"http://www.eol.org/search?q="
public static final java.lang.String
GO_LINK
"http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query="
public static final java.lang.String
GOOGLE_SCHOLAR_SEARCH
"http://scholar.google.com/scholar?q="
public static final java.lang.String
GOOGLE_WEB_SEARCH_LINK
"http://www.google.com/search?q="
public static final java.lang.String
NONE
"[none]"
public static final java.lang.String
PFAM_FAMILY_ID_LINK
"http://pfam.xfam.org/family/"
public static final java.lang.String
UNIPROT_TAXONOMY_ID_LINK
"http://www.uniprot.org/taxonomy/"
-
org.forester.util.DescriptiveStatistics Modifier and Type Constant Field Value public static final java.lang.String
PLUS_MINUS
"\u00b1"
-
org.forester.util.ForesterConstants Modifier and Type Constant Field Value public static final java.lang.String
FORESTER_DATE
"150513"
public static final java.lang.String
FORESTER_VERSION
"1.039"
public static final java.lang.String
LOCAL_PHYLOXML_XSD_RESOURCE
"resources/phyloxml.xsd"
public static final java.lang.String
PHYLO_XML_LOCATION
"http://www.phyloxml.org"
public static final java.lang.String
PHYLO_XML_REFERENCE
"Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356"
public static final java.lang.String
PHYLO_XML_SUFFIX
".xml"
public static final java.lang.String
PHYLO_XML_VERSION
"1.10"
public static final java.lang.String
PHYLO_XML_XSD
"phyloxml.xsd"
public static final boolean
RELEASE
false
public static final java.lang.String
UTF8
"UTF-8"
public static final java.lang.String
XML_SCHEMA_INSTANCE
"http://www.w3.org/2001/XMLSchema-instance"
-
org.forester.util.ForesterUtil Modifier and Type Constant Field Value public static final java.lang.String
NCBI_GI
"http://www.ncbi.nlm.nih.gov/protein/gi:"
public static final java.lang.String
NCBI_NUCCORE
"http://www.ncbi.nlm.nih.gov/nuccore/"
public static final java.lang.String
NCBI_PROTEIN
"http://www.ncbi.nlm.nih.gov/protein/"
public static final java.lang.String
PDB
"http://www.pdb.org/pdb/explore/explore.do?pdbId="
public static final java.lang.String
UNIPROT_KB
"http://www.uniprot.org/uniprot/"
public static final double
ZERO_DIFF
1.0E-9
-
org.forester.util.SequenceAccessionTools Modifier and Type Constant Field Value public static final java.lang.String
UNIPROT_KB_BASE_PATTERN_STR
"((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))"
-
org.forester.ws.seqdb.SequenceDbWsTools Modifier and Type Constant Field Value public static final java.lang.String
BASE_UNIPROT_URL
"http://www.uniprot.org/"
public static final int
DEFAULT_LINES_TO_RETURN
4000
public static final java.lang.String
EMBL_DBS_REFSEQ_N
"refseqn"
public static final java.lang.String
EMBL_DBS_REFSEQ_P
"refseqp"
public static final java.lang.String
EMBL_EMBL
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id="
public static final java.lang.String
EMBL_GENBANK
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id="
public static final java.lang.String
EMBL_REFSEQ
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id="
-
org.forester.ws.seqdb.UniProtTaxonomy Modifier and Type Constant Field Value public static final java.lang.String
ARCHAEA
"Archaea"
public static final java.lang.String
BACTERIA
"Bacteria"
public static final java.lang.String
CELLULAR_ORGANISMS
"cellular organisms"
public static final java.lang.String
EUKARYOTA
"Eukaryota"
public static final java.lang.String
VIRUSES
"Viruses"
public static final java.lang.String
X
"x"