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