Serialized Form

Package org.biojava.nbio.alignment

• Class org.biojava.nbio.alignment.SimpleGapPenalty

  class SimpleGapPenalty extends Object implements Serializable

  serialVersionUID:

  3945671344135815456L

  • Serialized Fields

    • gep

      int gep

    • gop

      int gop

    • type

      GapPenalty.Type type

Package org.biojava.nbio.core.alignment

• Class org.biojava.nbio.core.alignment.SimpleAlignedSequence

  class SimpleAlignedSequence extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • alignmentFromSequence

      int[] alignmentFromSequence

    • length

      int length

    • location

      Location location

    • numAfter

      int numAfter

    • numBefore

      int numBefore

    • numGapPositions

      int numGapPositions

    • numGaps

      int numGaps

    • original

      S extends Sequence<C> original

    • prev

      AlignedSequence<S extends Sequence<C>,C extends Compound> prev

    • sequenceFromAlignment

      int[] sequenceFromAlignment

• Class org.biojava.nbio.core.alignment.SimpleProfile

  class SimpleProfile extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • length

      int length

    • list

      List<AlignedSequence<S extends Sequence<C>,C extends Compound>> list

    • originals

      List<S extends Sequence<C>> originals

• Class org.biojava.nbio.core.alignment.SimpleProfilePair

  class SimpleProfilePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • query

      Profile<S extends Sequence<C>,C extends Compound> query

    • target

      Profile<S extends Sequence<C>,C extends Compound> target

• Class org.biojava.nbio.core.alignment.SimpleSequencePair

  class SimpleSequencePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • identicals

      int identicals

    • similars

      int similars

Package org.biojava.nbio.core.alignment.matrices

• Class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix

  class SimpleSubstitutionMatrix extends Object implements Serializable

  serialVersionUID:

  -2645265638108462479L

  • Serialized Fields

    • cols

      List<C extends Compound> cols

    • compoundSet

      CompoundSet<C extends Compound> compoundSet

    • description

      String description

    • matrix

      short[][] matrix

    • max

      short max

    • min

      short min

    • name

      String name

    • rows

      List<C extends Compound> rows

• Class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper

  class SubstitutionMatrixHelper extends Object implements Serializable

  serialVersionUID:

  148491724604653225L

Package org.biojava.nbio.core.exceptions

• Exception org.biojava.nbio.core.exceptions.CompoundNotFoundException

  class CompoundNotFoundException extends Exception implements Serializable

  serialVersionUID:

  1L

• Exception org.biojava.nbio.core.exceptions.ParserException

  class ParserException extends RuntimeException implements Serializable

  serialVersionUID:

  -4101924035353204493L

• Exception org.biojava.nbio.core.exceptions.TranslationException

  class TranslationException extends RuntimeException implements Serializable

  serialVersionUID:

  -3017433758219757440L

Package org.biojava.nbio.core.sequence.compound

• Class org.biojava.nbio.core.sequence.compound.AminoAcidCompound

  class AminoAcidCompound extends AbstractCompound implements Serializable

  serialVersionUID:

  -1955116496725902319L

  • Serialized Fields

    • compoundSet

      AminoAcidCompoundSet compoundSet

• Class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet

  class AminoAcidCompoundSet extends Object implements Serializable

  serialVersionUID:

  4000344194364133456L

  • Serialized Fields

    • aminoAcidCompoundCache

      Map<String,AminoAcidCompound> aminoAcidCompoundCache

    • aminoAcidCompoundCache3Letter

      Map<String,AminoAcidCompound> aminoAcidCompoundCache3Letter

    • equivalentsCache

      Map<AminoAcidCompound,Set<AminoAcidCompound>> equivalentsCache

Package org.biojava.nbio.core.sequence.location

• Class org.biojava.nbio.core.sequence.location.FuzzyPoint

  class FuzzyPoint extends SimplePoint implements Serializable

  • Serialized Fields

    • max

      int max

    • min

      int min

    • resolver

      Point.Resolver<FuzzyPoint> resolver

• Class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation

  class BondLocation extends AbstractLocation implements Serializable

• Class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation

  class GroupLocation extends SimpleLocation implements Serializable

• Class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation

  class OneOfLocation extends AbstractLocation implements Serializable

• Class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation

  class OrderLocation extends SimpleLocation implements Serializable

• Class org.biojava.nbio.core.sequence.location.SequenceLocation

  class SequenceLocation extends SimpleLocation implements Serializable

  • Serialized Fields

    • sequence

      S extends AbstractSequence<C> sequence

• Class org.biojava.nbio.core.sequence.location.SimpleLocation

  class SimpleLocation extends AbstractLocation implements Serializable

• Class org.biojava.nbio.core.sequence.location.SimplePoint

  class SimplePoint extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • position

      int position

    • uncertain

      boolean uncertain

    • unknown

      boolean unknown

Package org.biojava.nbio.core.sequence.location.template

• Class org.biojava.nbio.core.sequence.location.template.AbstractLocation

  class AbstractLocation extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • accession

      AccessionID accession

    • betweenCompounds

      boolean betweenCompounds

    • circular

      boolean circular

    • end

      Point end

    • partialOn3prime

      boolean partialOn3prime

    • partialOn5prime

      boolean partialOn5prime

    • start

      Point start

    • strand

      Strand strand

    • subLocations

      List<Location> subLocations

Package org.biojava.nbio.genome.parsers.cytoband

• Class org.biojava.nbio.genome.parsers.cytoband.Cytoband

  class Cytoband extends Object implements Serializable

  serialVersionUID:

  2805976387404499650L

  • Serialized Fields

    • chromosome

      String chromosome

    • end

      Integer end

    • locus

      String locus

    • start

      Integer start

    • type

      StainType type

Package org.biojava.nbio.genome.parsers.genename

• Class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition

  class GeneChromosomePosition extends Object implements Serializable

  serialVersionUID:

  -6886306238993367835L

  • Serialized Fields

    • cdsEnd

      Integer cdsEnd

    • cdsStart

      Integer cdsStart

    • chromosome

      String chromosome

    • exonCount

      int exonCount

    • exonEnds

      List<Integer> exonEnds

    • exonStarts

      List<Integer> exonStarts

    • genebankId

      String genebankId

    • geneName

      String geneName

    • orientation

      Character orientation

    • transcriptionEnd

      Integer transcriptionEnd

    • transcriptionStart

      Integer transcriptionStart

• Class org.biojava.nbio.genome.parsers.genename.GeneName

  class GeneName extends Object implements Serializable

  serialVersionUID:

  -7163977639324764020L

  • Serialized Fields

    • accessionNr

      String accessionNr

    • approvedName

      String approvedName

    • approvedSymbol

      String approvedSymbol

    • chromosome

      String chromosome

    • ensemblGeneId

      String ensemblGeneId

    • hgncId

      String hgncId

    • omimId

      String omimId

    • previousNames

      String previousNames

    • previousSymbols

      String previousSymbols

    • refseqIds

      String refseqIds

    • status

      String status

    • synonyms

      String synonyms

    • uniprot

      String uniprot

Package org.biojava.nbio.genome.parsers.gff

• Class org.biojava.nbio.genome.parsers.gff.FeatureList

  class FeatureList extends ArrayList<FeatureI> implements Serializable

  • Serialized Fields

    • featindex

      Map<String,Map<String,List<FeatureI>>> featindex

    • mLocation

      Location mLocation

Package org.biojava.nbio.ontology

• Exception org.biojava.nbio.ontology.AlreadyExistsException

  class AlreadyExistsException extends OntologyException implements Serializable

  serialVersionUID:

  1L

• Class org.biojava.nbio.ontology.DefaultOps

  class DefaultOps extends Object implements Serializable

  serialVersionUID:

  1L

• Exception org.biojava.nbio.ontology.InvalidTermException

  class InvalidTermException extends OntologyException implements Serializable

  serialVersionUID:

  1L

• Class org.biojava.nbio.ontology.Ontology.Impl

  class Impl extends Object implements Serializable

  serialVersionUID:

  -8064461497813727957L

  • Serialized Fields

    • description

      String description

    • localRemoteTerms

      Set<Term> localRemoteTerms

    • name

      String name

    • objectTriples

      Map<Term,Set<Triple>> objectTriples

    • ops

      OntologyOps ops

    • relationTriples

      Map<Term,Set<Triple>> relationTriples

    • remoteTerms

      Map<Term,RemoteTerm> remoteTerms

    • subjectTriples

      Map<Term,Set<Triple>> subjectTriples

    • terms

      Map<String,Term> terms

    • triples

      Set<Triple> triples

• Exception org.biojava.nbio.ontology.OntologyException

  class OntologyException extends Exception implements Serializable

  serialVersionUID:

  1L

• Class org.biojava.nbio.ontology.OntologyTerm.Impl

  class Impl extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • ontology

      Ontology ontology

    • synonyms

      Set synonyms

    • target

      Ontology target

• Class org.biojava.nbio.ontology.RemoteTerm.Impl

  class Impl extends AbstractTerm implements Serializable

  serialVersionUID:

  922700041939183676L

  • Serialized Fields

    • name

      String name

    • ontology

      Ontology ontology

    • remoteTerm

      Term remoteTerm

    • synonyms

      Set synonyms

• Class org.biojava.nbio.ontology.Term.Impl

  class Impl extends AbstractTerm implements Serializable

  serialVersionUID:

  6561668917514377417L

  • Serialized Fields

    • annotation

      Annotation annotation

    • name

      String name

    • ontology

      Ontology ontology

    • synonyms

      Set<Object> synonyms

• Class org.biojava.nbio.ontology.Triple.Impl

  class Impl extends Object implements Serializable

  serialVersionUID:

  3807331980372839221L

  • Serialized Fields

    • description

      String description

    • name

      String name

    • object

      Term object

    • predicate

      Term predicate

    • subject

      Term subject

    • synonyms

      Set<Object> synonyms

• Class org.biojava.nbio.ontology.Variable.Impl

  class Impl extends Term.Impl implements Serializable

  serialVersionUID:

  1L

Package org.biojava.nbio.ontology.utils

• Class org.biojava.nbio.ontology.utils.AbstractAnnotation

  class AbstractAnnotation extends Object implements Serializable

  serialVersionUID:

  2753449055959952873L

• Error org.biojava.nbio.ontology.utils.AssertionFailure

  class AssertionFailure extends AssertionError implements Serializable

• Class org.biojava.nbio.ontology.utils.SmallAnnotation

  class SmallAnnotation extends AbstractAnnotation implements Serializable

  • Serialized Fields

    • properties

      Map properties

• Class org.biojava.nbio.ontology.utils.SmallMap

  class SmallMap extends AbstractMap implements Serializable

  • Serialized Fields

    • mappings

      Object[] mappings

    • numMappings

      int numMappings

• Class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

  class StaticMemberPlaceHolder extends Object implements Serializable

  • Serialization Methods

    • readResolve

      public Object readResolve() throws ObjectStreamException

      Throws:

      ObjectStreamException

  • Serialized Fields

    • className

      String className

    • fieldName

      String fieldName

Package org.biojava.nbio.protmod.structure

• Class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

  class ModifiedCompoundImpl extends Object implements Serializable

  serialVersionUID:

  1656563037849815427L

  • Serialized Fields

    • atomLinkages

      Map<Set<StructureGroup>,Set<StructureAtomLinkage>> atomLinkages

    • groups

      Set<StructureGroup> groups

    • modification

      ProteinModification modification

    • originalModification

      ProteinModification originalModification

Package org.biojava.nbio.structure

• Class org.biojava.nbio.structure.AminoAcidImpl

  class AminoAcidImpl extends HetatomImpl implements Serializable

  serialVersionUID:

  -6018854413829044230L

  • Serialized Fields

    • amino_char

      Character amino_char

      IUPAC amino acid residue names

    • recordType

      String recordType

• Class org.biojava.nbio.structure.AtomImpl

  class AtomImpl extends Object implements Serializable

  serialVersionUID:

  -2258364127420562883L

  • Serialized Fields

    • altLoc

      char altLoc

    • bonds

      List<Bond> bonds

    • charge

      short charge

    • coords

      double[] coords

    • element

      Element element

    • name

      String name

    • occupancy

      float occupancy

    • parent

      Group parent

    • pdbserial

      int pdbserial

    • tempfactor

      float tempfactor

• Class org.biojava.nbio.structure.Author

  class Author extends Object implements Serializable

  serialVersionUID:

  4840370515056666418L

  • Serialized Fields

    • initials

      String initials

    • surname

      String surname

• Class org.biojava.nbio.structure.BondImpl

  class BondImpl extends Object implements Serializable

  serialVersionUID:

  8836120946858134380L

  • Serialized Fields

    • atomA

      Atom atomA

    • atomB

      Atom atomB

    • bondOrder

      int bondOrder

• Class org.biojava.nbio.structure.ChainImpl

  class ChainImpl extends Object implements Serializable

  serialVersionUID:

  1990171805277911840L

  • Serialized Fields

    • chainID

      String chainID

    • groups

      List<Group> groups

    • id

      Long id

    • internalChainID

      String internalChainID

    • mol

      Compound mol

    • parent

      Structure parent

    • pdbResnumMap

      Map<String,Integer> pdbResnumMap

    • seqMisMatches

      List<SeqMisMatch> seqMisMatches

    • seqResGroups

      List<Group> seqResGroups

    • swissprot_id

      String swissprot_id

• Class org.biojava.nbio.structure.Compound

  class Compound extends Object implements Serializable

  serialVersionUID:

  2991897825657586356L

  • Serialized Fields

    • atcc

      String atcc

    • biologicalUnit

      String biologicalUnit

    • cell

      String cell

    • cellLine

      String cellLine

    • cellularLocation

      String cellularLocation

    • chains

      List<Chain> chains

      The list of chains that are described by this Compound

    • chains2pdbResNums2ResSerials

      Map<String,Map<ResidueNumber,Integer>> chains2pdbResNums2ResSerials

      A map to cache residue number mapping, between ResidueNumbers and index (1-based) in aligned sequences (SEQRES). Initialised lazily upon call to Compound.getAlignedResIndex(Group, Chain)

    • details

      String details

    • ecNums

      List<String> ecNums

    • engineered

      String engineered

    • expressionSystem

      String expressionSystem

    • expressionSystemAtccNumber

      String expressionSystemAtccNumber

    • expressionSystemCell

      String expressionSystemCell

    • expressionSystemCellLine

      String expressionSystemCellLine

    • expressionSystemCellularLocation

      String expressionSystemCellularLocation

    • expressionSystemGene

      String expressionSystemGene

    • expressionSystemOrgan

      String expressionSystemOrgan

    • expressionSystemOrganelle

      String expressionSystemOrganelle

    • expressionSystemOtherDetails

      String expressionSystemOtherDetails

    • expressionSystemPlasmid

      String expressionSystemPlasmid

    • expressionSystemStrain

      String expressionSystemStrain

    • expressionSystemTaxId

      String expressionSystemTaxId

    • expressionSystemTissue

      String expressionSystemTissue

    • expressionSystemVariant

      String expressionSystemVariant

    • expressionSystemVector

      String expressionSystemVector

    • expressionSystemVectorType

      String expressionSystemVectorType

    • fragment

      String fragment

    • gene

      String gene

    • headerVars

      String headerVars

    • id

      Long id

    • molId

      int molId

      The Molecule identifier, called entity_id in mmCIF dictionary

    • molName

      String molName

    • mutation

      String mutation

    • numRes

      String numRes

    • organ

      String organ

    • organelle

      String organelle

    • organismCommon

      String organismCommon

    • organismScientific

      String organismScientific

    • organismTaxId

      String organismTaxId

    • refChainId

      String refChainId

    • resNames

      String resNames

    • secretion

      String secretion

    • strain

      String strain

    • synonyms

      List<String> synonyms

    • synthetic

      String synthetic

    • tissue

      String tissue

    • title

      String title

    • variant

      String variant

• Class org.biojava.nbio.structure.DBRef

  class DBRef extends Object implements Serializable

  serialVersionUID:

  -1050178577542224379L

  • Serialized Fields

    • chainId

      String chainId

    • database

      String database

    • dbAccession

      String dbAccession

    • dbIdCode

      String dbIdCode

    • dbSeqBegin

      int dbSeqBegin

    • dbSeqEnd

      int dbSeqEnd

    • id

      Long id

    • idbnsBegin

      char idbnsBegin

    • idbnsEnd

      char idbnsEnd

    • idCode

      String idCode

    • insertBegin

      char insertBegin

    • insertEnd

      char insertEnd

    • parent

      Structure parent

    • seqbegin

      int seqbegin

    • seqEnd

      int seqEnd

• Class org.biojava.nbio.structure.HetatomImpl

  class HetatomImpl extends Object implements Serializable

  serialVersionUID:

  4491470432023820382L

  • Serialized Fields

    • altLocs

      List<Group> altLocs

    • atomNameLookup

      Map<String,Atom> atomNameLookup

    • atoms

      List<Atom> atoms

    • chemComp

      ChemComp chemComp

    • id

      long id

    • parent

      Chain parent

    • pdb_flag

      boolean pdb_flag

      stores if 3d coordinates are available.

    • pdb_name

      String pdb_name

      3 letter name of amino acid in pdb file.

    • properties

      Map<String,Object> properties

    • residueNumber

      ResidueNumber residueNumber

• Class org.biojava.nbio.structure.JournalArticle

  class JournalArticle extends Object implements Serializable

  serialVersionUID:

  5062668226159515468L

  • Serialized Fields

    • authorList

      List<Author> authorList

    • doi

      String doi

    • editorList

      List<Author> editorList

    • journalName

      String journalName

    • pmid

      String pmid

    • publicationDate

      int publicationDate

    • published

      boolean published

    • publisher

      String publisher

    • ref

      String ref

    • refn

      String refn

    • startPage

      String startPage

    • title

      String title

    • volume

      String volume

• Class org.biojava.nbio.structure.NucleotideImpl

  class NucleotideImpl extends HetatomImpl implements Serializable

  serialVersionUID:

  -7467726932980288712L

• Class org.biojava.nbio.structure.PDBCrystallographicInfo

  class PDBCrystallographicInfo extends Object implements Serializable

  serialVersionUID:

  -7949886749566087669L

  • Serialized Fields

    • cell

      CrystalCell cell

    • ncsOperators

      javax.vecmath.Matrix4d[] ncsOperators

      Some PDB files contain NCS operators necessary to create the full AU. Usually this happens for viral proteins. See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn . Note that the "given" operators (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format) are not stored.

    • nonStandardCoordFrameConvention

      boolean nonStandardCoordFrameConvention

      Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect. There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will be remediated in the future. For more info see: https://github.com/eppic-team/owl/issues/4

      Since:

      4.2.5

    • nonStandardSg

      boolean nonStandardSg

      Whether this structure has a non-standard space group not supported by Biojava. If this is true the sg member will be null.

      Since:

      4.2.5

    • sg

      SpaceGroup sg

• Class org.biojava.nbio.structure.PDBHeader

  class PDBHeader extends Object implements Serializable

  serialVersionUID:

  -5834326174085429508L

  • Serialized Fields

    • authors

      String authors

    • bioAssemblies

      Map<Integer,BioAssemblyInfo> bioAssemblies

    • classification

      String classification

    • crystallographicInfo

      PDBCrystallographicInfo crystallographicInfo

    • dateFormat

      DateFormat dateFormat

    • depDate

      Date depDate

    • description

      String description

    • id

      Long id

    • idCode

      String idCode

    • journalArticle

      JournalArticle journalArticle

    • modDate

      Date modDate

    • resolution

      float resolution

    • revisionRecords

      List<DatabasePdbrevRecord> revisionRecords

    • rFree

      float rFree

    • techniques

      Set<ExperimentalTechnique> techniques

    • title

      String title

• Class org.biojava.nbio.structure.ResidueNumber

  class ResidueNumber extends Object implements Serializable

  serialVersionUID:

  1773011704758536083L

  • Serialized Fields

    • chainId

      String chainId

    • insCode

      Character insCode

    • seqNum

      Integer seqNum

• Class org.biojava.nbio.structure.SeqMisMatchImpl

  class SeqMisMatchImpl extends Object implements Serializable

  serialVersionUID:

  -3699285122925652562L

  • Serialized Fields

    • details

      String details

    • insCode

      String insCode

    • origGroup

      String origGroup

    • pdbGroup

      String pdbGroup

    • pdbResNum

      String pdbResNum

    • seqNum

      Integer seqNum

    • uniProtId

      String uniProtId

• Class org.biojava.nbio.structure.Site

  class Site extends Object implements Serializable

  serialVersionUID:

  -4577047072916341237L

  • Serialized Fields

    • description

      String description

    • evCode

      String evCode

    • groups

      List<Group> groups

    • siteID

      String siteID

• Exception org.biojava.nbio.structure.StructureException

  class StructureException extends Exception implements Serializable

  serialVersionUID:

  62946250941673093L

• Class org.biojava.nbio.structure.StructureImpl

  class StructureImpl extends Object implements Serializable

  serialVersionUID:

  -8344837138032851348L

  • Serialized Fields

    • biologicalAssembly

      boolean biologicalAssembly

    • compounds

      List<Compound> compounds

    • connections

      List<Map<String,Integer>> connections

    • dbrefs

      List<DBRef> dbrefs

    • hetAtoms

      List<Group> hetAtoms

    • id

      Long id

    • models

      List<List<Chain>> models

    • name

      String name

    • pdb_id

      String pdb_id

    • pdbHeader

      PDBHeader pdbHeader

    • sites

      List<Site> sites

    • ssbonds

      List<Bond> ssbonds

    • structureIdentifier

      StructureIdentifier structureIdentifier

• Class org.biojava.nbio.structure.SubstructureIdentifier

  class SubstructureIdentifier extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • pdbId

      String pdbId

    • ranges

      List<ResidueRange> ranges

Package org.biojava.nbio.structure.align.client

• Exception org.biojava.nbio.structure.align.client.JobKillException

  class JobKillException extends Exception implements Serializable

  serialVersionUID:

  1L

• Class org.biojava.nbio.structure.align.client.StructureName

  class StructureName extends Object implements Serializable

  serialVersionUID:

  4021229518711762957L

  • Serialized Fields

    • base

      StructureIdentifier base

    • chainId

      String chainId

    • mySource

      StructureName.Source mySource

    • name

      String name

    • pdbId

      String pdbId

Package org.biojava.nbio.structure.align.gui

• Class org.biojava.nbio.structure.align.gui.AlignmentGui

  class AlignmentGui extends JFrame implements Serializable

  serialVersionUID:

  0L

  • Serialized Fields

    • abortB

      JButton abortB

    • algorithm

      StructureAlignment algorithm

    • alicalc

      AlignmentCalculationRunnable alicalc

    • dbsearch

      DBSearchGUI dbsearch

    • masterPane

      JTabbedPane masterPane

    • progress

      JProgressBar progress

    • tab1

      SelectPDBPanel tab1

    • tab2

      PDBUploadPanel tab2

    • tab3

      ScopSelectPanel tab3

    • tabPane

      JTabbedPane tabPane

    • thread

      Thread thread

• Class org.biojava.nbio.structure.align.gui.AlignmentTextPanel

  class AlignmentTextPanel extends JPrintPanel implements Serializable

  serialVersionUID:

  5092386365924879073L

  • Serialized Fields

    • tp

      JEditorPane tp

• Class org.biojava.nbio.structure.align.gui.ChooseDirAction

  class ChooseDirAction extends AbstractAction implements Serializable

  serialVersionUID:

  0L

  • Serialized Fields

    • config

      UserConfiguration config

    • textField

      JTextField textField

• Class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel

  class ConfigPDBInstallPanel extends JPanel implements Serializable

  serialVersionUID:

  -1055193854675583808L

  • Serialized Fields

    • fileType

      JComboBox fileType

    • fromFtp

      JCheckBox fromFtp

    • pdbDir

      JTextField pdbDir

• Class org.biojava.nbio.structure.align.gui.DBSearchGUI

  class DBSearchGUI extends JPanel implements Serializable

  serialVersionUID:

  -5657960663049062301L

  • Serialized Fields

    • abortB

      JButton abortB

    • algorithm

      StructureAlignment algorithm

    • alicalc

      AlignmentCalcDB alicalc

    • drawer

      org.biojava.nbio.structure.align.gui.ProgressThreadDrawer drawer

    • listPane

      JPanel listPane

    • outFileLocation

      JTextField outFileLocation

    • progress

      JProgressBar progress

    • tab1

      SelectPDBPanel tab1

    • tab2

      PDBUploadPanel tab2

    • tab3

      ScopSelectPanel tab3

    • tabPane

      JTabbedPane tabPane

    • useDomainSplit

      Boolean useDomainSplit

• Class org.biojava.nbio.structure.align.gui.DotPlotPanel

  class DotPlotPanel extends ScaleableMatrixPanel implements Serializable

  serialVersionUID:

  -7641953255857483895L

• Class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener

  class GUIAlignmentProgressListener extends JPanel implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • alignmentsProcessed

      int alignmentsProcessed

    • farmJob

      FarmJob farmJob

    • progressBar

      JProgressBar progressBar

    • stopButton

      JButton stopButton

    • taskOutput

      JTextArea taskOutput

• Class org.biojava.nbio.structure.align.gui.JPrintPanel

  class JPrintPanel extends JPanel implements Serializable

  serialVersionUID:

  -3337337068138131455L

• Class org.biojava.nbio.structure.align.gui.MemoryMonitor

  class MemoryMonitor extends JPanel implements Serializable

  serialVersionUID:

  56289234782130L

  • Serialized Fields

    • controls

      JPanel controls

    • doControls

      boolean doControls

    • surf

      MemoryMonitor.Surface surf

    • tf

      JTextField tf

• Class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

  class Surface extends JPanel implements Serializable

  serialVersionUID:

  2387409854370432908L

  • Serialized Fields

    • ascent

      int ascent

    • big

      Graphics2D big

    • bimg

      BufferedImage bimg

    • columnInc

      int columnInc

    • descent

      int descent

    • font

      Font font

    • graphColor

      Color graphColor

    • graphLine

      Line2D graphLine

    • graphOutlineRect

      Rectangle graphOutlineRect

    • h

      int h

    • mfColor

      Color mfColor

    • mfRect

      Rectangle2D mfRect

    • muRect

      Rectangle2D muRect

    • ptNum

      int ptNum

    • pts

      int[] pts

    • r

      Runtime r

    • sleepAmount

      long sleepAmount

    • thread

      Thread thread

    • usedStr

      String usedStr

    • w

      int w

• Class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI

  class MultipleAlignmentGUI extends JFrame implements Serializable

  serialVersionUID:

  0L

  • Serialized Fields

    • abortB

      JButton abortB

    • alicalc

      AlignmentCalculationRunnable alicalc

    • multiple

      MultipleStructureAligner multiple

    • pairwise

      StructureAlignment pairwise

    • progress

      JProgressBar progress

    • tab

      SelectMultiplePanel tab

    • tabPane

      JTabbedPane tabPane

    • thread

      Thread thread

• Class org.biojava.nbio.structure.align.gui.ParameterGUI

  class ParameterGUI extends JFrame implements Serializable

  serialVersionUID:

  723386061184110161L

  • Serialized Fields

    • params

      ConfigStrucAligParams params

    • textFields

      List<Component> textFields

• Class org.biojava.nbio.structure.align.gui.SelectPDBPanel

  class SelectPDBPanel extends JPanel implements Serializable

  serialVersionUID:

  4002475313717172193L

  • Serialized Fields

    • c1

      JTextField c1

    • c2

      JTextField c2

    • config

      UserConfiguration config

    • configPane

      JTabbedPane configPane

    • debug

      boolean debug

    • f1

      JTextField f1

    • f2

      JTextField f2

    • r1

      JTextField r1

    • r2

      JTextField r2

Package org.biojava.nbio.structure.align.gui.aligpanel

• Class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel

  class AligPanel extends JPrintPanel implements Serializable

  serialVersionUID:

  -6892229111166263764L

  • Serialized Fields

    • afpChain

      AFPChain afpChain

    • ca1

      Atom[] ca1

    • ca2

      Atom[] ca2

    • colorByAlignmentBlock

      boolean colorByAlignmentBlock

    • colorBySimilarity

      boolean colorBySimilarity

    • coordManager

      AFPChainCoordManager coordManager

    • eqFont

      Font eqFont

    • jmol

      AbstractAlignmentJmol jmol

    • mouseMoLi

      AligPanelMouseMotionListener mouseMoLi

    • selection

      BitSet selection

    • selectionLocked

      boolean selectionLocked

    • seqFont

      Font seqFont

• Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

  class MultipleAligPanel extends JPrintPanel implements Serializable

  serialVersionUID:

  -6892229111166263764L

  • Serialized Fields

    • alnSeq

      List<String> alnSeq

    • colorByAlignmentBlock

      boolean colorByAlignmentBlock

    • colorBySimilarity

      boolean colorBySimilarity

    • coordManager

      MultipleAlignmentCoordManager coordManager

    • eqFont

      Font eqFont

    • jmol

      AbstractAlignmentJmol jmol

    • length

      int length

    • mapSeqToStruct

      List<Integer> mapSeqToStruct

    • mouseMoLi

      MultipleAligPanelMouseMotionListener mouseMoLi

    • multAln

      MultipleAlignment multAln

    • selection

      BitSet selection

    • selectionLocked

      boolean selectionLocked

    • seqFont

      Font seqFont

    • size

      int size

• Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay

  class MultipleStatusDisplay extends JTextField implements Serializable

  serialVersionUID:

  6939947266417830429L

  • Serialized Fields

    • panel

      MultipleAligPanel panel

• Class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay

  class StatusDisplay extends JTextField implements Serializable

  serialVersionUID:

  6939947266417830429L

  • Serialized Fields

    • afpChain

      AFPChain afpChain

    • ca1

      Atom[] ca1

    • ca2

      Atom[] ca2

Package org.biojava.nbio.structure.align.gui.autosuggest

• Class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest

  class JAutoSuggest extends JTextField implements Serializable

  serialVersionUID:

  8591734727984365156L

  • Serialized Fields

    • autoSuggestProvider

      AutoSuggestProvider autoSuggestProvider

    • busy

      Font busy

    • defaultText

      String defaultText

    • dialog

      JDialog dialog

    • lastWord

      String lastWord

      last word that was entered by user

    • list

      JList list

    • location

      Point location

    • matcher

      org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest.SuggestionFetcher matcher

    • regular

      Font regular

    • suggestions

      Vector<String> suggestions

Package org.biojava.nbio.structure.align.gui.jmol

• Class org.biojava.nbio.structure.align.gui.jmol.JmolPanel

  class JmolPanel extends JPrintPanel implements Serializable

  serialVersionUID:

  -3661941083797644242L

  • Serialized Fields

    • adapter

      org.jmol.api.JmolAdapter adapter

    • currentSize

      Dimension currentSize

    • rectClip

      Rectangle rectClip

    • statusListener

      org.jmol.api.JmolStatusListener statusListener

    • structure

      Structure structure

    • viewer

      org.jmol.api.JmolViewer viewer

Package org.biojava.nbio.structure.align.helper

• Class org.biojava.nbio.structure.align.helper.AligMatEl

  class AligMatEl extends IndexPair implements Serializable

  serialVersionUID:

  -4040926588803887471L

  • Serialized Fields

    • contig

      int contig

    • value

      int value

• Class org.biojava.nbio.structure.align.helper.IndexPair

  class IndexPair extends Object implements Serializable

  serialVersionUID:

  1832393751152650420L

  • Serialized Fields

    • col

      short col

    • row

      short row

Package org.biojava.nbio.structure.align.model

• Class org.biojava.nbio.structure.align.model.AFP

  class AFP extends Object implements Serializable

  serialVersionUID:

  3901209995477111829L

  • Serialized Fields

    • fragLen

      int fragLen

    • id

      long id

    • m

      Matrix m

    • p1

      int p1

    • p2

      int p2

    • rmsd

      double rmsd

    • score

      double score

    • t

      double[] t

• Class org.biojava.nbio.structure.align.model.AFPChain

  class AFPChain extends Object implements Serializable

  serialVersionUID:

  -4474029015606617947L

  • Serialized Fields

    • afpAftIndex

      int[][] afpAftIndex

    • afpBefIndex

      int[][] afpBefIndex

    • afpChainLen

      int afpChainLen

    • afpChainList

      int[] afpChainList

    • afpChainTwiBin

      double[] afpChainTwiBin

    • afpChainTwiList

      double[] afpChainTwiList

    • afpChainTwiNum

      int afpChainTwiNum

    • afpIndex

      int[][] afpIndex

    • afpSet

      List<AFP> afpSet

    • algorithmName

      String algorithmName

    • alignScore

      double alignScore

    • alignScoreUpdate

      double alignScoreUpdate

    • alnbeg1

      int alnbeg1

    • alnbeg2

      int alnbeg2

    • alnLength

      int alnLength

    • alnseq1

      char[] alnseq1

    • alnseq2

      char[] alnseq2

    • alnsymb

      char[] alnsymb

    • block2Afp

      int[] block2Afp

    • blockGap

      int[] blockGap

    • blockNum

      int blockNum

    • blockNumClu

      int blockNumClu

    • blockNumIni

      int blockNumIni

    • blockNumSpt

      int blockNumSpt

    • blockResList

      int[][][] blockResList

    • blockResSize

      int[] blockResSize

    • blockRmsd

      double[] blockRmsd

    • blockRotationMatrix

      Matrix[] blockRotationMatrix

    • blockScore

      double[] blockScore

    • blockShiftVector

      Atom[] blockShiftVector

    • blockSize

      int[] blockSize

    • ca1Length

      int ca1Length

    • ca2Length

      int ca2Length

    • calculationTime

      long calculationTime

    • chainLen

      int chainLen

    • chainRmsd

      double chainRmsd

    • conn

      Double conn

    • description2

      String description2

    • disTable1

      Matrix disTable1

    • disTable2

      Matrix disTable2

    • distanceMatrix

      Matrix distanceMatrix

    • dvar

      Double dvar

    • focusAfpList

      int[] focusAfpList

    • focusAfpn

      int focusAfpn

    • focusRes1

      int[] focusRes1

    • focusRes2

      int[] focusRes2

    • focusResn

      int focusResn

    • gapLen

      int gapLen

    • id

      long id

    • identity

      double identity

    • ioTime

      long ioTime

    • maxTra

      int maxTra

    • minLen

      int minLen

    • misLen

      int misLen

    • myResultsEQR

      int myResultsEQR

    • myResultsSimilarity1

      int myResultsSimilarity1

    • myResultsSimilarity2

      int myResultsSimilarity2

    • name1

      String name1

    • name2

      String name2

    • normAlignScore

      double normAlignScore

    • optAln

      int[][][] optAln

    • optLen

      int[] optLen

    • optLength

      int optLength

    • optRmsd

      double[] optRmsd

    • pdbAln

      String[][][] pdbAln

    • probability

      double probability

    • sequentialAlignment

      boolean sequentialAlignment

    • shortAlign

      boolean shortAlign

    • similarity

      double similarity

    • tmScore

      double tmScore

    • totalLenIni

      int totalLenIni

    • totalLenOpt

      int totalLenOpt

    • totalRmsdIni

      double totalRmsdIni

    • totalRmsdOpt

      double totalRmsdOpt

    • twi

      int[] twi

    • version

      String version

Package org.biojava.nbio.structure.align.multiple

• Class org.biojava.nbio.structure.align.multiple.BlockImpl

  class BlockImpl extends AbstractScoresCache implements Serializable

  serialVersionUID:

  -5804042669466177641L

  • Serialized Fields

    • alignRes

      List<List<Integer>> alignRes

    • alignResCounts

      List<Integer> alignResCounts

    • coreLength

      int coreLength

    • parent

      BlockSet parent

• Class org.biojava.nbio.structure.align.multiple.BlockSetImpl

  class BlockSetImpl extends AbstractScoresCache implements Serializable

  serialVersionUID:

  -1015791986000076089L

  • Serialized Fields

    • alignResCounts

      List<Integer> alignResCounts

    • blocks

      List<Block> blocks

    • coreLength

      int coreLength

    • length

      int length

    • parent

      MultipleAlignment parent

    • pose

      List<javax.vecmath.Matrix4d> pose

• Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

  class MultipleAlignmentEnsembleImpl extends AbstractScoresCache implements Serializable

  serialVersionUID:

  -5732485866623431898L

  • Serialized Fields

    • algorithmName

      String algorithmName

    • atomArrays

      List<Atom[]> atomArrays

    • calculationTime

      Long calculationTime

    • distanceMatrix

      List<Matrix> distanceMatrix

    • ioTime

      Long ioTime

    • multipleAlignments

      List<MultipleAlignment> multipleAlignments

    • structureIdentifiers

      List<StructureIdentifier> structureIdentifiers

    • version

      String version

• Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

  class MultipleAlignmentImpl extends AbstractScoresCache implements Serializable

  serialVersionUID:

  3432043794125805139L

  • Serialized Fields

    • alignResCounts

      List<Integer> alignResCounts

    • blockSets

      List<BlockSet> blockSets

    • coreLength

      int coreLength

    • coverages

      List<Double> coverages

    • length

      int length

    • parent

      MultipleAlignmentEnsemble parent

Package org.biojava.nbio.structure.align.pairwise

• Class org.biojava.nbio.structure.align.pairwise.AlignmentResult

  class AlignmentResult extends Object implements Serializable

  serialVersionUID:

  -4132105905712445473L

  • Serialized Fields

    • alignments

      AlternativeAlignment[] alignments

    • calculationTime

      long calculationTime

    • chain1

      String chain1

    • chain2

      String chain2

    • ioTime

      long ioTime

    • length1

      int length1

    • length2

      int length2

    • pdb1

      String pdb1

    • pdb2

      String pdb2

• Class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

  class AlternativeAlignment extends Object implements Serializable

  serialVersionUID:

  -6226717654562221241L

  • Serialized Fields

    • aligpath

      IndexPair[] aligpath

    • center

      Atom center

    • cluster

      int cluster

    • currentRotMatrix

      Matrix currentRotMatrix

    • currentTranMatrix

      Atom currentTranMatrix

    • distanceMatrix

      Matrix distanceMatrix

    • eqr0

      int eqr0

    • fromia

      int fromia

    • gaps0

      int gaps0

    • idx1

      int[] idx1

    • idx2

      int[] idx2

    • joined

      int joined

    • nfrags

      int nfrags

    • pdbresnum1

      String[] pdbresnum1

    • pdbresnum2

      String[] pdbresnum2

    • percId

      int percId

    • rms

      double rms

    • rms0

      int rms0

    • rot

      Matrix rot

    • score

      float score

    • tr

      Atom tr

Package org.biojava.nbio.structure.align.util

• Exception org.biojava.nbio.structure.align.util.ConfigurationException

  class ConfigurationException extends Exception implements Serializable

  serialVersionUID:

  -8047100079715000276L

Package org.biojava.nbio.structure.asa

• Class org.biojava.nbio.structure.asa.GroupAsa

  class GroupAsa extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • asaC

      double asaC

      ASA of complexed residue

    • asaU

      double asaU

      ASA of uncomplexed residue

    • atomAsaCs

      List<Double> atomAsaCs

      The individual atoms complexed ASAs

    • atomAsaUs

      List<Double> atomAsaUs

      The individual atoms uncomplexed ASAs

    • g

      Group g

Package org.biojava.nbio.structure.cath

• Class org.biojava.nbio.structure.cath.CathDomain

  class CathDomain extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • architectureId

      Integer architectureId

      The architecture number of this domain.

    • classId

      Integer classId

      The class number of this domain.

    • comment

      String comment

      A (potentially long) comment. Usually empty.

    • date

      Date date

    • domainCounter

      Integer domainCounter

      The count of this domain among the identical sequence family members.

    • domainName

      String domainName

      The CATH domain code. Always 7 characters in length, combining the PDB and chain letter with the number of the domain within CATH. Example: 1aoiA00 If the chain letter '0', domain refers to an entire PDB entry.

    • format

      String format

      The format and version of the CathDomainDescriptionFile.

    • homologyId

      Integer homologyId

      The homologous superfamily number of this domain.

    • identicalSequenceFamilyId

      Integer identicalSequenceFamilyId

      The identical sequence family (100% identity) number of this domain.

    • length

      Integer length

      The domain length..

    • likeSequenceFamilyId

      Integer likeSequenceFamilyId

      The "Like" sequence family (95% identity) number of this domain.

    • name

      String name

      The so-called name field holds a potentially long description of the domain.

    • orthologousSequenceFamilyId

      Integer orthologousSequenceFamilyId

      The "orthologous" sequence family (60% identity) number of this domain.

    • resolution

      Double resolution

      The resolution of the domain structure. Nominally in Angstroms, the values 999.000 and 1000.000 signify NMR structures and obsolete structures, respectively.

    • segments

      List<CathSegment> segments

      List of all sub-domain segments.

    • sequence

      String sequence

      FASTA sequence.

    • sequenceFamilyId

      Integer sequenceFamilyId

      The sequence family (35% identity) number of this domain.

    • sequenceHeader

      String sequenceHeader

      FASTA header.

    • source

      String source

      Complete source organism listing.

    • topologyId

      Integer topologyId

      The topology number of this domain.

    • version

      String version

      The CATH version.

• Class org.biojava.nbio.structure.cath.CathFragment

  class CathFragment extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • fragmentId

      Integer fragmentId

      The number of this segment within the domain.

    • length

      Integer length

      Number of residues in the segment. This value is parsed, not calculated.

    • start

      String start

      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).

    • stop

      String stop

      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).

• Class org.biojava.nbio.structure.cath.CathNode

  class CathNode extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • category

      CathCategory category

      This node's level within the hierarchy. One of CATH, not CATHSOLID.

    • description

      String description

      A name or description.

    • nodeId

      String nodeId

      The CATH code of the node, e.g. "1.10.8.10".

    • parentId

      String parentId

      The CATH code of the parent, e.g. "1.10.8". Calculated during parsing.

    • representative

      String representative

      The representative domain for this node.

• Class org.biojava.nbio.structure.cath.CathSegment

  class CathSegment extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • length

      Integer length

      Number of residues in the segment. This value is parsed, not calculated.

    • segmentId

      Integer segmentId

      The number of this segment within the domain.

    • sequence

      String sequence

      FASTA sequence.

    • sequenceHeader

      String sequenceHeader

      FASTA header.

    • start

      String start

      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).

    • stop

      String stop

      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).

Package org.biojava.nbio.structure.contact

• Class org.biojava.nbio.structure.contact.AtomContact

  class AtomContact extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • distance

      double distance

    • pair

      Pair<Atom> pair

• Class org.biojava.nbio.structure.contact.AtomContactSet

  class AtomContactSet extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • contacts

      HashMap<Pair<AtomIdentifier>,AtomContact> contacts

    • cutoff

      double cutoff

• Class org.biojava.nbio.structure.contact.AtomIdentifier

  class AtomIdentifier extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • chainId

      String chainId

    • pdbSerial

      int pdbSerial

• Class org.biojava.nbio.structure.contact.BoundingBox

  class BoundingBox extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • xmax

      double xmax

    • xmin

      double xmin

    • ymax

      double ymax

    • ymin

      double ymin

    • zmax

      double zmax

    • zmin

      double zmin

• Class org.biojava.nbio.structure.contact.GroupContact

  class GroupContact extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • atomContacts

      List<AtomContact> atomContacts

    • pair

      Pair<Group> pair

• Class org.biojava.nbio.structure.contact.GroupContactSet

  class GroupContactSet extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • contacts

      HashMap<Pair<org.biojava.nbio.structure.contact.ResidueIdentifier>,GroupContact> contacts

• Class org.biojava.nbio.structure.contact.Pair

  class Pair extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • first

      T first

    • second

      T second

• Class org.biojava.nbio.structure.contact.StructureInterface

  class StructureInterface extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • cluster

      StructureInterfaceCluster cluster

    • contacts

      AtomContactSet contacts

    • groupAsas1

      Map<ResidueNumber,GroupAsa> groupAsas1

    • groupAsas2

      Map<ResidueNumber,GroupAsa> groupAsas2

    • groupContacts

      GroupContactSet groupContacts

    • id

      int id

    • moleculeIds

      Pair<String> moleculeIds

      The identifier for each of the atom arrays (usually a chain identifier, i.e. a single capital letter) Serves to identify the molecules within the Asymmetric Unit of the crystal

    • molecules

      Pair<Atom[]> molecules

    • totalArea

      double totalArea

    • transforms

      Pair<CrystalTransform> transforms

      The transformations (crystal operators) applied to each molecule (if applicable)

• Class org.biojava.nbio.structure.contact.StructureInterfaceCluster

  class StructureInterfaceCluster extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • averageScore

      double averageScore

      The average similarity score between all pairs of members in the cluster.

    • id

      int id

    • members

      List<StructureInterface> members

• Class org.biojava.nbio.structure.contact.StructureInterfaceList

  class StructureInterfaceList extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • clusters

      List<StructureInterfaceCluster> clusters

    • list

      List<StructureInterface> list

Package org.biojava.nbio.structure.domain.pdp

• Class org.biojava.nbio.structure.domain.pdp.Domain

  class Domain extends Object implements Serializable

  serialVersionUID:

  -1293994033102271366L

  • Serialized Fields

    • id

      String id

    • nseg

      int nseg

    • score

      double score

    • segments

      List<Segment> segments

    • size

      int size

• Class org.biojava.nbio.structure.domain.pdp.Segment

  class Segment extends Object implements Serializable

  serialVersionUID:

  1393487067559539657L

  • Serialized Fields

    • from

      Integer from

    • score

      double score

    • to

      Integer to

Package org.biojava.nbio.structure.ecod

• Class org.biojava.nbio.structure.ecod.EcodDomain

  class EcodDomain extends Object implements Serializable

  serialVersionUID:

  -7760082165560332048L

  • Serialized Fields

    • architectureName

      String architectureName

    • assemblyId

      Long assemblyId

    • chainId

      String chainId

    • domainId

      String domainId

    • fGroup

      Integer fGroup

    • fGroupName

      String fGroupName

    • hGroup

      Integer hGroup

    • hGroupName

      String hGroupName

    • ligands

      Set<String> ligands

    • manual

      Boolean manual

    • pdbId

      String pdbId

    • range

      String range

    • seqIdRange

      String seqIdRange

    • tGroup

      Integer tGroup

    • tGroupName

      String tGroupName

    • uid

      Long uid

    • xGroup

      Integer xGroup

    • xGroupName

      String xGroupName

Package org.biojava.nbio.structure.gui

• Class org.biojava.nbio.structure.gui.JMatrixPanel

  class JMatrixPanel extends JPanel implements Serializable

  serialVersionUID:

  -1720879395453257846L

  • Serialized Fields

    • _bufImage

      BufferedImage _bufImage

    • aligs

      AlternativeAlignment[] aligs

    • cellColor

      ContinuousColorMapper cellColor

    • fragmentPairs

      FragmentPair[] fragmentPairs

    • matrix

      Matrix matrix

    • params

      StrucAligParameters params

    • scale

      float scale

    • selectedAlignmentPos

      int selectedAlignmentPos

• Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel

  class ScaleableMatrixPanel extends JPanel implements Serializable

  serialVersionUID:

  -8082261434322968652L

  • Serialized Fields

    • coloring

      JComboBox coloring

    • gradients

      Map<String,ContinuousColorMapper> gradients

    • mPanel

      JMatrixPanel mPanel

    • scroll

      JScrollPane scroll

    • slider

      JSlider slider

• Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer

  class GradientRenderer extends JPanel implements Serializable

  serialVersionUID:

  -2000575579184232365L

  • Serialized Fields

    • gradientContainer

      JPanel gradientContainer

    • max

      int max

    • min

      int min

    • title

      JLabel title

• Class org.biojava.nbio.structure.gui.SequenceDisplay

  class SequenceDisplay extends JPanel implements Serializable

  serialVersionUID:

  -1829252532712454236L

  • Serialized Fields

    • alig

      AlternativeAlignment alig

    • apos

      List<AlignedPosition> apos

    • idx1

      int[] idx1

    • idx2

      int[] idx2

    • label1

      JLabel label1

    • label2

      JLabel label2

    • mouseListener1

      SequenceMouseListener mouseListener1

    • mouseListener2

      SequenceMouseListener mouseListener2

    • panel1

      SequenceScalePanel panel1

    • panel2

      SequenceScalePanel panel2

    • percentageDisplay

      JLabel percentageDisplay

    • residueSizeSlider

      JSlider residueSizeSlider

    • scale

      float scale

    • structure1

      Structure structure1

    • structure2

      Structure structure2

    • structurePairAligner

      StructurePairAligner structurePairAligner

• Class org.biojava.nbio.structure.gui.WrapLayout

  class WrapLayout extends FlowLayout implements Serializable

  • Serialized Fields

    • preferredLayoutSize

      Dimension preferredLayoutSize

Package org.biojava.nbio.structure.gui.util

• Class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame

  class AlternativeAlignmentFrame extends JFrame implements Serializable

  serialVersionUID:

  0L

  • Serialized Fields

    • aligs

      AlternativeAlignment[] aligs

    • panel

      JPanel panel

    • structure1

      Structure structure1

    • structure2

      Structure structure2

    • structurePairAligner

      StructurePairAligner structurePairAligner

• Class org.biojava.nbio.structure.gui.util.PDBDirPanel

  class PDBDirPanel extends JPanel implements Serializable

  serialVersionUID:

  -5682120627824627408L

  • Serialized Fields

    • c1

      JTextField c1

    • c2

      JTextField c2

    • debug

      boolean debug

    • f1

      JTextField f1

    • f2

      JTextField f2

    • pdbDir

      JTextField pdbDir

• Class org.biojava.nbio.structure.gui.util.PDBServerPanel

  class PDBServerPanel extends JPanel implements Serializable

  serialVersionUID:

  -5682120627824627408L

  • Serialized Fields

    • c1

      JTextField c1

    • c2

      JTextField c2

    • debug

      boolean debug

    • f1

      JTextField f1

    • f2

      JTextField f2

    • pdbDir

      JTextField pdbDir

• Class org.biojava.nbio.structure.gui.util.PDBUploadPanel

  class PDBUploadPanel extends JPanel implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • chain1

      JTextField chain1

    • chain2

      JTextField chain2

    • filePath1

      JTextField filePath1

    • filePath2

      JTextField filePath2

    • fileType

      JComboBox fileType

• Class org.biojava.nbio.structure.gui.util.ScopSelectPanel

  class ScopSelectPanel extends JPanel implements Serializable

  serialVersionUID:

  757947454156959178L

  • Serialized Fields

    • dom1

      JAutoSuggest dom1

    • dom2

      JAutoSuggest dom2

• Class org.biojava.nbio.structure.gui.util.SelectMultiplePanel

  class SelectMultiplePanel extends JPanel implements Serializable

  serialVersionUID:

  757947454156959178L

  • Serialized Fields

    • input

      JTextField input

• Class org.biojava.nbio.structure.gui.util.SequenceScalePanel

  class SequenceScalePanel extends JPanel implements Serializable

  serialVersionUID:

  7893248902423L

  • Serialized Fields

    • apos

      List<AlignedPosition> apos

    • chain

      Chain chain

    • chainLength

      int chainLength

    • coordManager

      CoordManager coordManager

    • position

      int position

    • scale

      float scale

    • seqArr

      Character[] seqArr

Package org.biojava.nbio.structure.gui.util.color

• Class org.biojava.nbio.structure.gui.util.color.GradientPanel

  class GradientPanel extends JPanel implements Serializable

  serialVersionUID:

  -6387922432121206731L

  • Serialized Fields

    • mapper

      ContinuousColorMapper mapper

    • max

      double max

    • min

      double min

• Class org.biojava.nbio.structure.gui.util.color.HSVColorSpace

  class HSVColorSpace extends ColorSpace implements Serializable

  serialVersionUID:

  8324413992279510075L

Package org.biojava.nbio.structure.io

• Class org.biojava.nbio.structure.io.FileParsingParameters

  class FileParsingParameters extends Object implements Serializable

  serialVersionUID:

  5878292315163939027L

  • Serialized Fields

    • alignSeqRes

      boolean alignSeqRes

      Flag to control if SEQRES and ATOM records should be aligned

    • atomCaThreshold

      int atomCaThreshold

    • createAtomBonds

      boolean createAtomBonds

      Should we create bonds between atoms when parsing a file?

    • createAtomCharges

      boolean createAtomCharges

      Should we create charges on atoms when parsing a file?

    • fullAtomNames

      String[] fullAtomNames

    • headerOnly

      boolean headerOnly

      Flag to parse header only

    • maxAtoms

      int maxAtoms

    • parseBioAssembly

      boolean parseBioAssembly

      Should we parse the biological assembly information from a file?

    • parseCAOnly

      boolean parseCAOnly

      Flag to control reading in only Calpha atoms - this is useful for parsing large structures like 1htq.

    • parseSecStruc

      boolean parseSecStruc

      Flag to detect if the secondary structure info should be read

    • updateRemediatedFiles

      boolean updateRemediatedFiles

      Update locally cached files to the latest version of remediated files

    • useInternalChainId

      boolean useInternalChainId

      Should we use internal (asym_id) or public facing (author) chain ids

• Exception org.biojava.nbio.structure.io.PDBParseException

  class PDBParseException extends Exception implements Serializable

  serialVersionUID:

  219047230178423923L

• Class org.biojava.nbio.structure.io.SSBondImpl

  class SSBondImpl extends Object implements Serializable

  serialVersionUID:

  -8663681100691188647L

  • Serialized Fields

    • chainID1

      String chainID1

    • chainID2

      String chainID2

    • insCode1

      String insCode1

    • insCode2

      String insCode2

    • resnum1

      String resnum1

    • resnum2

      String resnum2

    • serNum

      int serNum

Package org.biojava.nbio.structure.io.mmcif.model

• Class org.biojava.nbio.structure.io.mmcif.model.ChemComp

  class ChemComp extends Object implements Serializable

  serialVersionUID:

  -4736341142030215915L

  • Serialized Fields

    • atoms

      List<ChemCompAtom> atoms

    • bonds

      List<ChemCompBond> bonds

    • descriptors

      List<ChemCompDescriptor> descriptors

    • formula

      String formula

    • formula_weight

      String formula_weight

    • id

      String id

    • mon_nstd_flag

      String mon_nstd_flag

    • mon_nstd_parent_comp_id

      String mon_nstd_parent_comp_id

    • name

      String name

    • one_letter_code

      String one_letter_code

    • pdbx_ambiguous_flag

      String pdbx_ambiguous_flag

    • pdbx_formal_charge

      String pdbx_formal_charge

    • pdbx_ideal_coordinates_details

      String pdbx_ideal_coordinates_details

    • pdbx_ideal_coordinates_missing_flag

      String pdbx_ideal_coordinates_missing_flag

    • pdbx_initial_date

      String pdbx_initial_date

    • pdbx_model_coordinates_db_code

      String pdbx_model_coordinates_db_code

    • pdbx_model_coordinates_details

      String pdbx_model_coordinates_details

    • pdbx_model_coordinates_missing_flag

      String pdbx_model_coordinates_missing_flag

    • pdbx_modified_date

      String pdbx_modified_date

    • pdbx_processing_site

      String pdbx_processing_site

    • pdbx_release_status

      String pdbx_release_status

    • pdbx_replaced_by

      String pdbx_replaced_by

    • pdbx_replaces

      String pdbx_replaces

    • pdbx_subcomponent_list

      String pdbx_subcomponent_list

    • pdbx_synonyms

      String pdbx_synonyms

    • pdbx_type

      String pdbx_type

    • polymerType

      PolymerType polymerType

    • residueType

      ResidueType residueType

    • standard

      boolean standard

    • three_letter_code

      String three_letter_code

    • type

      String type

• Class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom

  class ChemCompAtom extends Object implements Serializable

  serialVersionUID:

  4070599340294758941L

  • Serialized Fields

    • alt_atom_id

      String alt_atom_id

    • atom_id

      String atom_id

    • charge

      String charge

    • comp_id

      String comp_id

    • model_Cartn_x

      String model_Cartn_x

    • model_Cartn_y

      String model_Cartn_y

    • model_Cartn_z

      String model_Cartn_z

    • pdbx_align

      String pdbx_align

    • pdbx_aromatic_flag

      String pdbx_aromatic_flag

    • pdbx_component_atom_id

      String pdbx_component_atom_id

    • pdbx_component_comp_id

      String pdbx_component_comp_id

    • pdbx_component_id

      String pdbx_component_id

    • pdbx_leaving_atom_flag

      String pdbx_leaving_atom_flag

    • pdbx_model_Cartn_x_ideal

      String pdbx_model_Cartn_x_ideal

    • pdbx_model_Cartn_y_ideal

      String pdbx_model_Cartn_y_ideal

    • pdbx_model_Cartn_z_ideal

      String pdbx_model_Cartn_z_ideal

    • pdbx_ordinal

      String pdbx_ordinal

    • pdbx_polymer_type

      String pdbx_polymer_type

    • pdbx_ref_id

      String pdbx_ref_id

    • pdbx_residue_numbering

      String pdbx_residue_numbering

    • pdbx_stereo_config

      String pdbx_stereo_config

    • type_symbol

      String type_symbol

• Class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond

  class ChemCompBond extends Object implements Serializable

  serialVersionUID:

  5905371029161975421L

  • Serialized Fields

    • atom_id_1

      String atom_id_1

    • atom_id_2

      String atom_id_2

    • comp_id

      String comp_id

    • pdbx_aromatic_flag

      String pdbx_aromatic_flag

    • pdbx_ordinal

      String pdbx_ordinal

    • pdbx_stereo_config

      String pdbx_stereo_config

    • value_order

      String value_order

• Class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor

  class ChemCompDescriptor extends Object implements Serializable

  serialVersionUID:

  1078685833800736278L

  • Serialized Fields

    • comp_id

      String comp_id

    • descriptor

      String descriptor

    • program

      String program

    • program_version

      String program_version

    • type

      String type

• Class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord

  class DatabasePdbrevRecord extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • details

      String details

    • rev_num

      String rev_num

    • type

      String type

• Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly

  class PdbxStructAssembly extends Object implements Serializable

  serialVersionUID:

  3104504686693887219L

  • Serialized Fields

    • details

      String details

    • id

      String id

    • method_details

      String method_details

    • oligomeric_count

      String oligomeric_count

    • oligomeric_details

      String oligomeric_details

• Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen

  class PdbxStructAssemblyGen extends Object implements Serializable

  serialVersionUID:

  6739568389242514332L

  • Serialized Fields

    • assembly_id

      String assembly_id

    • asym_id_list

      String asym_id_list

    • oper_expression

      String oper_expression

• Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList

  class PdbxStructOperList extends Object implements Serializable

  serialVersionUID:

  8933552854747969787L

  • Serialized Fields

    • id

      String id

    • matrix

      Matrix matrix

    • matrix11

      String matrix11

    • matrix12

      String matrix12

    • matrix13

      String matrix13

    • matrix21

      String matrix21

    • matrix22

      String matrix22

    • matrix23

      String matrix23

    • matrix31

      String matrix31

    • matrix32

      String matrix32

    • matrix33

      String matrix33

    • name

      String name

    • symmetry_operation

      String symmetry_operation

    • type

      String type

    • vector

      double[] vector

    • vector1

      String vector1

    • vector2

      String vector2

    • vector3

      String vector3

Package org.biojava.nbio.structure.io.sifts

• Class org.biojava.nbio.structure.io.sifts.SiftsEntity

  class SiftsEntity extends Object implements Serializable

  serialVersionUID:

  750353252427491487L

  • Serialized Fields

    • entityId

      String entityId

    • segments

      List<SiftsSegment> segments

    • type

      String type

• Class org.biojava.nbio.structure.io.sifts.SiftsResidue

  class SiftsResidue extends Object implements Serializable

  serialVersionUID:

  3425769737629800828L

  • Serialized Fields

    • chainId

      String chainId

    • naturalPos

      Integer naturalPos

    • notObserved

      Boolean notObserved

    • pdbId

      String pdbId

    • pdbResName

      String pdbResName

    • pdbResNum

      String pdbResNum

    • seqResName

      String seqResName

    • uniProtAccessionId

      String uniProtAccessionId

    • uniProtPos

      Integer uniProtPos

    • uniProtResName

      String uniProtResName

• Class org.biojava.nbio.structure.io.sifts.SiftsSegment

  class SiftsSegment extends Object implements Serializable

  serialVersionUID:

  -8005129863256307153L

  • Serialized Fields

    • end

      String end

    • residues

      List<SiftsResidue> residues

    • segId

      String segId

    • start

      String start

Package org.biojava.nbio.structure.jama

• Class org.biojava.nbio.structure.jama.CholeskyDecomposition

  class CholeskyDecomposition extends Object implements Serializable

  serialVersionUID:

  224348942390823L

  • Serialized Fields

    • isspd

      boolean isspd

      Symmetric and positive definite flag.
      is symmetric and positive definite flag.

    • L

      double[][] L

      Array for internal storage of decomposition.
      internal array storage.

    • n

      int n

      Row and column dimension (square matrix).
      matrix dimension.

• Class org.biojava.nbio.structure.jama.EigenvalueDecomposition

  class EigenvalueDecomposition extends Object implements Serializable

  serialVersionUID:

  3557806515310435894L

  • Serialized Fields

    • d

      double[] d

      Arrays for internal storage of eigenvalues.
      internal storage of eigenvalues.

    • e

      double[] e

      Arrays for internal storage of eigenvalues.
      internal storage of eigenvalues.

    • H

      double[][] H

      Array for internal storage of nonsymmetric Hessenberg form.
      internal storage of nonsymmetric Hessenberg form.

    • issymmetric

      boolean issymmetric

      Symmetry flag.
      internal symmetry flag.

    • n

      int n

      Row and column dimension (square matrix).
      matrix dimension.

    • ort

      double[] ort

      Working storage for nonsymmetric algorithm.
      working storage for nonsymmetric algorithm.

    • V

      double[][] V

      Array for internal storage of eigenvectors.
      internal storage of eigenvectors.

• Class org.biojava.nbio.structure.jama.LUDecomposition

  class LUDecomposition extends Object implements Serializable

  serialVersionUID:

  9271028462937843L

  • Serialized Fields

    • LU

      double[][] LU

      Array for internal storage of decomposition.
      internal array storage.

    • m

      int m

      Row and column dimensions, and pivot sign.
      column dimension.

    • n

      int n

      Row and column dimensions, and pivot sign.
      column dimension.

    • piv

      int[] piv

      Internal storage of pivot vector.
      pivot vector.

    • pivsign

      int pivsign

      Row and column dimensions, and pivot sign.
      column dimension.

• Class org.biojava.nbio.structure.jama.Matrix

  class Matrix extends Object implements Serializable

  serialVersionUID:

  8492558293015348719L

  • Serialized Fields

    • A

      double[][] A

      Array for internal storage of elements.
      internal array storage.

    • m

      int m

      Row and column dimensions.
      row dimension.

    • n

      int n

      Row and column dimensions.
      row dimension.

• Class org.biojava.nbio.structure.jama.QRDecomposition

  class QRDecomposition extends Object implements Serializable

  serialVersionUID:

  10293720387423L

  • Serialized Fields

    • m

      int m

      Row and column dimensions.
      column dimension.

    • n

      int n

      Row and column dimensions.
      column dimension.

    • QR

      double[][] QR

      Array for internal storage of decomposition.
      internal array storage.

    • Rdiag

      double[] Rdiag

      Array for internal storage of diagonal of R.
      diagonal of R.

• Class org.biojava.nbio.structure.jama.SingularValueDecomposition

  class SingularValueDecomposition extends Object implements Serializable

  serialVersionUID:

  640239472093534756L

  • Serialized Fields

    • m

      int m

      Row and column dimensions.
      row dimension.

    • n

      int n

      Row and column dimensions.
      row dimension.

    • s

      double[] s

      Array for internal storage of singular values.
      internal storage of singular values.

    • U

      double[][] U

      Arrays for internal storage of U and V.
      internal storage of U.

    • V

      double[][] V

      Arrays for internal storage of U and V.
      internal storage of U.

Package org.biojava.nbio.structure.math

• Class org.biojava.nbio.structure.math.SparseSquareMatrix

  class SparseSquareMatrix extends Object implements Serializable

  serialVersionUID:

  -5217767192992868955L

  • Serialized Fields

    • N

      int N

    • rows

      SparseVector[] rows

• Class org.biojava.nbio.structure.math.SparseVector

  class SparseVector extends Object implements Serializable

  serialVersionUID:

  1174668523213431927L

  • Serialized Fields

    • N

      int N

    • symbolTable

      SymbolTable<Integer,Double> symbolTable

• Class org.biojava.nbio.structure.math.SymbolTable

  class SymbolTable extends Object implements Serializable

  serialVersionUID:

  -4417561575046471931L

  • Serialized Fields

    • st

      TreeMap<Key extends Comparable<Key>,Value> st

Package org.biojava.nbio.structure.quaternary

• Class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

  class BioAssemblyInfo extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • id

      int id

    • macromolecularSize

      int macromolecularSize

    • transforms

      List<BiologicalAssemblyTransformation> transforms

• Class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

  class BiologicalAssemblyTransformation extends Object implements Serializable

  serialVersionUID:

  -6388503076022480391L

  • Serialized Fields

    • chainId

      String chainId

    • id

      String id

    • transformation

      javax.vecmath.Matrix4d transformation

Package org.biojava.nbio.structure.scop

• Class org.biojava.nbio.structure.scop.ScopDescription

  class ScopDescription extends Object implements Serializable

  serialVersionUID:

  8579808155176839161L

  • Serialized Fields

    • category

      ScopCategory category

    • classificationId

      String classificationId

    • description

      String description

    • name

      String name

    • sunID

      int sunID

• Class org.biojava.nbio.structure.scop.ScopDomain

  class ScopDomain extends Object implements Serializable

  serialVersionUID:

  5890476209571654301L

  • Serialized Fields

    • classId

      int classId

    • classificationId

      String classificationId

    • domainId

      int domainId

    • familyId

      int familyId

    • foldId

      int foldId

    • pdbId

      String pdbId

    • px

      int px

    • ranges

      List<String> ranges

    • scopId

      String scopId

    • speciesId

      int speciesId

    • sunid

      Integer sunid

    • superfamilyId

      int superfamilyId

• Exception org.biojava.nbio.structure.scop.ScopIOException

  class ScopIOException extends RuntimeException implements Serializable

  serialVersionUID:

  1L

• Class org.biojava.nbio.structure.scop.ScopNode

  class ScopNode extends Object implements Serializable

  serialVersionUID:

  1187083944488580995L

  • Serialized Fields

    • children

      List<Integer> children

    • parentSunid

      int parentSunid

    • sunid

      int sunid

Package org.biojava.nbio.structure.scop.server

• Class org.biojava.nbio.structure.scop.server.ListStringWrapper

  class ListStringWrapper extends Object implements Serializable

  serialVersionUID:

  4193799052494327416L

  • Serialized Fields

    • data

      List<String> data

• Class org.biojava.nbio.structure.scop.server.ScopDescriptions

  class ScopDescriptions extends Object implements Serializable

  serialVersionUID:

  4924350548761431852L

  • Serialized Fields

    • scopDescriptions

      List<ScopDescription> scopDescriptions

• Class org.biojava.nbio.structure.scop.server.ScopDomains

  class ScopDomains extends Object implements Serializable

  serialVersionUID:

  7693404355005856746L

  • Serialized Fields

    • domains

      List<ScopDomain> domains

• Class org.biojava.nbio.structure.scop.server.ScopNodes

  class ScopNodes extends Object implements Serializable

  serialVersionUID:

  5327454882500340305L

  • Serialized Fields

    • scopNodes

      List<ScopNode> scopNodes

• Class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper

  class TreeSetStringWrapper extends Object implements Serializable

  serialVersionUID:

  4193799052494327416L

  • Serialized Fields

    • data

      TreeSet<String> data

Package org.biojava.nbio.structure.symmetry.core

• Class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

  class QuatSymmetryParameters extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • absoluteMinimumSequenceLength

      int absoluteMinimumSequenceLength

    • alignmentFractionThreshold

      double alignmentFractionThreshold

    • angleThreshold

      double angleThreshold

    • helixRmsdThreshold

      double helixRmsdThreshold

    • helixRmsdToRiseRatio

      double helixRmsdToRiseRatio

    • localSymmetry

      boolean localSymmetry

    • localTimeLimit

      double localTimeLimit

    • maximumLocalCombinations

      int maximumLocalCombinations

    • maximumLocalResults

      int maximumLocalResults

    • maximumLocalSubunits

      int maximumLocalSubunits

    • minimumHelixAngle

      double minimumHelixAngle

    • minimumHelixRise

      double minimumHelixRise

    • minimumSequenceLength

      int minimumSequenceLength

    • minimumSequenceLengthFraction

      double minimumSequenceLengthFraction

    • onTheFly

      boolean onTheFly

    • rmsdThreshold

      double rmsdThreshold

    • sequenceIdentityThresholds

      double[] sequenceIdentityThresholds

    • sequencePseudoSymmetryThreshold

      double sequencePseudoSymmetryThreshold

    • verbose

      boolean verbose

Package org.biojava.nbio.structure.symmetry.gui

• Class org.biojava.nbio.structure.symmetry.gui.SymmetryGui

  class SymmetryGui extends JFrame implements Serializable

  serialVersionUID:

  0L

  • Serialized Fields

    • abortB

      JButton abortB

    • alicalc

      AlignmentCalculationRunnable alicalc

    • masterPane

      JTabbedPane masterPane

    • params

      CESymmParameters params

    • progress

      JProgressBar progress

    • tab1

      SelectPDBPanel tab1

    • tab2

      PDBUploadPanel tab2

    • tab3

      ScopSelectPanel tab3

    • tabPane

      JTabbedPane tabPane

    • thread

      Thread thread

Package org.biojava.nbio.structure.symmetry.internal

• Exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

  class RefinerFailedException extends Exception implements Serializable

  serialVersionUID:

  -3592155787060329421L

Package org.biojava.nbio.structure.symmetry.utils

• Class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

  class BlastClustReader extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • clusters

      List<List<String>> clusters

    • sequenceIdentity

      int sequenceIdentity

Package org.biojava.nbio.structure.validation

• Class org.biojava.nbio.structure.validation.WwPDBValidationInformation

  class WwPDBValidationInformation extends Object implements Serializable

  serialVersionUID:

  -996804963717482650L

  • Serialized Fields

    • entry

      Entry entry

    • modelledSubgroup

      List<ModelledSubgroup> modelledSubgroup

    • programs

      Programs programs

Package org.biojava.nbio.structure.xtal

• Class org.biojava.nbio.structure.xtal.CrystalCell

  class CrystalCell extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • a

      double a

    • alpha

      double alpha

    • alphaRad

      double alphaRad

    • b

      double b

    • beta

      double beta

    • betaRad

      double betaRad

    • c

      double c

    • gamma

      double gamma

    • gammaRad

      double gammaRad

    • M

      javax.vecmath.Matrix3d M

    • maxDimension

      double maxDimension

    • Minv

      javax.vecmath.Matrix3d Minv

    • Mtransp

      javax.vecmath.Matrix3d Mtransp

    • MtranspInv

      javax.vecmath.Matrix3d MtranspInv

    • volume

      double volume

• Class org.biojava.nbio.structure.xtal.CrystalTransform

  class CrystalTransform extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • crystalTranslation

      javax.vecmath.Point3i crystalTranslation

      The crystal translation (always integer)

    • matTransform

      javax.vecmath.Matrix4d matTransform

      The 4-dimensional matrix transformation in crystal basis. Note that the translational component of this matrix is not necessarily identical to crystalTranslation since some operators have fractional translations within the cell

    • sg

      SpaceGroup sg

      The space group to which this transform belongs

    • transformId

      int transformId

      The transform id corresponding to the SpaceGroup's transform indices. From 0 (identity) to m (m=number of symmetry operations of the space group) It is unique within the unit cell but equivalent units of different crystal unit cells will have same id

• Class org.biojava.nbio.structure.xtal.SpaceGroup

  class SpaceGroup extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • altShortSymbol

      String altShortSymbol

    • axisAngles

      javax.vecmath.AxisAngle4d[] axisAngles

    • axisTypes

      int[] axisTypes

    • bravLattice

      BravaisLattice bravLattice

    • cellTranslations

      javax.vecmath.Vector3d[] cellTranslations

    • id

      int id

    • multiplicity

      int multiplicity

    • primitiveMultiplicity

      int primitiveMultiplicity

    • shortSymbol

      String shortSymbol

    • transfAlgebraic

      List<String> transfAlgebraic

    • transformations

      List<javax.vecmath.Matrix4d> transformations

Package org.biojava.nbio.structure.xtal.io

• Class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

  class TreeMapSpaceGroupWrapper extends Object implements Serializable

  serialVersionUID:

  4193799052494327416L

  • Serialized Fields

    • data

      TreeMap<Integer,SpaceGroup> data

Package org.biojava.nbio.survival.data

• Class org.biojava.nbio.survival.data.CompactCharSequence

  class CompactCharSequence extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • data

      byte[] data

    • end

      int end

    • nullstring

      boolean nullstring

    • offset

      int offset

Package org.biojava.nbio.survival.kaplanmeier.figure

• Class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

  class ExpressionFigure extends JPanel implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • bottom

      int bottom

    • df

      DecimalFormat df

    • fileName

      String fileName

    • fm

      FontMetrics fm

    • kmfi

      KMFigureInfo kmfi

    • labelWidth

      int labelWidth

    • left

      int left

    • lineInfoList

      ArrayList<String> lineInfoList

    • maxTime

      Double maxTime

    • maxX

      Double maxX

    • maxY

      Double maxY

    • mean

      Double mean

    • minX

      Double minX

    • minY

      Double minY

    • right

      int right

    • siList

      ArrayList<SurvivalInfo> siList

    • title

      ArrayList<String> title

    • titleHeight

      int titleHeight

    • top

      int top

    • variable

      String variable

    • xAxisLabelHeight

      int xAxisLabelHeight

• Class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure

  class KaplanMeierFigure extends JPanel implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • adjustedPercentIncrement

      Double adjustedPercentIncrement

    • bottom

      int bottom

    • df

      DecimalFormat df

    • fileName

      String fileName

    • fm

      FontMetrics fm

    • kmfi

      KMFigureInfo kmfi

    • labelWidth

      int labelWidth

    • left

      int left

    • lineInfoList

      ArrayList<String> lineInfoList

    • maxPercentage

      double maxPercentage

    • maxTime

      double maxTime

    • minPercentage

      double minPercentage

    • minTime

      double minTime

    • right

      int right

    • sfi

      SurvFitInfo sfi

    • survivalData

      LinkedHashMap<String,ArrayList<CensorStatus>> survivalData

    • title

      ArrayList<String> title

    • titleHeight

      int titleHeight

    • top

      int top

    • xAxisLabelHeight

      int xAxisLabelHeight

    • xAxisTimeCoordinates

      ArrayList<Integer> xAxisTimeCoordinates

    • xAxisTimeValues

      ArrayList<Double> xAxisTimeValues

    • yaxisLabel

      int yaxisLabel

• Class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel

  class NumbersAtRiskPanel extends JPanel implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • kmf

      KaplanMeierFigure kmf

    • timePercentage

      Double timePercentage

Package org.biojava.nbio.ws.alignment

Package org.biojava.nbio.ws.alignment.qblast

• Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

  class NCBIQBlastAlignmentProperties extends Object implements Serializable

  serialVersionUID:

  7158270364392309841L

  • Serialized Fields

    • param

      Map<BlastAlignmentParameterEnum,String> param

• Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

  class NCBIQBlastOutputProperties extends Object implements Serializable

  serialVersionUID:

  -9202060390925345163L

  • Serialized Fields

    • param

      Map<BlastOutputParameterEnum,String> param

Package org.biojava.nbio.ws.hmmer

• Class org.biojava.nbio.ws.hmmer.HmmerDomain

  class HmmerDomain extends Object implements Serializable

  serialVersionUID:

  8004302800150892757L

  • Serialized Fields

    • aliLenth

      Integer aliLenth

    • evalue

      Float evalue

    • hmmAcc

      String hmmAcc

    • hmmDesc

      String hmmDesc

    • hmmFrom

      Integer hmmFrom

    • hmmName

      String hmmName

    • hmmTo

      Integer hmmTo

    • simCount

      Integer simCount

    • sqFrom

      Integer sqFrom

    • sqTo

      Integer sqTo

• Class org.biojava.nbio.ws.hmmer.HmmerResult

  class HmmerResult extends Object implements Serializable

  serialVersionUID:

  -6016026193090737943L

  • Serialized Fields

    • acc

      String acc

    • dcl

      Integer dcl

    • desc

      String desc

    • domains

      SortedSet<HmmerDomain> domains

    • evalue

      Float evalue

    • name

      String name

    • ndom

      Integer ndom

    • nreported

      Integer nreported

    • pvalue

      Double pvalue

    • score

      Float score

Package org.forester.analysis

• Exception org.forester.analysis.AncestralTaxonomyInferenceException

  class AncestralTaxonomyInferenceException extends Exception implements Serializable

  serialVersionUID:

  1L

Package org.forester.archaeopteryx

• Class org.forester.archaeopteryx.ArchaeopteryxA

  class ArchaeopteryxA extends JApplet implements Serializable

  serialVersionUID:

  2314899014580484146L

  • Serialized Fields

    • _mainframe_applet

      MainFrameApplet _mainframe_applet

    • _message_1

      String _message_1

    • _message_2

      String _message_2

    • _species_tree_url_str

      String _species_tree_url_str

    • _tree_url_str

      String _tree_url_str

• Class org.forester.archaeopteryx.ArchaeopteryxE

  class ArchaeopteryxE extends JApplet implements Serializable

  serialVersionUID:

  -1220055577935759443L

  • Serialized Fields

    • _abbreviate_scientific_names

      JCheckBoxMenuItem _abbreviate_scientific_names

    • _about_item

      JMenuItem _about_item

    • _analysis_menu

      JMenu _analysis_menu

    • _antialias_print_cbmi

      JCheckBoxMenuItem _antialias_print_cbmi

    • _aptx_ref_item

      JMenuItem _aptx_ref_item

    • _background_gradient_cbmi

      JCheckBoxMenuItem _background_gradient_cbmi

    • _choose_font_mi

      JMenuItem _choose_font_mi

    • _choose_minimal_confidence_mi

      JMenuItem _choose_minimal_confidence_mi

    • _choose_node_size_mi

      JMenuItem _choose_node_size_mi

    • _choose_pdf_width_mi

      JMenuItem _choose_pdf_width_mi

    • _circular_type_cbmi

      JCheckBoxMenuItem _circular_type_cbmi

    • _collapse_species_specific_subtrees

      JMenuItem _collapse_species_specific_subtrees

    • _color_by_taxonomic_group_cbmi

      JCheckBoxMenuItem _color_by_taxonomic_group_cbmi

    • _color_labels_same_as_parent_branch

      JCheckBoxMenuItem _color_labels_same_as_parent_branch

    • _confcolor_item

      JMenuItem _confcolor_item

    • _configuration

      Configuration _configuration

    • _convex_type_cbmi

      JCheckBoxMenuItem _convex_type_cbmi

    • _current_dir

      File _current_dir

    • _curved_type_cbmi

      JCheckBoxMenuItem _curved_type_cbmi

    • _cycle_node_fill_mi

      JMenuItem _cycle_node_fill_mi

    • _cycle_node_shape_mi

      JMenuItem _cycle_node_shape_mi

    • _display_basic_information_item

      JMenuItem _display_basic_information_item

    • _euro_type_cbmi

      JCheckBoxMenuItem _euro_type_cbmi

    • _ext_node_dependent_cladogram_rbmi

      JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

    • _file_jmenu

      JMenu _file_jmenu

    • _font_size_menu

      JMenu _font_size_menu

    • _graphics_export_using_actual_size_cbmi

      JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi

    • _graphics_export_visible_only_cbmi

      JCheckBoxMenuItem _graphics_export_visible_only_cbmi

    • _gsdi_item

      JMenuItem _gsdi_item

    • _gsdir_item

      JMenuItem _gsdir_item

    • _help_item

      JMenuItem _help_item

    • _help_jmenu

      JMenu _help_jmenu

    • _inverse_search_result_cbmi

      JCheckBoxMenuItem _inverse_search_result_cbmi

    • _jmenubar

      JMenuBar _jmenubar

    • _label_direction_cbmi

      JCheckBoxMenuItem _label_direction_cbmi

    • _large_fonts_mi

      JMenuItem _large_fonts_mi

    • _line_up_renderable_data_cbmi

      JCheckBoxMenuItem _line_up_renderable_data_cbmi

    • _mainpanel

      MainPanel _mainpanel

    • _medium_fonts_mi

      JMenuItem _medium_fonts_mi

    • _midpoint_root_item

      JMenuItem _midpoint_root_item

    • _non_lined_up_cladograms_rbmi

      JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

    • _options

      Options _options

    • _options_jmenu

      JMenu _options_jmenu

    • _overview_placment_mi

      JMenuItem _overview_placment_mi

    • _phyloxml_ref_item

      JMenuItem _phyloxml_ref_item

    • _phyloxml_website_item

      JMenuItem _phyloxml_website_item

    • _print_black_and_white_cbmi

      JCheckBoxMenuItem _print_black_and_white_cbmi

    • _print_item

      JMenuItem _print_item

    • _print_size_mi

      JMenuItem _print_size_mi

    • _print_using_actual_size_cbmi

      JCheckBoxMenuItem _print_using_actual_size_cbmi

    • _radio_group_1

      ButtonGroup _radio_group_1

    • _rectangular_type_cbmi

      JCheckBoxMenuItem _rectangular_type_cbmi

    • _remove_branch_color_item

      JMenuItem _remove_branch_color_item

    • _remove_visual_styles_item

      JMenuItem _remove_visual_styles_item

    • _right_line_up_domains_cbmi

      JCheckBoxMenuItem _right_line_up_domains_cbmi

    • _rounded_type_cbmi

      JCheckBoxMenuItem _rounded_type_cbmi

    • _save_filechooser

      JFileChooser _save_filechooser

    • _save_item

      JMenuItem _save_item

    • _screen_antialias_cbmi

      JCheckBoxMenuItem _screen_antialias_cbmi

    • _search_case_senstive_cbmi

      JCheckBoxMenuItem _search_case_senstive_cbmi

    • _search_whole_words_only_cbmi

      JCheckBoxMenuItem _search_whole_words_only_cbmi

    • _search_with_regex_cbmi

      JCheckBoxMenuItem _search_with_regex_cbmi

    • _show_annotation_ref_source

      JCheckBoxMenuItem _show_annotation_ref_source

    • _show_confidence_stddev_cbmi

      JCheckBoxMenuItem _show_confidence_stddev_cbmi

    • _show_default_node_shapes_external_cbmi

      JCheckBoxMenuItem _show_default_node_shapes_external_cbmi

    • _show_default_node_shapes_for_marked_cbmi

      JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi

    • _show_default_node_shapes_internal_cbmi

      JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi

    • _show_domain_labels

      JCheckBoxMenuItem _show_domain_labels

    • _show_overview_cbmi

      JCheckBoxMenuItem _show_overview_cbmi

    • _show_scale_cbmi

      JCheckBoxMenuItem _show_scale_cbmi

    • _small_fonts_mi

      JMenuItem _small_fonts_mi

    • _species_tree

      Phylogeny _species_tree

    • _super_tiny_fonts_mi

      JMenuItem _super_tiny_fonts_mi

    • _switch_colors_mi

      JMenuItem _switch_colors_mi

    • _taxcolor_item

      JMenuItem _taxcolor_item

    • _textframes

      LinkedList<org.forester.archaeopteryx.TextFrame> _textframes

    • _tiny_fonts_mi

      JMenuItem _tiny_fonts_mi

    • _tools_menu

      JMenu _tools_menu

    • _triangular_type_cbmi

      JCheckBoxMenuItem _triangular_type_cbmi

    • _type_menu

      JMenu _type_menu

    • _uniform_cladograms_rbmi

      JRadioButtonMenuItem _uniform_cladograms_rbmi

    • _unrooted_type_cbmi

      JCheckBoxMenuItem _unrooted_type_cbmi

    • _view_as_nexus_item

      JMenuItem _view_as_nexus_item

    • _view_as_NH_item

      JMenuItem _view_as_NH_item

    • _view_as_XML_item

      JMenuItem _view_as_XML_item

    • _view_jmenu

      JMenu _view_jmenu

    • _website_item

      JMenuItem _website_item

    • _write_to_bmp_item

      JMenuItem _write_to_bmp_item

    • _write_to_gif_item

      JMenuItem _write_to_gif_item

    • _write_to_jpg_item

      JMenuItem _write_to_jpg_item

    • _write_to_pdf_item

      JMenuItem _write_to_pdf_item

    • _write_to_png_item

      JMenuItem _write_to_png_item

    • _write_to_tif_item

      JMenuItem _write_to_tif_item

    • _writetographics_filechooser

      JFileChooser _writetographics_filechooser

    • _writetopdf_filechooser

      JFileChooser _writetopdf_filechooser

• Class org.forester.archaeopteryx.FontChooser

  class FontChooser extends JDialog implements Serializable

  serialVersionUID:

  62256323L

  • Serialized Fields

    • _cancel_button

      JButton _cancel_button

    • _font

      Font _font

    • _font_jsp

      JScrollPane _font_jsp

    • _font_list

      JList<String> _font_list

    • _fonts_label

      JLabel _fonts_label

    • _fonts_tf

      JTextField _fonts_tf

    • _ok_button

      JButton _ok_button

    • _option

      int _option

    • _size

      int _size

    • _size_jsp

      JScrollPane _size_jsp

    • _size_label

      JLabel _size_label

    • _size_list

      JList<String> _size_list

    • _size_tf

      JTextField _size_tf

    • _style

      int _style

    • _style_jsp

      JScrollPane _style_jsp

    • _style_label

      JLabel _style_label

    • _style_list

      JList<String> _style_list

    • _style_tf

      JTextField _style_tf

    • _test_tf

      JTextField _test_tf

    • _type

      String _type

• Class org.forester.archaeopteryx.MainFrame

  class MainFrame extends JFrame implements Serializable

  serialVersionUID:

  3655000897845508358L

  • Serialized Fields

    • _abbreviate_scientific_names

      JCheckBoxMenuItem _abbreviate_scientific_names

    • _about_item

      JMenuItem _about_item

    • _allow_errors_in_distance_to_parent_cbmi

      JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi

    • _analysis_menu

      JMenu _analysis_menu

    • _annotate_item

      JMenuItem _annotate_item

    • _antialias_print_cbmi

      JCheckBoxMenuItem _antialias_print_cbmi

    • _aptx_ref_item

      JMenuItem _aptx_ref_item

    • _background_gradient_cbmi

      JCheckBoxMenuItem _background_gradient_cbmi

    • _choose_font_mi

      JMenuItem _choose_font_mi

    • _choose_minimal_confidence_mi

      JMenuItem _choose_minimal_confidence_mi

    • _choose_node_size_mi

      JMenuItem _choose_node_size_mi

    • _choose_pdf_width_mi

      JMenuItem _choose_pdf_width_mi

    • _circular_type_cbmi

      JCheckBoxMenuItem _circular_type_cbmi

    • _close_item

      JMenuItem _close_item

    • _collapse_species_specific_subtrees

      JMenuItem _collapse_species_specific_subtrees

    • _color_by_taxonomic_group_cbmi

      JCheckBoxMenuItem _color_by_taxonomic_group_cbmi

    • _color_labels_same_as_parent_branch

      JCheckBoxMenuItem _color_labels_same_as_parent_branch

    • _color_rank_jmi

      JMenuItem _color_rank_jmi

    • _confcolor_item

      JMenuItem _confcolor_item

    • _configuration

      Configuration _configuration

    • _contentpane

      Container _contentpane

    • _convex_type_cbmi

      JCheckBoxMenuItem _convex_type_cbmi

    • _current_dir

      File _current_dir

    • _curved_type_cbmi

      JCheckBoxMenuItem _curved_type_cbmi

    • _cycle_data_return

      JMenuItem _cycle_data_return

    • _cycle_node_fill_mi

      JMenuItem _cycle_node_fill_mi

    • _cycle_node_shape_mi

      JMenuItem _cycle_node_shape_mi

    • _delete_not_selected_nodes_item

      JMenuItem _delete_not_selected_nodes_item

    • _delete_selected_nodes_item

      JMenuItem _delete_selected_nodes_item

    • _display_basic_information_item

      JMenuItem _display_basic_information_item

    • _euro_type_cbmi

      JCheckBoxMenuItem _euro_type_cbmi

    • _exit_item

      JMenuItem _exit_item

    • _ext_node_dependent_cladogram_rbmi

      JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi

    • _extract_tax_code_from_node_names_jmi

      JMenuItem _extract_tax_code_from_node_names_jmi

    • _extract_taxonomy_agressive_rbmi

      JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi

    • _extract_taxonomy_no_rbmi

      JRadioButtonMenuItem _extract_taxonomy_no_rbmi

    • _extract_taxonomy_pfam_relaxed_rbmi

      JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi

    • _extract_taxonomy_pfam_strict_rbmi

      JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi

    • _file_jmenu

      JMenu _file_jmenu

    • _font_size_menu

      JMenu _font_size_menu

    • _graphics_export_using_actual_size_cbmi

      JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi

    • _graphics_export_visible_only_cbmi

      JCheckBoxMenuItem _graphics_export_visible_only_cbmi

    • _gsdi_item

      JMenuItem _gsdi_item

    • _gsdir_item

      JMenuItem _gsdir_item

    • _help_item

      JMenuItem _help_item

    • _help_jmenu

      JMenu _help_jmenu

    • _inference_manager

      InferenceManager _inference_manager

    • _internal_number_are_confidence_for_nh_parsing_cbmi

      JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi

    • _inverse_search_result_cbmi

      JCheckBoxMenuItem _inverse_search_result_cbmi

    • _jmenubar

      JMenuBar _jmenubar

    • _label_direction_cbmi

      JCheckBoxMenuItem _label_direction_cbmi

    • _large_fonts_item

      JMenuItem _large_fonts_item

    • _line_up_renderable_data_cbmi

      JCheckBoxMenuItem _line_up_renderable_data_cbmi

    • _lineage_inference

      JMenuItem _lineage_inference

    • _load_phylogeny_from_webservice_menu_items

      JMenuItem[] _load_phylogeny_from_webservice_menu_items

    • _load_species_tree_item

      JMenuItem _load_species_tree_item

    • _mainpanel

      MainPanel _mainpanel

    • _medium_fonts_item

      JMenuItem _medium_fonts_item

    • _midpoint_root_item

      JMenuItem _midpoint_root_item

    • _move_node_names_to_seq_names_jmi

      JMenuItem _move_node_names_to_seq_names_jmi

    • _move_node_names_to_tax_sn_jmi

      JMenuItem _move_node_names_to_tax_sn_jmi

    • _new_item

      JMenuItem _new_item

    • _non_lined_up_cladograms_rbmi

      JRadioButtonMenuItem _non_lined_up_cladograms_rbmi

    • _obtain_detailed_taxonomic_information_deleting_jmi

      JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi

    • _obtain_detailed_taxonomic_information_jmi

      JMenuItem _obtain_detailed_taxonomic_information_jmi

    • _obtain_seq_information_jmi

      JMenuItem _obtain_seq_information_jmi

    • _open_item

      JMenuItem _open_item

    • _open_url_item

      JMenuItem _open_url_item

    • _options

      Options _options

    • _options_jmenu

      JMenu _options_jmenu

    • _overview_placment_mi

      JMenuItem _overview_placment_mi

    • _phyloxml_ref_item

      JMenuItem _phyloxml_ref_item

    • _phyloxml_website_item

      JMenuItem _phyloxml_website_item

    • _previous_node_annotation_ref

      String _previous_node_annotation_ref

    • _print_black_and_white_cbmi

      JCheckBoxMenuItem _print_black_and_white_cbmi

    • _print_item

      JMenuItem _print_item

    • _print_size_mi

      JMenuItem _print_size_mi

    • _print_using_actual_size_cbmi

      JCheckBoxMenuItem _print_using_actual_size_cbmi

    • _process_menu

      JMenu _process_menu

    • _process_pool

      ProcessPool _process_pool

    • _rectangular_type_cbmi

      JCheckBoxMenuItem _rectangular_type_cbmi

    • _remove_branch_color_item

      JMenuItem _remove_branch_color_item

    • _remove_visual_styles_item

      JMenuItem _remove_visual_styles_item

    • _replace_underscores_cbmi

      JCheckBoxMenuItem _replace_underscores_cbmi

    • _right_line_up_domains_cbmi

      JCheckBoxMenuItem _right_line_up_domains_cbmi

    • _rounded_type_cbmi

      JCheckBoxMenuItem _rounded_type_cbmi

    • _save_all_item

      JMenuItem _save_all_item

    • _save_filechooser

      JFileChooser _save_filechooser

    • _save_item

      JMenuItem _save_item

    • _screen_antialias_cbmi

      JCheckBoxMenuItem _screen_antialias_cbmi

    • _search_case_senstive_cbmi

      JCheckBoxMenuItem _search_case_senstive_cbmi

    • _search_whole_words_only_cbmi

      JCheckBoxMenuItem _search_whole_words_only_cbmi

    • _search_with_regex_cbmi

      JCheckBoxMenuItem _search_with_regex_cbmi

    • _show_annotation_ref_source

      JCheckBoxMenuItem _show_annotation_ref_source

    • _show_confidence_stddev_cbmi

      JCheckBoxMenuItem _show_confidence_stddev_cbmi

    • _show_default_node_shapes_external_cbmi

      JCheckBoxMenuItem _show_default_node_shapes_external_cbmi

    • _show_default_node_shapes_for_marked_cbmi

      JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi

    • _show_default_node_shapes_internal_cbmi

      JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi

    • _show_domain_labels

      JCheckBoxMenuItem _show_domain_labels

    • _show_overview_cbmi

      JCheckBoxMenuItem _show_overview_cbmi

    • _show_scale_cbmi

      JCheckBoxMenuItem _show_scale_cbmi

    • _small_fonts_item

      JMenuItem _small_fonts_item

    • _species_tree

      Phylogeny _species_tree

    • _super_tiny_fonts_item

      JMenuItem _super_tiny_fonts_item

    • _switch_colors_mi

      JMenuItem _switch_colors_mi

    • _taxcolor_item

      JMenuItem _taxcolor_item

    • _textframes

      LinkedList<org.forester.archaeopteryx.TextFrame> _textframes

    • _tiny_fonts_item

      JMenuItem _tiny_fonts_item

    • _tools_menu

      JMenu _tools_menu

    • _triangular_type_cbmi

      JCheckBoxMenuItem _triangular_type_cbmi

    • _type_menu

      JMenu _type_menu

    • _uniform_cladograms_rbmi

      JRadioButtonMenuItem _uniform_cladograms_rbmi

    • _unrooted_type_cbmi

      JCheckBoxMenuItem _unrooted_type_cbmi

    • _use_brackets_for_conf_in_nh_export_cbmi

      JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi

    • _use_internal_names_for_conf_in_nh_export_cbmi

      JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi

    • _view_as_nexus_item

      JMenuItem _view_as_nexus_item

    • _view_as_NH_item

      JMenuItem _view_as_NH_item

    • _view_as_XML_item

      JMenuItem _view_as_XML_item

    • _view_jmenu

      JMenu _view_jmenu

    • _website_item

      JMenuItem _website_item

    • _write_to_bmp_item

      JMenuItem _write_to_bmp_item

    • _write_to_gif_item

      JMenuItem _write_to_gif_item

    • _write_to_jpg_item

      JMenuItem _write_to_jpg_item

    • _write_to_pdf_item

      JMenuItem _write_to_pdf_item

    • _write_to_png_item

      JMenuItem _write_to_png_item

    • _write_to_tif_item

      JMenuItem _write_to_tif_item

    • _writetographics_filechooser

      JFileChooser _writetographics_filechooser

    • _writetopdf_filechooser

      JFileChooser _writetopdf_filechooser

• Class org.forester.archaeopteryx.MainFrameApplet

  class MainFrameApplet extends MainFrame implements Serializable

  serialVersionUID:

  1941019292746717053L

  • Serialized Fields

    • _applet

      ArchaeopteryxA _applet

    • _radio_group_1

      ButtonGroup _radio_group_1

• Class org.forester.archaeopteryx.MainFrameApplication

  class MainFrameApplication extends MainFrame implements Serializable

  serialVersionUID:

  -799735726778865234L

  • Serialized Fields

    • _collapse_below_branch_length

      JMenuItem _collapse_below_branch_length

    • _collapse_below_threshold

      JMenuItem _collapse_below_threshold

    • _inference_from_msa_item

      JMenuItem _inference_from_msa_item

    • _inference_from_seqs_item

      JMenuItem _inference_from_seqs_item

    • _inference_menu

      JMenu _inference_menu

    • _min_not_collapse

      double _min_not_collapse

    • _min_not_collapse_bl

      double _min_not_collapse_bl

    • _msa

      Msa _msa

    • _msa_file

      File _msa_file

    • _msa_filechooser

      JFileChooser _msa_filechooser

    • _open_filechooser

      JFileChooser _open_filechooser

    • _open_filechooser_for_species_tree

      JFileChooser _open_filechooser_for_species_tree

    • _phylogenetic_inference_options

      PhylogeneticInferenceOptions _phylogenetic_inference_options

    • _radio_group_1

      ButtonGroup _radio_group_1

    • _radio_group_2

      ButtonGroup _radio_group_2

    • _read_seqs_jmi

      JMenuItem _read_seqs_jmi

    • _read_values_jmi

      JMenuItem _read_values_jmi

    • _seqs

      List<MolecularSequence> _seqs

    • _seqs_file

      File _seqs_file

    • _seqs_pi_filechooser

      JFileChooser _seqs_pi_filechooser

    • _sequences_filechooser

      JFileChooser _sequences_filechooser

    • _values_filechooser

      JFileChooser _values_filechooser

• Class org.forester.archaeopteryx.MainPanel

  class MainPanel extends JPanel implements Serializable

  serialVersionUID:

  -2682765312661416435L

  • Serialized Fields

    • _colorset

      TreeColorSet _colorset

    • _configuration

      Configuration _configuration

    • _control_panel

      org.forester.archaeopteryx.ControlPanel _control_panel

    • _copied_and_pasted_nodes

      Set<Long> _copied_and_pasted_nodes

    • _cut_or_copied_tree

      Phylogeny _cut_or_copied_tree

    • _fontset

      TreeFontSet _fontset

    • _image_map

      Hashtable<String,BufferedImage> _image_map

    • _mainframe

      MainFrame _mainframe

    • _tabbed_pane

      JTabbedPane _tabbed_pane

    • _treegraphic_scroll_pane_panels

      List<JPanel> _treegraphic_scroll_pane_panels

    • _treegraphic_scroll_panes

      List<JScrollPane> _treegraphic_scroll_panes

    • _treepanels

      List<TreePanel> _treepanels

• Class org.forester.archaeopteryx.TreePanel

  class TreePanel extends JPanel implements Serializable

  serialVersionUID:

  -978349745916505029L

  • Serialized Fields

    • _arc

      Arc2D _arc

    • _at

      AffineTransform _at

    • _circ_max_depth

      int _circ_max_depth

    • _collapsed_external_nodeid_set

      Set<Long> _collapsed_external_nodeid_set

    • _color_chooser

      JColorChooser _color_chooser

    • _configuration

      Configuration _configuration

    • _control_panel

      org.forester.archaeopteryx.ControlPanel _control_panel

    • _cubic_curve

      CubicCurve2D _cubic_curve

    • _current_external_nodes

      Set<Long> _current_external_nodes

    • _current_external_nodes_data_buffer

      StringBuilder _current_external_nodes_data_buffer

    • _current_external_nodes_data_buffer_change_counter

      int _current_external_nodes_data_buffer_change_counter

    • _domain_structure_e_value_thr_exp

      int _domain_structure_e_value_thr_exp

    • _domain_structure_width

      double _domain_structure_width

    • _dynamic_hiding_factor

      int _dynamic_hiding_factor

    • _edited

      boolean _edited

    • _ellipse

      Ellipse2D _ellipse

    • _ext_node_with_longest_txt_info

      PhylogenyNode _ext_node_with_longest_txt_info

    • _external_node_index

      int _external_node_index

    • _found_nodes_0

      Set<Long> _found_nodes_0

    • _found_nodes_1

      Set<Long> _found_nodes_1

    • _frc

      FontRenderContext _frc

    • _graphics_type

      Options.PHYLOGENY_GRAPHICS_TYPE _graphics_type

    • _highlight_node

      PhylogenyNode _highlight_node

    • _in_ov

      boolean _in_ov

    • _in_ov_rect

      boolean _in_ov_rect

    • _last_drag_point_x

      float _last_drag_point_x

    • _last_drag_point_y

      float _last_drag_point_y

    • _length_of_longest_text

      int _length_of_longest_text

    • _line

      Line2D _line

    • _longest_domain

      int _longest_domain

    • _longest_ext_node_info

      int _longest_ext_node_info

    • _main_panel

      MainPanel _main_panel

    • _max_distance_to_root

      double _max_distance_to_root

    • _node_desc_popup

      Popup _node_desc_popup

    • _node_frame_index

      int _node_frame_index

    • _node_frames

      org.forester.archaeopteryx.NodeFrame[] _node_frames

    • _node_popup_menu

      JPopupMenu _node_popup_menu

    • _node_popup_menu_items

      JMenuItem[] _node_popup_menu_items

    • _nodeid_dist_to_leaf

      HashMap<Long,Short> _nodeid_dist_to_leaf

    • _nodes_in_preorder

      PhylogenyNode[] _nodes_in_preorder

    • _options

      Options _options

    • _ov_max_height

      float _ov_max_height

    • _ov_max_width

      float _ov_max_width

    • _ov_on

      boolean _ov_on

    • _ov_rectangle

      Rectangle2D _ov_rectangle

    • _ov_virtual_rectangle

      Rectangle _ov_virtual_rectangle

    • _ov_x_correction_factor

      float _ov_x_correction_factor

    • _ov_x_distance

      float _ov_x_distance

    • _ov_x_position

      int _ov_x_position

    • _ov_y_distance

      float _ov_y_distance

    • _ov_y_position

      int _ov_y_position

    • _ov_y_start

      int _ov_y_start

    • _phy_has_branch_lengths

      boolean _phy_has_branch_lengths

    • _phylogeny

      Phylogeny _phylogeny

    • _polygon

      Path2D.Float _polygon

    • _popup_buffer

      StringBuffer _popup_buffer

    • _quad_curve

      QuadCurve2D _quad_curve

    • _query_sequence

      Sequence _query_sequence

    • _rectangle

      Rectangle2D _rectangle

    • _rendering_hints

      RenderingHints _rendering_hints

    • _rollover_popup

      JTextArea _rollover_popup

    • _root

      PhylogenyNode _root

    • _sb

      StringBuilder _sb

    • _scale_distance

      double _scale_distance

    • _scale_label

      String _scale_label

    • _statistics_for_vector_data

      DescriptiveStatistics _statistics_for_vector_data

    • _sub_phylogenies

      Phylogeny[] _sub_phylogenies

    • _sub_phylogenies_temp_roots

      PhylogenyNode[] _sub_phylogenies_temp_roots

    • _subtree_index

      int _subtree_index

    • _treefile

      File _treefile

    • _urt_factor

      float _urt_factor

    • _urt_factor_ov

      float _urt_factor_ov

    • _urt_nodeid_angle_map

      HashMap<Long,Double> _urt_nodeid_angle_map

    • _urt_nodeid_index_map

      HashMap<Long,Integer> _urt_nodeid_index_map

    • _urt_starting_angle

      double _urt_starting_angle

    • _x_correction_factor

      float _x_correction_factor

    • _x_distance

      float _x_distance

    • _y_distance

      float _y_distance