GapPenalty.Type type
int gop
int gep
AlignedSequence<S extends Sequence<C>,C extends Compound> prev
Sequence<C extends Compound> original
int length
int numBefore
int numAfter
Location location
int numGaps
int[] alignmentFromSequence
int[] sequenceFromAlignment
java.util.List<E> list
java.util.List<E> originals
int length
int identicals
int similars
CompoundSet<C extends Compound> compoundSet
java.lang.String description
java.lang.String name
short[][] matrix
short max
short min
java.util.List<E> rows
java.util.List<E> cols
AminoAcidCompoundSet compoundSet
java.util.Map<K,V> aminoAcidCompoundCache
java.util.Map<K,V> aminoAcidCompoundCache3Letter
java.util.Map<K,V> equivalentsCache
int min
int max
Point.Resolver<T extends Point> resolver
AbstractSequence<C extends Compound> sequence
int position
boolean unknown
boolean uncertain
Point start
Point end
Strand strand
java.util.List<E> subLocations
boolean circular
boolean betweenCompounds
AccessionID accession
boolean partialOn5prime
boolean partialOn3prime
java.lang.String chromosome
java.lang.Integer start
java.lang.Integer end
java.lang.String locus
StainType type
java.lang.String geneName
java.lang.String genebankId
java.lang.String chromosome
java.lang.Character orientation
java.lang.Integer transcriptionStart
java.lang.Integer transcriptionEnd
java.lang.Integer cdsStart
java.lang.Integer cdsEnd
int exonCount
java.util.List<E> exonStarts
java.util.List<E> exonEnds
java.lang.String hgncId
java.lang.String approvedSymbol
java.lang.String approvedName
java.lang.String status
java.lang.String previousSymbols
java.lang.String previousNames
java.lang.String synonyms
java.lang.String chromosome
java.lang.String accessionNr
java.lang.String refseqIds
java.lang.String uniprot
java.lang.String omimId
java.lang.String ensemblGeneId
java.util.Map<K,V> featindex
Location mLocation
java.util.Map<K,V> terms
java.util.Set<E> triples
java.util.Map<K,V> subjectTriples
java.util.Map<K,V> objectTriples
java.util.Map<K,V> relationTriples
java.util.Map<K,V> remoteTerms
java.util.Set<E> localRemoteTerms
java.lang.String name
java.lang.String description
OntologyOps ops
java.lang.String name
Ontology ontology
Annotation annotation
java.util.Set<E> synonyms
java.util.Map<K,V> properties
java.lang.Object[] mappings
int numMappings
public java.lang.Object readResolve() throws java.io.ObjectStreamException
java.io.ObjectStreamException
java.lang.String className
java.lang.String fieldName
ProteinModification originalModification
ProteinModification modification
java.util.Set<E> groups
java.util.Map<K,V> atomLinkages
java.lang.Character amino_char
java.lang.String recordType
java.lang.String surname
java.lang.String initials
java.lang.String swissprot_id
java.lang.String chainID
java.util.List<E> groups
java.util.List<E> seqResGroups
java.lang.Long id
Compound mol
Structure parent
java.util.Map<K,V> pdbResnumMap
java.lang.String internalChainID
java.util.List<E> seqMisMatches
java.util.List<E> chains
int molId
java.util.Map<K,V> chains2pdbResNums2ResSerials
Compound.getAlignedResIndex(Group, Chain)
java.lang.String refChainId
java.lang.String molName
java.lang.String title
java.util.List<E> synonyms
java.util.List<E> ecNums
java.lang.String engineered
java.lang.String mutation
java.lang.String biologicalUnit
java.lang.String details
java.lang.String numRes
java.lang.String resNames
java.lang.String headerVars
java.lang.String synthetic
java.lang.String fragment
java.lang.String organismScientific
java.lang.String organismTaxId
java.lang.String organismCommon
java.lang.String strain
java.lang.String variant
java.lang.String cellLine
java.lang.String atcc
java.lang.String organ
java.lang.String tissue
java.lang.String cell
java.lang.String organelle
java.lang.String secretion
java.lang.String gene
java.lang.String cellularLocation
java.lang.String expressionSystem
java.lang.String expressionSystemTaxId
java.lang.String expressionSystemStrain
java.lang.String expressionSystemVariant
java.lang.String expressionSystemCellLine
java.lang.String expressionSystemAtccNumber
java.lang.String expressionSystemOrgan
java.lang.String expressionSystemTissue
java.lang.String expressionSystemCell
java.lang.String expressionSystemOrganelle
java.lang.String expressionSystemCellularLocation
java.lang.String expressionSystemVectorType
java.lang.String expressionSystemVector
java.lang.String expressionSystemPlasmid
java.lang.String expressionSystemGene
java.lang.String expressionSystemOtherDetails
java.lang.Long id
Structure parent
java.lang.String idCode
java.lang.String chainId
int seqbegin
char insertBegin
int seqEnd
char insertEnd
java.lang.String database
java.lang.String dbAccession
java.lang.String dbIdCode
int dbSeqBegin
char idbnsBegin
int dbSeqEnd
char idbnsEnd
java.lang.Long id
java.util.Map<K,V> properties
long id
boolean pdb_flag
java.lang.String pdb_name
ResidueNumber residueNumber
java.util.List<E> atoms
Chain parent
java.util.Map<K,V> atomNameLookup
ChemComp chemComp
java.util.List<E> altLocs
java.util.List<E> authorList
java.util.List<E> editorList
java.lang.String title
java.lang.String ref
java.lang.String journalName
java.lang.String volume
java.lang.String startPage
int publicationDate
java.lang.String publisher
java.lang.String refn
java.lang.String pmid
java.lang.String doi
boolean published
CrystalCell cell
SpaceGroup sg
Matrix4d[] ncsOperators
java.lang.String title
java.lang.String description
java.lang.String idCode
java.lang.String classification
java.util.Date depDate
java.util.Date modDate
java.util.Set<E> techniques
PDBCrystallographicInfo crystallographicInfo
float resolution
float rFree
JournalArticle journalArticle
java.lang.String authors
java.lang.Long id
java.text.DateFormat dateFormat
java.util.Map<K,V> bioAssemblies
java.util.List<E> revisionRecords
java.lang.String chainId
java.lang.Character insCode
java.lang.Integer seqNum
java.lang.Integer seqNum
java.lang.String origGroup
java.lang.String pdbGroup
java.lang.String details
java.lang.String uniProtId
java.lang.String insCode
java.lang.String pdbResNum
java.lang.String siteID
java.util.List<E> groups
java.lang.String evCode
java.lang.String description
java.lang.String pdb_id
java.util.List<E> models
java.util.List<E> connections
java.util.List<E> compounds
java.util.List<E> dbrefs
java.util.List<E> ssbonds
java.util.List<E> sites
java.util.List<E> hetAtoms
java.lang.String name
StructureIdentifier structureIdentifier
PDBHeader pdbHeader
java.lang.Long id
boolean biologicalAssembly
java.lang.String pdbId
java.util.List<E> ranges
java.lang.String name
java.lang.String pdbId
java.lang.String chainId
StructureName.Source mySource
StructureIdentifier base
StructureAlignment algorithm
javax.swing.JButton abortB
SelectPDBPanel tab1
PDBUploadPanel tab2
ScopSelectPanel tab3
java.lang.Thread thread
AlignmentCalculationRunnable alicalc
javax.swing.JTabbedPane masterPane
javax.swing.JTabbedPane tabPane
javax.swing.JProgressBar progress
DBSearchGUI dbsearch
javax.swing.JEditorPane tp
javax.swing.JTextField textField
UserConfiguration config
javax.swing.JCheckBox fromFtp
javax.swing.JComboBox<E> fileType
javax.swing.JTextField pdbDir
StructureAlignment algorithm
SelectPDBPanel tab1
javax.swing.JTabbedPane tabPane
PDBUploadPanel tab2
ScopSelectPanel tab3
javax.swing.JPanel listPane
javax.swing.JButton abortB
AlignmentCalcDB alicalc
javax.swing.JProgressBar progress
org.biojava.nbio.structure.align.gui.ProgressThreadDrawer drawer
javax.swing.JTextField outFileLocation
java.lang.Boolean useDomainSplit
int alignmentsProcessed
javax.swing.JProgressBar progressBar
javax.swing.JTextArea taskOutput
javax.swing.JButton stopButton
FarmJob farmJob
MemoryMonitor.Surface surf
javax.swing.JPanel controls
boolean doControls
javax.swing.JTextField tf
java.lang.Thread thread
long sleepAmount
int w
int h
java.awt.image.BufferedImage bimg
java.awt.Graphics2D big
java.awt.Font font
java.lang.Runtime r
int columnInc
int[] pts
int ptNum
int ascent
int descent
java.awt.Rectangle graphOutlineRect
java.awt.geom.Rectangle2D mfRect
java.awt.geom.Rectangle2D muRect
java.awt.geom.Line2D graphLine
java.awt.Color graphColor
java.awt.Color mfColor
java.lang.String usedStr
MultipleStructureAligner multiple
StructureAlignment pairwise
SelectMultiplePanel tab
javax.swing.JTabbedPane tabPane
java.lang.Thread thread
AlignmentCalculationRunnable alicalc
javax.swing.JProgressBar progress
javax.swing.JButton abortB
ConfigStrucAligParams params
java.util.List<E> textFields
boolean debug
javax.swing.JTextField f1
javax.swing.JTextField f2
javax.swing.JTextField c1
javax.swing.JTextField c2
javax.swing.JTextField r1
javax.swing.JTextField r2
UserConfiguration config
javax.swing.JTabbedPane configPane
AFPChain afpChain
AFPChainCoordManager coordManager
java.awt.Font seqFont
java.awt.Font eqFont
AbstractAlignmentJmol jmol
AligPanelMouseMotionListener mouseMoLi
java.util.BitSet selection
boolean selectionLocked
Atom[] ca1
Atom[] ca2
boolean colorBySimilarity
boolean colorByAlignmentBlock
MultipleAlignment multAln
java.util.List<E> alnSeq
java.util.List<E> mapSeqToStruct
int size
int length
java.awt.Font seqFont
java.awt.Font eqFont
AbstractAlignmentJmol jmol
MultipleAligPanelMouseMotionListener mouseMoLi
MultipleAlignmentCoordManager coordManager
java.util.BitSet selection
boolean selectionLocked
boolean colorBySimilarity
boolean colorByAlignmentBlock
MultipleAligPanel panel
java.lang.String defaultText
javax.swing.JDialog dialog
java.awt.Point location
javax.swing.JList<E> list
java.util.Vector<E> suggestions
java.lang.String lastWord
AutoSuggestProvider autoSuggestProvider
java.awt.Font regular
java.awt.Font busy
org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest.SuggestionFetcher matcher
JmolViewer viewer
JmolAdapter adapter
JmolStatusListener statusListener
java.awt.Dimension currentSize
java.awt.Rectangle rectClip
Structure structure
boolean verbose
int value
int contig
short row
short col
int p1
int p2
int fragLen
double rmsd
Matrix m
double[] t
double score
long id
java.lang.String algorithmName
java.lang.String version
java.lang.String name1
java.lang.String name2
long ioTime
long calculationTime
long id
double alignScore
double alignScoreUpdate
int afpChainTwiNum
double tmScore
int minLen
java.util.List<E> afpSet
int[][] afpIndex
int[][] afpAftIndex
int[][] afpBefIndex
Matrix disTable1
Matrix disTable2
int[] twi
int afpChainLen
int[] afpChainList
double[] afpChainTwiBin
double[] afpChainTwiList
double chainRmsd
int chainLen
int misLen
int gapLen
int blockNum
int blockNumIni
int blockNumClu
int blockNumSpt
double[] blockRmsd
int[] block2Afp
int[] blockSize
double[] blockScore
int[] blockGap
int[] blockResSize
int[][][] blockResList
Matrix[] blockRotationMatrix
Atom[] blockShiftVector
int focusResn
int[] focusRes1
int[] focusRes2
int focusAfpn
int[] focusAfpList
boolean shortAlign
java.lang.String[][][] pdbAln
int[][][] optAln
int[] optLen
double[] optRmsd
int optLength
char[] alnsymb
char[] alnseq1
char[] alnseq2
int alnLength
int alnbeg1
int alnbeg2
int totalLenIni
int totalLenOpt
double totalRmsdIni
double totalRmsdOpt
int ca1Length
int ca2Length
int maxTra
java.lang.Double conn
java.lang.Double dvar
double probability
double identity
double similarity
double normAlignScore
int myResultsEQR
int myResultsSimilarity1
int myResultsSimilarity2
boolean sequentialAlignment
Matrix distanceMatrix
java.lang.String description2
BlockSet parent
java.util.List<E> alignRes
int coreLength
java.util.List<E> alignResCounts
MultipleAlignment parent
java.util.List<E> blocks
java.util.List<E> pose
int length
int coreLength
java.util.List<E> alignResCounts
java.lang.String algorithmName
java.lang.String version
java.lang.Long ioTime
java.lang.Long calculationTime
java.util.List<E> structureIdentifiers
java.util.List<E> atomArrays
java.util.List<E> distanceMatrix
java.util.List<E> multipleAlignments
MultipleAlignmentEnsemble parent
java.util.List<E> blockSets
int length
int coreLength
java.util.List<E> alignResCounts
java.util.List<E> coverages
AlternativeAlignment[] alignments
java.lang.String pdb1
java.lang.String pdb2
java.lang.String chain1
java.lang.String chain2
int length1
int length2
long calculationTime
long ioTime
int[] idx1
int[] idx2
java.lang.String[] pdbresnum1
java.lang.String[] pdbresnum2
int nfrags
Atom center
Matrix rot
Atom tr
int gaps0
int eqr0
int rms0
int joined
int percId
int cluster
float score
IndexPair[] aligpath
int fromia
Matrix currentRotMatrix
Atom currentTranMatrix
double rms
Matrix distanceMatrix
Group g
double asaU
double asaC
java.util.List<E> atomAsaUs
java.util.List<E> atomAsaCs
java.lang.String domainName
java.lang.Integer classId
java.lang.Integer architectureId
java.lang.Integer topologyId
java.lang.Integer homologyId
java.lang.Integer sequenceFamilyId
java.lang.Integer orthologousSequenceFamilyId
java.lang.Integer likeSequenceFamilyId
java.lang.Integer identicalSequenceFamilyId
java.lang.Integer domainCounter
java.lang.Integer length
java.lang.Double resolution
java.lang.String format
java.lang.String version
java.util.Date date
java.lang.String name
java.lang.String source
java.lang.String sequenceHeader
java.lang.String sequence
java.util.List<E> segments
java.lang.String comment
java.lang.Integer fragmentId
java.lang.String start
java.lang.String stop
java.lang.Integer length
java.lang.String nodeId
java.lang.String parentId
java.lang.String representative
java.lang.String description
CathCategory category
java.lang.Integer segmentId
java.lang.String start
java.lang.String stop
java.lang.Integer length
java.lang.String sequenceHeader
java.lang.String sequence
java.util.HashMap<K,V> contacts
double cutoff
int pdbSerial
java.lang.String chainId
double xmin
double xmax
double ymin
double ymax
double zmin
double zmax
java.util.HashMap<K,V> contacts
java.lang.Object first
java.lang.Object second
int id
double totalArea
AtomContactSet contacts
GroupContactSet groupContacts
Pair<T> molecules
Pair<T> moleculeIds
Pair<T> transforms
java.util.Map<K,V> groupAsas1
java.util.Map<K,V> groupAsas2
StructureInterfaceCluster cluster
int id
java.util.List<E> members
double averageScore
java.util.List<E> list
java.util.List<E> clusters
java.lang.String id
int size
int nseg
double score
java.util.List<E> segments
java.lang.Integer from
java.lang.Integer to
double score
java.lang.Long uid
java.lang.String domainId
java.lang.Boolean manual
java.lang.Integer xGroup
java.lang.Integer hGroup
java.lang.Integer tGroup
java.lang.Integer fGroup
java.lang.String pdbId
java.lang.String chainId
java.lang.String range
java.lang.String seqIdRange
java.lang.String architectureName
java.lang.String xGroupName
java.lang.String hGroupName
java.lang.String tGroupName
java.lang.String fGroupName
java.lang.Long assemblyId
java.util.Set<E> ligands
java.awt.image.BufferedImage _bufImage
Matrix matrix
ContinuousColorMapper cellColor
float scale
FragmentPair[] fragmentPairs
AlternativeAlignment[] aligs
int selectedAlignmentPos
StrucAligParameters params
JMatrixPanel mPanel
javax.swing.JSlider slider
javax.swing.JScrollPane scroll
javax.swing.JComboBox<E> coloring
java.util.Map<K,V> gradients
int min
int max
javax.swing.JLabel title
javax.swing.JPanel gradientContainer
Structure structure1
Structure structure2
AlternativeAlignment alig
StructurePairAligner structurePairAligner
SequenceScalePanel panel1
SequenceScalePanel panel2
javax.swing.JSlider residueSizeSlider
javax.swing.JLabel percentageDisplay
int[] idx1
int[] idx2
java.util.List<E> apos
float scale
SequenceMouseListener mouseListener1
SequenceMouseListener mouseListener2
javax.swing.JLabel label1
javax.swing.JLabel label2
AlternativeAlignment[] aligs
javax.swing.JPanel panel
Structure structure1
Structure structure2
StructurePairAligner structurePairAligner
boolean debug
javax.swing.JTextField pdbDir
javax.swing.JTextField f1
javax.swing.JTextField f2
javax.swing.JTextField c1
javax.swing.JTextField c2
boolean debug
javax.swing.JTextField pdbDir
javax.swing.JTextField f1
javax.swing.JTextField f2
javax.swing.JTextField c1
javax.swing.JTextField c2
javax.swing.JComboBox<E> fileType
javax.swing.JTextField filePath1
javax.swing.JTextField filePath2
javax.swing.JTextField chain1
javax.swing.JTextField chain2
JAutoSuggest dom1
JAutoSuggest dom2
javax.swing.JTextField input
Chain chain
int chainLength
float scale
java.lang.Character[] seqArr
CoordManager coordManager
int position
java.util.List<E> apos
ContinuousColorMapper mapper
double min
double max
boolean parseSecStruc
boolean alignSeqRes
boolean parseCAOnly
boolean headerOnly
boolean updateRemediatedFiles
int atomCaThreshold
boolean parseBioAssembly
boolean createAtomBonds
boolean createAtomCharges
boolean useInternalChainId
int maxAtoms
java.lang.String[] fullAtomNames
int serNum
java.lang.String chainID1
java.lang.String chainID2
java.lang.String resnum1
java.lang.String resnum2
java.lang.String insCode1
java.lang.String insCode2
java.lang.String id
java.lang.String name
java.lang.String type
java.lang.String pdbx_type
java.lang.String formula
java.lang.String mon_nstd_parent_comp_id
java.lang.String pdbx_synonyms
java.lang.String pdbx_formal_charge
java.lang.String pdbx_initial_date
java.lang.String pdbx_modified_date
java.lang.String pdbx_ambiguous_flag
java.lang.String pdbx_release_status
java.lang.String pdbx_replaced_by
java.lang.String pdbx_replaces
java.lang.String formula_weight
java.lang.String one_letter_code
java.lang.String three_letter_code
java.lang.String pdbx_model_coordinates_details
java.lang.String pdbx_model_coordinates_missing_flag
java.lang.String pdbx_ideal_coordinates_details
java.lang.String pdbx_ideal_coordinates_missing_flag
java.lang.String pdbx_model_coordinates_db_code
java.lang.String pdbx_subcomponent_list
java.lang.String pdbx_processing_site
java.lang.String mon_nstd_flag
java.util.List<E> descriptors
java.util.List<E> bonds
java.util.List<E> atoms
ResidueType residueType
PolymerType polymerType
boolean standard
java.lang.String comp_id
java.lang.String atom_id
java.lang.String alt_atom_id
java.lang.String type_symbol
java.lang.String charge
java.lang.String pdbx_align
java.lang.String pdbx_aromatic_flag
java.lang.String pdbx_leaving_atom_flag
java.lang.String pdbx_stereo_config
java.lang.String model_Cartn_x
java.lang.String model_Cartn_y
java.lang.String model_Cartn_z
java.lang.String pdbx_model_Cartn_x_ideal
java.lang.String pdbx_model_Cartn_y_ideal
java.lang.String pdbx_model_Cartn_z_ideal
java.lang.String pdbx_component_comp_id
java.lang.String pdbx_residue_numbering
java.lang.String pdbx_component_atom_id
java.lang.String pdbx_polymer_type
java.lang.String pdbx_ref_id
java.lang.String pdbx_component_id
java.lang.String pdbx_ordinal
java.lang.String comp_id
java.lang.String atom_id_1
java.lang.String atom_id_2
java.lang.String value_order
java.lang.String pdbx_aromatic_flag
java.lang.String pdbx_stereo_config
java.lang.String pdbx_ordinal
java.lang.String comp_id
java.lang.String type
java.lang.String program
java.lang.String program_version
java.lang.String descriptor
java.lang.String rev_num
java.lang.String type
java.lang.String details
java.lang.String id
java.lang.String details
java.lang.String method_details
java.lang.String oligomeric_details
java.lang.String oligomeric_count
java.lang.String assembly_id
java.lang.String oper_expression
java.lang.String asym_id_list
java.lang.String id
java.lang.String type
java.lang.String symmetry_operation
java.lang.String matrix11
java.lang.String matrix12
java.lang.String matrix13
java.lang.String vector1
java.lang.String matrix21
java.lang.String matrix22
java.lang.String matrix23
java.lang.String vector2
java.lang.String matrix31
java.lang.String matrix32
java.lang.String matrix33
java.lang.String vector3
java.lang.String name
Matrix matrix
double[] vector
java.lang.String type
java.lang.String entityId
java.util.List<E> segments
java.lang.String pdbResNum
java.lang.String pdbResName
java.lang.String chainId
java.lang.String uniProtResName
java.lang.Integer uniProtPos
java.lang.Integer naturalPos
java.lang.String seqResName
java.lang.String pdbId
java.lang.String uniProtAccessionId
java.lang.Boolean notObserved
java.lang.String segId
java.lang.String start
java.lang.String end
java.util.List<E> residues
double[][] L
int n
boolean isspd
int n
boolean issymmetric
double[] d
double[] e
double[][] V
double[][] H
double[] ort
double[][] LU
int m
int n
int pivsign
int[] piv
double[][] A
int m
int n
double[][] QR
int m
int n
double[] Rdiag
double[][] U
double[][] V
double[] s
int m
int n
int N
SparseVector[] rows
int N
SymbolTable<Key extends java.lang.Comparable<Key>,Value> symbolTable
java.util.TreeMap<K,V> st
int id
java.util.List<E> transforms
int macromolecularSize
java.lang.String id
java.lang.String chainId
Matrix4d transformation
int sunID
ScopCategory category
java.lang.String classificationId
java.lang.String name
java.lang.String description
java.lang.String scopId
java.lang.String pdbId
java.util.List<E> ranges
java.lang.String classificationId
java.lang.Integer sunid
int classId
int foldId
int superfamilyId
int familyId
int domainId
int speciesId
int px
int sunid
int parentSunid
java.util.List<E> children
java.util.List<E> data
java.util.List<E> scopDescriptions
java.util.List<E> domains
java.util.List<E> scopNodes
java.util.TreeSet<E> data
int minimumSequenceLength
int absoluteMinimumSequenceLength
double minimumSequenceLengthFraction
double[] sequenceIdentityThresholds
double sequencePseudoSymmetryThreshold
double alignmentFractionThreshold
double rmsdThreshold
double angleThreshold
double helixRmsdThreshold
double helixRmsdToRiseRatio
double minimumHelixRise
double minimumHelixAngle
int maximumLocalCombinations
int maximumLocalResults
int maximumLocalSubunits
boolean localSymmetry
double localTimeLimit
boolean onTheFly
boolean verbose
CESymmParameters params
javax.swing.JButton abortB
SelectPDBPanel tab1
PDBUploadPanel tab2
ScopSelectPanel tab3
java.lang.Thread thread
AlignmentCalculationRunnable alicalc
javax.swing.JTabbedPane masterPane
javax.swing.JTabbedPane tabPane
javax.swing.JProgressBar progress
int sequenceIdentity
java.util.List<E> clusters
double a
double b
double c
double alpha
double beta
double gamma
double alphaRad
double betaRad
double gammaRad
double volume
double maxDimension
Matrix3d M
Matrix3d Minv
Matrix3d Mtransp
Matrix3d MtranspInv
SpaceGroup sg
int transformId
Matrix4d matTransform
Point3i crystalTranslation
int id
int multiplicity
int primitiveMultiplicity
java.lang.String shortSymbol
java.lang.String altShortSymbol
java.util.List<E> transformations
java.util.List<E> transfAlgebraic
Vector3d[] cellTranslations
AxisAngle4d[] axisAngles
int[] axisTypes
BravaisLattice bravLattice
java.util.TreeMap<K,V> data
int offset
int end
byte[] data
boolean nullstring
java.util.ArrayList<E> title
int top
int bottom
int left
int right
int titleHeight
int xAxisLabelHeight
int labelWidth
java.lang.Double maxTime
java.lang.Double minX
java.lang.Double maxX
java.lang.Double minY
java.lang.Double maxY
java.lang.Double mean
java.awt.FontMetrics fm
KMFigureInfo kmfi
java.util.ArrayList<E> lineInfoList
java.util.ArrayList<E> siList
java.lang.String variable
java.lang.String fileName
java.text.DecimalFormat df
java.util.ArrayList<E> title
int top
int bottom
int left
int yaxisLabel
int right
int titleHeight
int xAxisLabelHeight
int labelWidth
double minTime
double maxTime
double minPercentage
double maxPercentage
java.awt.FontMetrics fm
KMFigureInfo kmfi
java.util.LinkedHashMap<K,V> survivalData
java.util.ArrayList<E> lineInfoList
SurvFitInfo sfi
java.lang.String fileName
java.util.ArrayList<E> xAxisTimeValues
java.util.ArrayList<E> xAxisTimeCoordinates
java.text.DecimalFormat df
java.lang.Double adjustedPercentIncrement
KaplanMeierFigure kmf
java.lang.Double timePercentage
java.util.Map<K,V> param
java.util.Map<K,V> param
java.lang.Integer sqFrom
java.lang.Integer sqTo
java.lang.Integer aliLenth
java.lang.Integer simCount
java.lang.Integer hmmFrom
java.lang.Integer hmmTo
java.lang.String hmmName
java.lang.String hmmDesc
java.lang.String hmmAcc
java.lang.Float evalue
java.lang.String desc
java.lang.Float score
java.lang.Float evalue
java.lang.Double pvalue
java.lang.String acc
java.lang.Integer dcl
java.lang.String name
java.lang.Integer ndom
java.lang.Integer nreported
java.util.SortedSet<E> domains
MainFrameApplet _mainframe_applet
java.lang.String _tree_url_str
java.lang.String _species_tree_url_str
java.lang.String _message_1
java.lang.String _message_2
Configuration _configuration
MainPanel _mainpanel
javax.swing.JMenuBar _jmenubar
javax.swing.JMenu _options_jmenu
javax.swing.JMenu _font_size_menu
javax.swing.JMenuItem _super_tiny_fonts_mi
javax.swing.JMenuItem _tiny_fonts_mi
javax.swing.JMenuItem _small_fonts_mi
javax.swing.JMenuItem _medium_fonts_mi
javax.swing.JMenuItem _large_fonts_mi
javax.swing.JMenu _tools_menu
javax.swing.JMenuItem _taxcolor_item
javax.swing.JMenuItem _confcolor_item
javax.swing.JMenuItem _midpoint_root_item
javax.swing.JMenu _view_jmenu
javax.swing.JMenuItem _view_as_XML_item
javax.swing.JMenuItem _view_as_NH_item
javax.swing.JMenuItem _view_as_nexus_item
javax.swing.JMenuItem _display_basic_information_item
javax.swing.JMenu _type_menu
javax.swing.JCheckBoxMenuItem _rectangular_type_cbmi
javax.swing.JCheckBoxMenuItem _triangular_type_cbmi
javax.swing.JCheckBoxMenuItem _curved_type_cbmi
javax.swing.JCheckBoxMenuItem _convex_type_cbmi
javax.swing.JCheckBoxMenuItem _euro_type_cbmi
javax.swing.JCheckBoxMenuItem _rounded_type_cbmi
javax.swing.JCheckBoxMenuItem _unrooted_type_cbmi
javax.swing.JCheckBoxMenuItem _circular_type_cbmi
javax.swing.JMenuItem _help_item
javax.swing.JMenuItem _about_item
javax.swing.JMenu _help_jmenu
javax.swing.JMenuItem _website_item
javax.swing.JMenuItem _phyloxml_website_item
javax.swing.JMenuItem _phyloxml_ref_item
javax.swing.JMenuItem _aptx_ref_item
javax.swing.JMenuItem _remove_branch_color_item
javax.swing.JMenuItem _remove_visual_styles_item
javax.swing.JCheckBoxMenuItem _show_domain_labels
javax.swing.JCheckBoxMenuItem _show_annotation_ref_source
javax.swing.JCheckBoxMenuItem _color_labels_same_as_parent_branch
javax.swing.JCheckBoxMenuItem _abbreviate_scientific_names
javax.swing.JCheckBoxMenuItem _screen_antialias_cbmi
javax.swing.JCheckBoxMenuItem _background_gradient_cbmi
javax.swing.JCheckBoxMenuItem _color_by_taxonomic_group_cbmi
javax.swing.JRadioButtonMenuItem _non_lined_up_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _uniform_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi
Options _options
javax.swing.JMenuItem _choose_font_mi
javax.swing.JMenuItem _switch_colors_mi
javax.swing.JCheckBoxMenuItem _label_direction_cbmi
javax.swing.JCheckBoxMenuItem _show_scale_cbmi
javax.swing.JCheckBoxMenuItem _search_case_senstive_cbmi
javax.swing.JCheckBoxMenuItem _search_whole_words_only_cbmi
javax.swing.JCheckBoxMenuItem _inverse_search_result_cbmi
javax.swing.JCheckBoxMenuItem _search_with_regex_cbmi
javax.swing.JCheckBoxMenuItem _show_overview_cbmi
javax.swing.JMenuItem _choose_minimal_confidence_mi
javax.swing.JMenuItem _collapse_species_specific_subtrees
javax.swing.JMenuItem _overview_placment_mi
javax.swing.ButtonGroup _radio_group_1
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_external_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi
javax.swing.JMenuItem _cycle_node_shape_mi
javax.swing.JMenuItem _cycle_node_fill_mi
javax.swing.JMenuItem _choose_node_size_mi
javax.swing.JCheckBoxMenuItem _show_confidence_stddev_cbmi
java.util.LinkedList<E> _textframes
javax.swing.JMenu _analysis_menu
javax.swing.JMenuItem _gsdi_item
javax.swing.JMenuItem _gsdir_item
Phylogeny _species_tree
javax.swing.JCheckBoxMenuItem _right_line_up_domains_cbmi
javax.swing.JCheckBoxMenuItem _line_up_renderable_data_cbmi
javax.swing.JMenuItem _save_item
javax.swing.JMenuItem _print_item
javax.swing.JMenuItem _write_to_pdf_item
javax.swing.JMenuItem _write_to_jpg_item
javax.swing.JMenuItem _write_to_gif_item
javax.swing.JMenuItem _write_to_tif_item
javax.swing.JMenuItem _write_to_png_item
javax.swing.JMenuItem _write_to_bmp_item
javax.swing.JMenu _file_jmenu
javax.swing.JFileChooser _writetopdf_filechooser
java.io.File _current_dir
javax.swing.JFileChooser _save_filechooser
javax.swing.JFileChooser _writetographics_filechooser
javax.swing.JCheckBoxMenuItem _graphics_export_visible_only_cbmi
javax.swing.JCheckBoxMenuItem _antialias_print_cbmi
javax.swing.JCheckBoxMenuItem _print_black_and_white_cbmi
javax.swing.JCheckBoxMenuItem _print_using_actual_size_cbmi
javax.swing.JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi
javax.swing.JMenuItem _print_size_mi
javax.swing.JMenuItem _choose_pdf_width_mi
java.awt.Font _font
int _option
java.lang.String _type
int _style
int _size
javax.swing.JList<E> _font_list
javax.swing.JList<E> _style_list
javax.swing.JList<E> _size_list
javax.swing.JTextField _fonts_tf
javax.swing.JTextField _style_tf
javax.swing.JTextField _size_tf
javax.swing.JLabel _fonts_label
javax.swing.JLabel _style_label
javax.swing.JLabel _size_label
javax.swing.JScrollPane _font_jsp
javax.swing.JScrollPane _style_jsp
javax.swing.JScrollPane _size_jsp
javax.swing.JButton _ok_button
javax.swing.JButton _cancel_button
javax.swing.JTextField _test_tf
javax.swing.JMenuBar _jmenubar
javax.swing.JMenu _file_jmenu
javax.swing.JMenu _tools_menu
javax.swing.JMenu _view_jmenu
javax.swing.JMenu _options_jmenu
javax.swing.JMenu _font_size_menu
javax.swing.JMenu _help_jmenu
javax.swing.JMenuItem[] _load_phylogeny_from_webservice_menu_items
javax.swing.JMenu _analysis_menu
javax.swing.JMenuItem _load_species_tree_item
javax.swing.JMenuItem _gsdi_item
javax.swing.JMenuItem _gsdir_item
javax.swing.JMenuItem _lineage_inference
javax.swing.JMenuItem _open_item
javax.swing.JMenuItem _open_url_item
javax.swing.JMenuItem _save_item
javax.swing.JMenuItem _save_all_item
javax.swing.JMenuItem _close_item
javax.swing.JMenuItem _exit_item
javax.swing.JMenuItem _new_item
javax.swing.JMenuItem _print_item
javax.swing.JMenuItem _write_to_pdf_item
javax.swing.JMenuItem _write_to_jpg_item
javax.swing.JMenuItem _write_to_gif_item
javax.swing.JMenuItem _write_to_tif_item
javax.swing.JMenuItem _write_to_png_item
javax.swing.JMenuItem _write_to_bmp_item
javax.swing.JMenuItem _midpoint_root_item
javax.swing.JMenuItem _taxcolor_item
javax.swing.JMenuItem _confcolor_item
javax.swing.JMenuItem _color_rank_jmi
javax.swing.JMenuItem _collapse_species_specific_subtrees
javax.swing.JMenuItem _obtain_detailed_taxonomic_information_jmi
javax.swing.JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi
javax.swing.JMenuItem _obtain_seq_information_jmi
javax.swing.JMenuItem _move_node_names_to_tax_sn_jmi
javax.swing.JMenuItem _move_node_names_to_seq_names_jmi
javax.swing.JMenuItem _extract_tax_code_from_node_names_jmi
javax.swing.JMenuItem _annotate_item
javax.swing.JMenuItem _remove_branch_color_item
javax.swing.JMenuItem _remove_visual_styles_item
javax.swing.JMenuItem _delete_selected_nodes_item
javax.swing.JMenuItem _delete_not_selected_nodes_item
javax.swing.JMenuItem _super_tiny_fonts_item
javax.swing.JMenuItem _tiny_fonts_item
javax.swing.JMenuItem _small_fonts_item
javax.swing.JMenuItem _medium_fonts_item
javax.swing.JMenuItem _large_fonts_item
javax.swing.JMenuItem _choose_font_mi
javax.swing.JMenuItem _switch_colors_mi
javax.swing.JCheckBoxMenuItem _label_direction_cbmi
javax.swing.JCheckBoxMenuItem _screen_antialias_cbmi
javax.swing.JCheckBoxMenuItem _background_gradient_cbmi
javax.swing.JRadioButtonMenuItem _non_lined_up_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _uniform_cladograms_rbmi
javax.swing.JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi
javax.swing.JCheckBoxMenuItem _color_by_taxonomic_group_cbmi
javax.swing.JCheckBoxMenuItem _show_scale_cbmi
javax.swing.JCheckBoxMenuItem _show_overview_cbmi
javax.swing.JCheckBoxMenuItem _show_domain_labels
javax.swing.JCheckBoxMenuItem _show_annotation_ref_source
javax.swing.JCheckBoxMenuItem _abbreviate_scientific_names
javax.swing.JCheckBoxMenuItem _color_labels_same_as_parent_branch
javax.swing.JMenuItem _overview_placment_mi
javax.swing.JMenuItem _choose_minimal_confidence_mi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_external_cbmi
javax.swing.JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi
javax.swing.JMenuItem _cycle_node_shape_mi
javax.swing.JMenuItem _cycle_node_fill_mi
javax.swing.JMenuItem _choose_node_size_mi
javax.swing.JMenuItem _cycle_data_return
javax.swing.JCheckBoxMenuItem _show_confidence_stddev_cbmi
javax.swing.JCheckBoxMenuItem _right_line_up_domains_cbmi
javax.swing.JCheckBoxMenuItem _line_up_renderable_data_cbmi
javax.swing.JCheckBoxMenuItem _graphics_export_visible_only_cbmi
javax.swing.JCheckBoxMenuItem _antialias_print_cbmi
javax.swing.JCheckBoxMenuItem _print_black_and_white_cbmi
javax.swing.JCheckBoxMenuItem _print_using_actual_size_cbmi
javax.swing.JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi
javax.swing.JMenuItem _print_size_mi
javax.swing.JMenuItem _choose_pdf_width_mi
javax.swing.JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_no_rbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi
javax.swing.JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi
javax.swing.JCheckBoxMenuItem _replace_underscores_cbmi
javax.swing.JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi
javax.swing.JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi
javax.swing.JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi
javax.swing.JCheckBoxMenuItem _search_case_senstive_cbmi
javax.swing.JCheckBoxMenuItem _search_whole_words_only_cbmi
javax.swing.JCheckBoxMenuItem _inverse_search_result_cbmi
javax.swing.JCheckBoxMenuItem _search_with_regex_cbmi
javax.swing.JMenu _type_menu
javax.swing.JCheckBoxMenuItem _rectangular_type_cbmi
javax.swing.JCheckBoxMenuItem _triangular_type_cbmi
javax.swing.JCheckBoxMenuItem _curved_type_cbmi
javax.swing.JCheckBoxMenuItem _convex_type_cbmi
javax.swing.JCheckBoxMenuItem _euro_type_cbmi
javax.swing.JCheckBoxMenuItem _rounded_type_cbmi
javax.swing.JCheckBoxMenuItem _unrooted_type_cbmi
javax.swing.JCheckBoxMenuItem _circular_type_cbmi
javax.swing.JMenuItem _view_as_NH_item
javax.swing.JMenuItem _view_as_XML_item
javax.swing.JMenuItem _view_as_nexus_item
javax.swing.JMenuItem _display_basic_information_item
javax.swing.JMenuItem _about_item
javax.swing.JMenuItem _help_item
javax.swing.JMenuItem _website_item
javax.swing.JMenuItem _phyloxml_website_item
javax.swing.JMenuItem _phyloxml_ref_item
javax.swing.JMenuItem _aptx_ref_item
java.io.File _current_dir
javax.swing.JFileChooser _writetopdf_filechooser
javax.swing.JFileChooser _save_filechooser
javax.swing.JFileChooser _writetographics_filechooser
javax.swing.JMenu _process_menu
MainPanel _mainpanel
java.awt.Container _contentpane
java.util.LinkedList<E> _textframes
Configuration _configuration
Options _options
Phylogeny _species_tree
InferenceManager _inference_manager
ProcessPool _process_pool
java.lang.String _previous_node_annotation_ref
ArchaeopteryxA _applet
javax.swing.ButtonGroup _radio_group_1
javax.swing.JFileChooser _values_filechooser
javax.swing.JFileChooser _sequences_filechooser
javax.swing.JFileChooser _open_filechooser
javax.swing.JFileChooser _msa_filechooser
javax.swing.JFileChooser _seqs_pi_filechooser
javax.swing.JFileChooser _open_filechooser_for_species_tree
javax.swing.JMenuItem _collapse_below_threshold
javax.swing.JMenuItem _collapse_below_branch_length
javax.swing.ButtonGroup _radio_group_1
javax.swing.ButtonGroup _radio_group_2
double _min_not_collapse
double _min_not_collapse_bl
javax.swing.JMenu _inference_menu
javax.swing.JMenuItem _inference_from_msa_item
javax.swing.JMenuItem _inference_from_seqs_item
PhylogeneticInferenceOptions _phylogenetic_inference_options
Msa _msa
java.io.File _msa_file
java.util.List<E> _seqs
java.io.File _seqs_file
javax.swing.JMenuItem _read_values_jmi
javax.swing.JMenuItem _read_seqs_jmi
MainFrame _mainframe
java.util.List<E> _treepanels
org.forester.archaeopteryx.ControlPanel _control_panel
java.util.List<E> _treegraphic_scroll_panes
java.util.List<E> _treegraphic_scroll_pane_panels
Configuration _configuration
javax.swing.JTabbedPane _tabbed_pane
TreeColorSet _colorset
TreeFontSet _fontset
Phylogeny _cut_or_copied_tree
java.util.Set<E> _copied_and_pasted_nodes
java.util.Hashtable<K,V> _image_map
java.util.HashMap<K,V> _nodeid_dist_to_leaf
java.awt.geom.Arc2D _arc
java.awt.geom.AffineTransform _at
int _circ_max_depth
java.util.Set<E> _collapsed_external_nodeid_set
javax.swing.JColorChooser _color_chooser
Configuration _configuration
org.forester.archaeopteryx.ControlPanel _control_panel
java.awt.geom.CubicCurve2D _cubic_curve
java.util.Set<E> _current_external_nodes
java.lang.StringBuilder _current_external_nodes_data_buffer
int _current_external_nodes_data_buffer_change_counter
int _domain_structure_e_value_thr_exp
double _domain_structure_width
int _dynamic_hiding_factor
boolean _edited
java.awt.geom.Ellipse2D _ellipse
int _external_node_index
java.util.Set<E> _found_nodes_0
java.util.Set<E> _found_nodes_1
java.awt.font.FontRenderContext _frc
Options.PHYLOGENY_GRAPHICS_TYPE _graphics_type
PhylogenyNode _highlight_node
boolean _in_ov
boolean _in_ov_rect
float _last_drag_point_x
float _last_drag_point_y
java.awt.geom.Line2D _line
int _longest_ext_node_info
PhylogenyNode _ext_node_with_longest_txt_info
MainPanel _main_panel
double _max_distance_to_root
javax.swing.Popup _node_desc_popup
int _node_frame_index
org.forester.archaeopteryx.NodeFrame[] _node_frames
javax.swing.JPopupMenu _node_popup_menu
javax.swing.JMenuItem[] _node_popup_menu_items
PhylogenyNode[] _nodes_in_preorder
Options _options
float _ov_max_height
float _ov_max_width
boolean _ov_on
java.awt.geom.Rectangle2D _ov_rectangle
java.awt.Rectangle _ov_virtual_rectangle
float _ov_x_correction_factor
float _ov_x_distance
int _ov_x_position
float _ov_y_distance
int _ov_y_position
int _ov_y_start
boolean _phy_has_branch_lengths
Phylogeny _phylogeny
java.awt.geom.Path2D.Float _polygon
java.lang.StringBuffer _popup_buffer
java.awt.geom.QuadCurve2D _quad_curve
Sequence _query_sequence
java.awt.geom.Rectangle2D _rectangle
java.awt.RenderingHints _rendering_hints
javax.swing.JTextArea _rollover_popup
PhylogenyNode _root
java.lang.StringBuilder _sb
double _scale_distance
java.lang.String _scale_label
DescriptiveStatistics _statistics_for_vector_data
Phylogeny[] _sub_phylogenies
PhylogenyNode[] _sub_phylogenies_temp_roots
int _subtree_index
java.io.File _treefile
float _urt_factor
float _urt_factor_ov
java.util.HashMap<K,V> _urt_nodeid_angle_map
java.util.HashMap<K,V> _urt_nodeid_index_map
double _urt_starting_angle
float _x_correction_factor
float _x_distance
float _y_distance
int _length_of_longest_text
int _longest_domain
javax.swing.JPanel _pnl
javax.swing.JButton _launch_btn
javax.swing.JButton _cancel_btn
javax.swing.JFormattedTextField _bootstrap_tf
javax.swing.JCheckBox _bootstrap_cb
PhylogeneticInferenceOptions _opts
javax.swing.JTextField _input_msa_file_tf
javax.swing.JButton _select_input_msa_btn
MainFrameApplication _parent_frame
javax.swing.JTextField _msa_length_tf
javax.swing.JTextField _msa_size_tf
javax.swing.JTextField _msa_type_tf
javax.swing.JRadioButton _distance_calc_kimura_rb
javax.swing.JRadioButton _distance_calc_poisson_rb
javax.swing.JRadioButton _distance_calc_fract_dissimilarity_rb
int _value
javax.swing.JTextField _input_seqs_tf
javax.swing.JButton _select_input_seqs_btn
javax.swing.JTextField _input_seqs_number_tf
javax.swing.JTextField _input_seqs_median_length_tf
javax.swing.JTextField _input_seqs_min_length_tf
javax.swing.JTextField _input_seqs_max_length_tf
javax.swing.JTextField _input_seqs_type_tf
javax.swing.JTextField _mafft_paramenters_tf
javax.swing.JTextField _msa_processing_max_allowed_gap_ratio_tf
javax.swing.JTextField _msa_processing_min_allowed_length_tf
javax.swing.JTextField _random_seed_tf
javax.swing.JCheckBox _execute_msa_processing_cb
javax.swing.JCheckBox _msa_processing_remove_all_gap_columns_cb
javax.swing.JCheckBox _mafft_cb
javax.swing.JCheckBox _save_pwd_file_cb
javax.swing.JCheckBox _save_processed_msa_cb
javax.swing.JCheckBox _save_original_msa_cb
javax.swing.JTextField _pwd_outfile_tf
javax.swing.JTextField _processed_msa_outfile_tf
javax.swing.JTextField _original_msa_outfile_tf
int _x
int _y
int _well_size
byte _status
int _rows
int _columns
int _wellSize
AbstractRenderer[][] _wells
double _min
double _max
double _mean
java.awt.Color _minColor
java.awt.Color _maxColor
java.awt.Color _meanColor
boolean _useMean
Msa _msa
javax.swing.JComponent _parent
char _value
java.awt.Color _wellColor
boolean _isMarked
boolean _isSelected
MsaRenderer _parentPlateRenderer
int _initial_number_of_seqs
javax.swing.JMenuItem _m_exit
java.util.List<E> _msa_props
boolean _show_msa_qual
java.lang.String _title
java.awt.Window parent
javax.swing.JPanel innerPanel
javax.swing.JColorChooser colorChooser
java.awt.Color startingColor
ColorBrewer startingColorBrewer
boolean okWasPressed
ColorBrewer brewer