Class Hierarchy

java.lang.Object
- org.forester.applications.aa
- org.forester.applications.aaa
- org.biojava.nbio.core.alignment.matrices.AAindexFactory
- org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
- org.biojava.nbio.structure.align.gui.AboutDialog
- javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
  - org.biojava.nbio.structure.align.gui.ChooseDirAction
- org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol (implements java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener)
  - org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
  - org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
- org.biojava.nbio.ontology.utils.AbstractAnnotation (implements org.biojava.nbio.ontology.utils.Annotation, java.io.Serializable)
  - org.biojava.nbio.ontology.utils.SmallAnnotation
- org.biojava.nbio.structure.io.mmcif.model.AbstractBean
  - org.biojava.nbio.structure.io.mmcif.model.AtomSite
  - org.biojava.nbio.structure.io.mmcif.model.AtomSites
  - org.biojava.nbio.structure.io.mmcif.model.Cell
  - org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
  - org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
  - org.biojava.nbio.structure.io.mmcif.model.Exptl
  - org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
  - org.biojava.nbio.structure.io.mmcif.model.StructAsym
  - org.biojava.nbio.structure.io.mmcif.model.StructConn
  - org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
  - org.biojava.nbio.structure.io.mmcif.model.StructRef
  - org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
  - org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
  - org.biojava.nbio.structure.io.mmcif.model.Symmetry
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
  - java.util.AbstractList<E> (implements java.util.List<E>)
    - java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
      - org.biojava.nbio.genome.parsers.gff.FeatureList
- org.biojava.nbio.core.sequence.template.AbstractCompound (implements org.biojava.nbio.core.sequence.template.Compound)
  - org.biojava.nbio.core.sequence.compound.AminoAcidCompound (implements java.io.Serializable)
  - org.biojava.nbio.core.sequence.compound.CodonCompound
  - org.biojava.nbio.core.sequence.compound.NucleotideCompound (implements org.biojava.nbio.core.sequence.template.ComplementCompound)
- org.biojava.nbio.core.sequence.template.AbstractCompoundSet<C> (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>)
  - org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet<C>
    - org.biojava.nbio.core.sequence.compound.DNACompoundSet
      - org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
      - org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
    - org.biojava.nbio.core.sequence.compound.RNACompoundSet
      - org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
- org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator<F,T> (implements org.biojava.nbio.core.sequence.template.CompoundTranslator<F,T>)
  - org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
  - org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
- org.biojava.nbio.core.sequence.features.AbstractFeature<S,C> (implements org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>)
  - org.biojava.nbio.core.sequence.features.QualityFeature<S,C>
  - org.biojava.nbio.core.sequence.features.QuantityFeature<S,C>
  - org.biojava.nbio.core.sequence.features.TextFeature<S,C>
- org.biojava.nbio.core.sequence.location.template.AbstractLocation (implements org.biojava.nbio.core.sequence.location.template.Location, java.io.Serializable)
  - org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
  - org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
  - org.biojava.nbio.core.sequence.location.SimpleLocation
    - org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
    - org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
    - org.biojava.nbio.core.sequence.location.SequenceLocation<S,C>
- java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
  - org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap<K>
  - org.biojava.nbio.ontology.utils.SmallMap (implements java.io.Serializable)
  - org.biojava.nbio.core.util.SoftHashMap<K,V>
  - org.biojava.nbio.ontology.utils.WeakValueHashMap
- org.biojava.nbio.alignment.template.AbstractScorer (implements org.biojava.nbio.alignment.template.Scorer)
  - org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C> (implements org.biojava.nbio.alignment.template.MatrixAligner<S,C>)
    - org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C>)
      - org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>
        
        org.biojava.nbio.alignment.routines.GuanUberbacher<S,C>
        
        org.biojava.nbio.alignment.NeedlemanWunsch<S,C>
      - org.biojava.nbio.alignment.SmithWaterman<S,C>
    - org.biojava.nbio.alignment.template.AbstractProfileProfileAligner<S,C> (implements org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C>)
      - org.biojava.nbio.alignment.SimpleProfileProfileAligner<S,C>
  - org.biojava.nbio.alignment.FractionalIdentityScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
    - org.biojava.nbio.alignment.FractionalIdentityInProfileScorer<S,C> (implements org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>)
  - org.biojava.nbio.alignment.FractionalSimilarityScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
    - org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer<S,C> (implements org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>)
  - org.biojava.nbio.alignment.StandardRescoreRefiner<S,C> (implements org.biojava.nbio.alignment.template.RescoreRefiner<S,C>)
  - org.biojava.nbio.alignment.SubstitutionMatrixScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
- org.biojava.nbio.structure.align.multiple.AbstractScoresCache (implements org.biojava.nbio.structure.align.multiple.ScoresCache)
  - org.biojava.nbio.structure.align.multiple.BlockImpl (implements org.biojava.nbio.structure.align.multiple.Block, java.lang.Cloneable, java.io.Serializable)
  - org.biojava.nbio.structure.align.multiple.BlockSetImpl (implements org.biojava.nbio.structure.align.multiple.BlockSet, java.lang.Cloneable, java.io.Serializable)
  - org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble, java.io.Serializable)
  - org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.MultipleAlignment, java.io.Serializable)
- org.biojava.nbio.core.sequence.template.AbstractSequence<C> (implements org.biojava.nbio.core.sequence.template.Sequence<C>)
  - org.biojava.nbio.core.sequence.BasicSequence<C>
  - org.biojava.nbio.core.sequence.DNASequence
    - org.biojava.nbio.core.sequence.CDSSequence
    - org.biojava.nbio.core.sequence.ChromosomeSequence
    - org.biojava.nbio.core.sequence.ExonSequence
    - org.biojava.nbio.core.sequence.GeneSequence
    - org.biojava.nbio.core.sequence.IntronSequence
    - org.biojava.nbio.core.sequence.StartCodonSequence
    - org.biojava.nbio.core.sequence.StopCodonSequence
    - org.biojava.nbio.core.sequence.TranscriptSequence
  - org.biojava.nbio.core.sequence.ProteinSequence
  - org.biojava.nbio.core.sequence.RNASequence
- org.biojava.nbio.structure.align.AbstractStructureAlignment (implements org.biojava.nbio.structure.align.StructureAlignment)
  - org.biojava.nbio.structure.align.ce.CeMain (implements org.biojava.nbio.structure.align.StructureAlignment)
    - org.biojava.nbio.structure.align.ce.CeCPMain
    - org.biojava.nbio.structure.align.ce.CeSideChainMain (implements org.biojava.nbio.structure.align.StructureAlignment)
    - org.biojava.nbio.structure.align.ce.OptimalCECPMain
  - org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner (implements org.biojava.nbio.structure.align.StructureAlignment)
- org.biojava.nbio.ontology.AbstractTerm (implements org.biojava.nbio.ontology.Term)
  - org.biojava.nbio.ontology.RemoteTerm.Impl (implements org.biojava.nbio.ontology.RemoteTerm, java.io.Serializable)
  - org.biojava.nbio.ontology.Term.Impl (implements java.io.Serializable, org.biojava.nbio.ontology.Term)
    - org.biojava.nbio.ontology.Variable.Impl (implements org.biojava.nbio.ontology.Variable)
- org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor (implements org.biojava.nbio.structure.align.ce.UserArgumentProcessor)
  - org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
    - org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
    - org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
  - org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
  - org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
- org.forester.phylogeny.data.Accession (implements java.lang.Comparable<T>, org.forester.phylogeny.data.PhylogenyData)
- org.biojava.nbio.core.sequence.AccessionID
- org.forester.io.parsers.phyloxml.data.AccessionParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.align.model.AFP (implements java.io.Serializable)
- org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
- org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
- org.biojava.nbio.structure.align.model.AFPChain (implements java.lang.Cloneable, java.io.Serializable)
- org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
- org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
- org.biojava.nbio.structure.align.xml.AFPChainFlipper
- org.biojava.nbio.structure.align.util.AFPChainScorer
- org.biojava.nbio.structure.align.model.AfpChainWriter
- org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
- org.biojava.nbio.structure.align.xml.AFPChainXMLParser
- org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
- org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
- org.biojava.nbio.structure.align.AFPTwister
- org.biojava.nbio.survival.cox.stats.AgScore
- org.biojava.nbio.structure.gui.util.AlignedPosition
- org.biojava.nbio.alignment.routines.AlignerHelper
- org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
- org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.alignment.routines.AlignerHelper.Cut
- org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
- org.biojava.nbio.structure.align.gui.AlignmentCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
- org.biojava.nbio.structure.gui.util.AlignmentCalc (implements java.lang.Runnable)
- org.biojava.nbio.structure.align.gui.AlignmentCalcDB (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
- org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
- org.biojava.nbio.structure.align.pairwise.AlignmentResult (implements java.io.Serializable)
- org.biojava.nbio.alignment.Alignments
- org.biojava.nbio.structure.align.util.AlignmentTools
- org.biojava.nbio.structure.align.pairwise.AligNPE
- org.biojava.nbio.structure.align.helper.AlignTools
- org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
- org.biojava.nbio.structure.align.webstart.AligUIManager
- org.biojava.nbio.structure.io.mmcif.AllChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider, java.lang.Runnable)
- org.biojava.nbio.structure.align.pairwise.AltAligComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.structure.align.pairwise.AlternativeAlignment (implements java.io.Serializable)
- org.biojava.nbio.aaproperties.xml.AminoAcidComposition
- org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
- org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>, java.io.Serializable)
- org.forester.analysis.AncestralTaxonomyInference
- org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
- org.biojava.nbio.structure.validation.AngleOutlier
- org.forester.phylogeny.data.Annotation (implements java.lang.Comparable<T>, org.forester.phylogeny.data.MultipleUris, org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.AnnotationParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.forester.application.annotator
- org.biojava.nbio.genome.App
- org.biojava.nbio.ontology.App
- org.forester.archaeopteryx.AptxUtil
- org.forester.archaeopteryx.Archaeopteryx
- org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.SequenceReader<C>)
  - org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
- org.biojava.nbio.structure.asa.AsaCalculator
- org.forester.util.AsciiHistogram
- org.biojava.nbio.structure.domain.AssignmentXMLSerializer
- org.biojava.nbio.structure.scop.Astral
- org.biojava.nbio.structure.align.util.AtomCache
- org.biojava.nbio.structure.contact.AtomContact (implements java.io.Serializable)
- org.biojava.nbio.structure.contact.AtomContactSet (implements java.lang.Iterable<T>, java.io.Serializable)
- org.biojava.nbio.structure.contact.AtomIdentifier (implements java.io.Serializable)
- org.biojava.nbio.structure.AtomImpl (implements org.biojava.nbio.structure.Atom, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
- org.biojava.nbio.structure.align.gui.jmol.AtomInfo
- org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
- org.biojava.nbio.structure.AtomIterator (implements java.util.Iterator<E>)
- org.biojava.nbio.structure.AtomPositionMap
- org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
- org.biojava.nbio.structure.Author (implements java.io.Serializable)
- org.biojava.nbio.structure.symmetry.core.AxisAligner
  - org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
  - org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
- org.forester.surfacing.BasicBinaryDomainCombination (implements org.forester.protein.BinaryDomainCombination)
  - org.forester.surfacing.AdjactantDirectedBinaryDomainCombination
  - org.forester.surfacing.DirectedBinaryDomainCombination
- org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<S> (implements org.forester.evoinference.matrix.character.CharacterStateMatrix<S>)
- org.forester.surfacing.BasicCombinableDomains (implements org.forester.surfacing.CombinableDomains)
  - org.forester.surfacing.AdjactantDirectedCombinableDomains
  - org.forester.surfacing.DirectedCombinableDomains
- org.forester.util.BasicDescriptiveStatistics (implements org.forester.util.DescriptiveStatistics)
- org.forester.protein.BasicDomain (implements org.forester.protein.Domain)
- org.forester.surfacing.BasicDomainSimilarityCalculator (implements org.forester.surfacing.DomainSimilarityCalculator)
- org.forester.pccx.BasicExternalNodeBasedCoverageExtender (implements org.forester.pccx.CoverageExtender)
- org.forester.surfacing.BasicGenomeWideCombinableDomains (implements org.forester.surfacing.GenomeWideCombinableDomains)
- org.forester.go.BasicGoRelationship (implements org.forester.go.GoRelationship)
- org.forester.go.BasicGoSubset (implements org.forester.go.GoSubset)
- org.forester.go.BasicGoTerm (implements org.forester.go.GoTerm)
- org.forester.go.BasicGoXRef (implements org.forester.go.GoXRef)
- org.forester.msa.BasicMsa (implements org.forester.msa.Msa)
  - org.forester.msa.DeleteableMsa
  - org.forester.msa.ResampleableMsa
- org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient (implements org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient)
- org.forester.protein.BasicProtein (implements org.forester.protein.Protein)
- org.forester.sequence.BasicSequence (implements org.forester.sequence.MolecularSequence)
- org.forester.species.BasicSpecies (implements org.forester.species.Species)
- org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix (implements org.forester.evoinference.matrix.distance.DistanceMatrix)
- org.forester.util.BasicTable<E>
- org.forester.util.BasicTableParser
- org.biojava.nbio.structure.secstruc.BetaBridge
- org.forester.phylogeny.data.BinaryCharacters (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.BinaryCharactersParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.BioAssemblyIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
- org.biojava.nbio.structure.quaternary.BioAssemblyInfo (implements java.io.Serializable)
- org.biojava.nbio.structure.quaternary.BioAssemblyTools
- org.biojava.nbio.structure.gui.BiojavaJmol
- org.biojava.nbio.structure.align.BioJavaStructureAlignment (implements org.biojava.nbio.structure.align.StructureAlignment)
- org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
- org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation (implements java.lang.Cloneable, java.io.Serializable)
- org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
- org.biojava.nbio.core.sequence.storage.BitSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  - org.biojava.nbio.core.sequence.storage.FourBitSequenceReader<C>
  - org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader<C>
- org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
  - org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker<C>
  - org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker<C>
- org.forester.archaeopteryx.tools.Blast
- org.biojava.nbio.structure.symmetry.utils.BlastClustReader (implements java.io.Serializable)
- org.biojava.nbio.core.search.io.blast.BlastHitBuilder
- org.biojava.nbio.genome.homology.BlastHomologyHits
- org.biojava.nbio.core.search.io.blast.BlastHspBuilder
- org.biojava.nbio.ws.alignment.qblast.BlastJob
- org.biojava.nbio.core.search.io.blast.BlastResultBuilder
- org.biojava.nbio.core.search.io.blast.BlastTabularParser (implements org.biojava.nbio.core.search.io.ResultFactory)
- org.biojava.nbio.core.search.io.blast.BlastXMLParser (implements org.biojava.nbio.core.search.io.ResultFactory)
- org.biojava.nbio.genome.query.BlastXMLQuery
- org.biojava.nbio.structure.BondImpl (implements org.biojava.nbio.structure.Bond, java.io.Serializable)
- org.biojava.nbio.structure.io.BondMaker
- org.biojava.nbio.structure.validation.BondOutlier
- org.forester.evoinference.tools.BootstrapResampler
- org.biojava.nbio.structure.contact.BoundingBox (implements java.io.Serializable)
- org.forester.phylogeny.data.BranchColor (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.pccx.BranchCountingBasedScoringMethod (implements org.forester.pccx.ScoringMethodForExternalNode)
  - org.forester.pccx.BranchLengthBasedScoringMethod
  - org.forester.pccx.LogBranchLengthBasedScoringMethod
- org.forester.phylogeny.data.BranchData (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.phylogeny.data.BranchWidth (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.BranchWidthParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.align.webstart.BrowserOpener
- org.biojava.nbio.structure.symmetry.core.C2RotationSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
- org.biojava.nbio.structure.align.util.CacheFactory
- org.biojava.nbio.structure.io.CAConverter
- org.biojava.nbio.structure.Calc
- org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
- org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner<S,C> (implements java.util.concurrent.Callable<V>)
- org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer<S,C> (implements java.util.concurrent.Callable<V>)
- org.biojava.nbio.alignment.template.CallableProfileProfileAligner<S,C> (implements java.util.concurrent.Callable<V>)
- org.biojava.nbio.structure.align.CallableStructureAlignment (implements java.util.concurrent.Callable<V>)
- org.biojava.nbio.structure.quaternary.CartesianProduct<T>
- org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>)
- org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound (implements org.biojava.nbio.core.sequence.template.Compound)
- org.biojava.nbio.structure.cath.CathDomain (implements java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
- org.biojava.nbio.structure.cath.CathFactory
- org.biojava.nbio.structure.cath.CathFragment (implements java.io.Serializable)
- org.biojava.nbio.structure.cath.CathInstallation (implements org.biojava.nbio.structure.cath.CathDatabase)
- org.biojava.nbio.structure.cath.CathNode (implements java.io.Serializable)
- org.biojava.nbio.structure.cath.CathSegment (implements java.io.Serializable)
- org.biojava.nbio.core.sequence.CDSComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.structure.align.ce.CECalculator
- org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
- org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
- org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus (implements java.lang.Comparable<T>)
- org.biojava.nbio.structure.align.ce.CeParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
  - org.biojava.nbio.structure.align.ce.CECPParameters
  - org.biojava.nbio.structure.symmetry.internal.CESymmParameters
  - org.biojava.nbio.structure.align.ce.OptimalCECPParameters
- org.biojava.nbio.structure.symmetry.internal.CeSymm
- org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
- org.biojava.nbio.structure.symmetry.internal.CeSymmResult
- org.biojava.nbio.structure.symmetry.core.ChainClusterer
- org.biojava.nbio.structure.ChainImpl (implements org.biojava.nbio.structure.Chain, java.io.Serializable)
- org.biojava.nbio.structure.symmetry.misc.ChainSignature (implements java.lang.Comparable<T>)
- org.biojava.nbio.structure.io.ChargeAdder
- org.forester.application.check_fasta
- org.biojava.nbio.structure.io.mmcif.model.ChemComp (implements java.lang.Comparable<T>, java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom (implements java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.model.ChemCompBond (implements java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.ChemCompConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
- org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor (implements java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
- org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
- org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
- org.biojava.nbio.survival.cox.stats.ChiSq
- org.biojava.nbio.survival.cox.stats.Cholesky2
- org.biojava.nbio.structure.jama.CholeskyDecomposition (implements java.io.Serializable)
- org.biojava.nbio.genome.util.ChromosomeMappingTools
- org.biojava.nbio.genome.parsers.genename.ChromPos
- org.biojava.nbio.survival.cox.stats.Chsolve2
- org.biojava.nbio.structure.validation.Clash
- org.biojava.nbio.core.sequence.io.util.ClasspathResource
- org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
- org.biojava.nbio.structure.align.util.CliTools
- org.biojava.nbio.structure.align.ClusterAltAligs
- org.biojava.nbio.structure.domain.pdp.ClusterDomains
- org.biojava.nbio.structure.symmetry.core.ClusterMerger
- org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
- org.biojava.nbio.structure.align.util.CollectionTools
- org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
- org.forester.io.parsers.phyloxml.data.ColorParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- java.awt.color.ColorSpace (implements java.io.Serializable)
  - org.biojava.nbio.structure.gui.util.color.HSVColorSpace
- org.biojava.nbio.structure.gui.util.color.ColorUtils
- org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
- org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity (implements org.forester.surfacing.PairwiseDomainSimilarity)
- org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
- org.forester.util.CommandLineArguments
- org.forester.util.CommandProcessBuilder
- org.biojava.nbio.aaproperties.CommandPrompt
- org.biojava.nbio.survival.data.CompactCharSequence (implements java.lang.CharSequence, java.io.Serializable)
- org.biojava.nbio.phylo.Comparison
- java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
  - java.awt.Container
    - javax.swing.JComponent (implements java.io.Serializable)
      - org.forester.development.AbstractRenderer
        
        org.forester.development.ResidueRenderer
      - javax.swing.JPanel (implements javax.accessibility.Accessible)
        
        javax.swing.colorchooser.AbstractColorChooserPanel
        
        org.jcolorbrewer.ui.DivergingColorPalettePanel (implements java.awt.event.ActionListener)
        
        org.jcolorbrewer.ui.QualitativeColorPalettePanel (implements java.awt.event.ActionListener)
        
        org.jcolorbrewer.ui.SequentialColorPalettePanel (implements java.awt.event.ActionListener)
        
        org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
        
        org.biojava.nbio.structure.align.gui.DBSearchGUI
        
        org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
        
        org.biojava.nbio.structure.gui.util.color.GradientPanel
        
        org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener (implements java.awt.event.ActionListener, org.biojava.nbio.structure.align.events.AlignmentProgressListener)
        
        org.biojava.nbio.structure.gui.JMatrixPanel
        
        org.biojava.nbio.structure.align.gui.JPrintPanel (implements java.awt.event.ActionListener, java.awt.print.Printable)
        
        org.biojava.nbio.structure.align.gui.AlignmentTextPanel
        
        org.biojava.nbio.structure.align.gui.aligpanel.AligPanel (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
        
        org.biojava.nbio.structure.align.gui.jmol.JmolPanel (implements java.awt.event.ActionListener)
        
        org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
        
        org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
        
        org.forester.archaeopteryx.MainPanel (implements java.awt.event.ComponentListener)
        
        org.biojava.nbio.structure.align.gui.MemoryMonitor
        
        org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface (implements java.lang.Runnable)
        
        org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
        
        org.biojava.nbio.structure.gui.util.PDBDirPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
        
        org.biojava.nbio.structure.gui.util.PDBServerPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
        
        org.biojava.nbio.structure.gui.util.PDBUploadPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
        
        org.biojava.nbio.structure.gui.ScaleableMatrixPanel (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener)
        
        org.biojava.nbio.structure.align.gui.DotPlotPanel
        
        org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer (implements javax.swing.ListCellRenderer<E>)
        
        org.biojava.nbio.structure.gui.util.ScopSelectPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
        
        org.biojava.nbio.structure.gui.util.SelectMultiplePanel
        
        org.biojava.nbio.structure.align.gui.SelectPDBPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
        
        org.biojava.nbio.structure.gui.SequenceDisplay (implements javax.swing.event.ChangeListener)
        
        org.biojava.nbio.structure.gui.util.SequenceScalePanel
        
        org.forester.archaeopteryx.TreePanel (implements java.awt.event.ActionListener, java.awt.event.MouseWheelListener, java.awt.print.Printable)
      - javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
        
        javax.swing.JTextField (implements javax.swing.SwingConstants)
        
        org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
        
        org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
        
        org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
      - org.forester.development.MsaRenderer
    - java.awt.Panel (implements javax.accessibility.Accessible)
      - java.applet.Applet
        
        javax.swing.JApplet (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer)
        
        org.forester.archaeopteryx.ArchaeopteryxA
        
        org.forester.archaeopteryx.ArchaeopteryxE (implements java.awt.event.ActionListener)
    - java.awt.Window (implements javax.accessibility.Accessible)
      - java.awt.Dialog
        
        javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
        
        org.forester.msa_compactor.Chart (implements java.awt.event.ActionListener)
        
        org.jcolorbrewer.ui.ColorPaletteChooserDialog
        
        org.forester.archaeopteryx.FontChooser (implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener)
        
        org.forester.archaeopteryx.tools.PhyloInferenceDialog (implements java.awt.event.ActionListener)
      - java.awt.Frame (implements java.awt.MenuContainer)
        
        javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
        
        org.biojava.nbio.structure.align.gui.AlignmentGui
        
        org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
        
        org.forester.archaeopteryx.MainFrame (implements java.awt.event.ActionListener)
        
        org.forester.archaeopteryx.MainFrameApplet
        
        org.forester.archaeopteryx.MainFrameApplication
        
        org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
        
        org.biojava.nbio.structure.align.gui.ParameterGUI
        
        org.biojava.nbio.structure.symmetry.gui.SymmetryGui
- org.biojava.nbio.protmod.Component
- org.biojava.nbio.protmod.io.ComponentXMLConverter
- org.biojava.nbio.structure.Compound (implements java.io.Serializable)
- org.biojava.nbio.structure.io.CompoundFinder
- org.biojava.nbio.core.util.ConcurrencyTools
- org.forester.application.confadd
- org.forester.phylogeny.data.Confidence (implements java.lang.Comparable<T>, org.forester.phylogeny.data.PhylogenyData)
- org.forester.tools.ConfidenceAssessor
- org.forester.io.parsers.phyloxml.data.ConfidenceParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.forester.archaeopteryx.Configuration
- org.forester.archaeopteryx.Constants
- org.biojava.nbio.aaproperties.Constraints
- org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper)
  - org.biojava.nbio.structure.gui.util.color.LogColorMapper
  - org.biojava.nbio.structure.gui.util.color.SqrtColorMapper
- org.biojava.nbio.aaproperties.profeat.convertor.Convertor
  - org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
  - org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
  - org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
  - org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
  - org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
  - org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
  - org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
- org.biojava.nbio.structure.gui.util.CoordManager
- org.forester.applications.core_chars
- org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer (implements org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer)
- org.forester.application.count_support
- org.biojava.nbio.structure.align.client.CountProgressListener (implements org.biojava.nbio.structure.align.events.AlignmentProgressListener)
- org.forester.surfacing.CountsBasedPairwiseDomainSimilarity (implements org.forester.surfacing.PairwiseDomainSimilarity)
- org.forester.pccx.CoverageCalculator
- org.biojava.nbio.survival.cox.CoxCC
- org.biojava.nbio.survival.cox.CoxCoefficient
- org.biojava.nbio.survival.cox.CoxHelper
- org.biojava.nbio.survival.cox.CoxInfo
- org.biojava.nbio.survival.cox.CoxMart
- org.biojava.nbio.survival.cox.CoxR
- org.biojava.nbio.survival.cox.CoxScore
- org.biojava.nbio.survival.cox.CoxVariables
- org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator (implements org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface)
- org.biojava.nbio.core.util.CRC64Checksum (implements java.util.zip.Checksum)
- org.biojava.nbio.structure.xtal.CrystalBuilder
- org.biojava.nbio.structure.xtal.CrystalCell (implements java.io.Serializable)
- org.biojava.nbio.structure.xtal.CrystalTransform (implements java.io.Serializable)
- org.biojava.nbio.structure.domain.pdp.Cut
- org.biojava.nbio.structure.domain.pdp.CutDomain
- org.biojava.nbio.structure.domain.pdp.CutSites
- org.biojava.nbio.structure.domain.pdp.CutValues
- org.biojava.nbio.genome.parsers.cytoband.Cytoband (implements java.lang.Comparable<T>, java.io.Serializable)
- org.biojava.nbio.genome.parsers.cytoband.CytobandParser
- org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
- org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord (implements java.io.Serializable)
- org.biojava.nbio.phosphosite.Dataset
- org.forester.phylogeny.data.Date (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.DateParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.DBRef (implements org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
- org.biojava.nbio.structure.align.gui.DBResultTable (implements java.awt.event.ActionListener)
- org.forester.application.decorator
- org.forester.application.decoratorX
- org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider (implements org.biojava.nbio.core.alignment.matrices.AAIndexProvider)
- org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider (implements org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider)
- javax.swing.colorchooser.DefaultColorSelectionModel (implements javax.swing.colorchooser.ColorSelectionModel, java.io.Serializable)
  - org.jcolorbrewer.ui.ColorPanelSelectionModel
- org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
  - org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
  - org.forester.io.parsers.phyloxml.PhyloXmlHandler
  - org.forester.io.parsers.tol.TolXmlHandler
- org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper)
- org.biojava.nbio.ontology.DefaultOps (implements org.biojava.nbio.ontology.OntologyOps, java.io.Serializable)
- org.forester.development.DevelopmentTools
- org.biojava.nbio.structure.align.gui.DisplayAFP
- org.biojava.nbio.structure.symmetry.geometry.DistanceBox<T>
- org.biojava.nbio.phylo.DistanceMatrixCalculator
- org.biojava.nbio.phylo.DistanceTreeEvaluator
- org.forester.phylogeny.data.Distribution (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.DistributionParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.core.sequence.io.DNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
- org.forester.evoinference.parsimony.DolloParsimony
- org.forester.application.dom_dup
- org.biojava.nbio.structure.domain.pdp.Domain (implements java.lang.Comparable<T>, java.io.Serializable)
- org.forester.phylogeny.data.DomainArchitecture (implements org.forester.phylogeny.data.PhylogenyData)
  - org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture (implements org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData)
- org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
- org.forester.io.parsers.phyloxml.data.DomainArchitectureParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
- org.forester.surfacing.DomainCountsDifferenceUtil
- org.forester.surfacing.DomainLengths
- org.forester.surfacing.DomainLengthsTable
- org.forester.applications.domainloss_replacement
- org.forester.surfacing.DomainParsimonyCalculator
- org.biojava.nbio.structure.domain.DomainProviderFactory
- org.forester.surfacing.DomainSimilarity (implements java.lang.Comparable<T>)
- org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)
- org.biojava.nbio.structure.secstruc.DSSPParser
- org.forester.ws.seqdb.EbiDbEntry (implements org.forester.ws.seqdb.SequenceDatabaseEntry)
- org.biojava.nbio.structure.ecod.EcodDomain (implements java.lang.Cloneable, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
- org.biojava.nbio.structure.ecod.EcodFactory
- org.biojava.nbio.structure.ecod.EcodInstallation (implements org.biojava.nbio.structure.ecod.EcodDatabase)
- org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
- org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit<C> (implements org.biojava.nbio.core.sequence.edits.Edit<C>)
  - org.biojava.nbio.core.sequence.edits.Edit.Delete<C>
  - org.biojava.nbio.core.sequence.edits.Edit.Insert<C>
  - org.biojava.nbio.core.sequence.edits.Edit.Substitute<C>
- org.biojava.nbio.structure.jama.EigenvalueDecomposition (implements java.io.Serializable)
- org.biojava.nbio.aaproperties.xml.Element
- org.biojava.nbio.aaproperties.xml.ElementTable
- org.biojava.nbio.structure.io.mmcif.model.Entity
- org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
- org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
- org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
- org.biojava.nbio.structure.validation.Entry
- org.biojava.nbio.core.util.Equals
- org.forester.phylogeny.data.Event (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.EventParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.forester.test.examples.Example1
- org.forester.test.examples.Example2
- org.forester.test.examples.Example3
- org.forester.test.examples.Example4
- org.forester.test.examples.Example5
- org.biojava.nbio.core.sequence.ExonComparator (implements java.util.Comparator<T>)
- org.forester.phylogeny.iterators.ExternalForwardIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
- org.forester.pccx.ExternalNodeBasedCoverage (implements org.forester.pccx.Coverage)
- org.forester.pccx.ExternalNodeBasedCoverageMethod (implements org.forester.pccx.CoverageCalculationMethod)
- org.forester.pccx.ExternalNodeBasedCoverageMethodOptions (implements org.forester.pccx.CoverageCalculationOptions)
- org.forester.util.ExternalProgram
- org.biojava.nbio.structure.align.FarmJob (implements java.lang.Runnable)
- org.biojava.nbio.structure.align.client.FarmJobParameters
- org.biojava.nbio.structure.align.client.FarmJobRunnable (implements java.lang.Runnable)
- org.forester.application.fasta_split
- org.biojava.nbio.structure.io.FastaAFPChainConverter
- org.biojava.nbio.core.sequence.io.FastaGeneWriter
- org.forester.io.parsers.FastaParser
- org.biojava.nbio.core.sequence.io.FastaReader<S,C>
- org.biojava.nbio.core.sequence.io.FastaReaderHelper
- org.biojava.nbio.data.sequence.FastaSequence (implements java.lang.Comparable<T>)
- org.biojava.nbio.core.sequence.io.FastaSequenceParser (implements org.biojava.nbio.core.sequence.io.template.SequenceParserInterface)
- org.biojava.nbio.structure.io.FastaStructureParser
- org.biojava.nbio.core.sequence.io.FastaWriter<S,C>
- org.biojava.nbio.core.sequence.io.FastaWriterHelper
- org.biojava.nbio.sequencing.io.fastq.Fastq
- org.biojava.nbio.sequencing.io.fastq.FastqBuilder
- org.biojava.nbio.sequencing.io.fastq.FastqTools
- org.biojava.nbio.structure.align.fatcat.FatCat
  - org.biojava.nbio.structure.align.fatcat.FatCatFlexible (implements org.biojava.nbio.structure.align.StructureAlignment)
  - org.biojava.nbio.structure.align.fatcat.FatCatRigid (implements org.biojava.nbio.structure.align.StructureAlignment)
- org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
- org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
- org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
- org.biojava.nbio.genome.parsers.gff.Feature (implements org.biojava.nbio.genome.parsers.gff.FeatureI)
- org.biojava.nbio.genome.parsers.gff.FeatureHelper
- org.biojava.nbio.structure.io.FileConvert
- org.biojava.nbio.structure.io.util.FileDownloadUtils
- org.biojava.nbio.structure.io.FileParsingParameters (implements java.io.Serializable)
- org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
- org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
- org.forester.evoinference.parsimony.FitchParsimony<STATE_TYPE>
- org.biojava.nbio.core.util.FlatFileCache
- java.awt.FlowLayout (implements java.awt.LayoutManager, java.io.Serializable)
  - org.biojava.nbio.structure.gui.WrapLayout
- org.forester.util.ForesterConstants
- org.forester.util.ForesterUtil
- org.biojava.nbio.phylo.ForesterWrapper
- org.biojava.nbio.structure.align.pairwise.FragmentJoiner
- org.biojava.nbio.structure.align.pairwise.FragmentPair
- org.biojava.nbio.structure.align.helper.GapArray
- org.forester.msa_compactor.GapContribution (implements java.lang.Comparable<T>)
- org.biojava.nbio.genome.parsers.gff.GCStats
- org.biojava.nbio.core.sequence.io.GenbankReader<S,C>
- org.biojava.nbio.core.sequence.io.GenbankReaderHelper
- org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceParserInterface)
- org.biojava.nbio.core.sequence.io.GenbankWriter<S,C>
- org.biojava.nbio.core.sequence.io.GenbankWriterHelper
- org.forester.application.gene_tree_preprocess
- org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition (implements java.lang.Comparable<T>, java.io.Serializable)
- org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
- org.biojava.nbio.genome.GeneFeatureHelper
- org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
- org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
- org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
- org.biojava.nbio.genome.parsers.genename.GeneName (implements java.lang.Comparable<T>, java.io.Serializable)
- org.biojava.nbio.genome.parsers.genename.GeneNamesParser
- org.forester.io.parsers.GeneralMsaParser
- org.forester.util.GeneralTable<IDENTIFIER_TYPE,VALUE_TYPE>
- org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat<S,C> (implements org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface<S,C>)
- org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
- org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
- org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat<S,C>
  - org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat<S,C> (implements org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S,C>)
- org.forester.applications.genome_counts_for_once_appearing_dcs
- org.forester.applications.get_distances
- org.forester.applications.get_genome_counts_per_char
- org.forester.applications.get_loss_nodes
- org.forester.applications.get_shared_chars
- org.forester.applications.get_subtree_specific_chars
- org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
- org.biojava.nbio.structure.rcsb.GetRepresentatives
- org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
- org.biojava.nbio.genome.parsers.gff.GFF3Reader
- org.biojava.nbio.genome.parsers.gff.GFF3Writer
- org.forester.application.goac
- org.forester.go.GoId (implements java.lang.Comparable<T>)
- org.forester.go.GoNameSpace
- org.biojava.nbio.ontology.io.GOParser
- org.biojava.nbio.structure.align.pairwise.Gotoh
- org.forester.go.GoUtils
- org.biojava.nbio.structure.gui.util.color.GradientMapper (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper, java.util.Map<K,V>)
- org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
- org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner (implements org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner)
- org.biojava.nbio.structure.contact.Grid
- org.biojava.nbio.structure.contact.GridCell
- org.biojava.nbio.structure.asa.GroupAsa (implements java.io.Serializable)
- org.biojava.nbio.structure.contact.GroupContact (implements java.io.Serializable)
- org.biojava.nbio.structure.contact.GroupContactSet (implements java.lang.Iterable<T>, java.io.Serializable)
- org.biojava.nbio.structure.GroupIterator (implements java.util.Iterator<E>)
- org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
- org.biojava.nbio.structure.io.GroupToSDF
- org.forester.application.gsdi
- org.forester.sdi.GSDI (implements org.forester.sdi.GSDII)
- org.forester.sdi.GSDIR (implements org.forester.sdi.GSDII)
- org.biojava.nbio.alignment.GuideTree<S,C> (implements java.lang.Iterable<T>)
- org.biojava.nbio.alignment.GuideTree.Node (implements org.biojava.nbio.alignment.template.GuideTreeNode<S,C>)
- org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable (implements java.lang.Runnable)
- org.biojava.nbio.structure.align.ce.GuiWrapper
- org.biojava.nbio.core.util.Hashcoder
- org.biojava.nbio.structure.align.xml.HasResultXMLConverter
- org.biojava.nbio.structure.secstruc.HBond
- org.biojava.nbio.survival.data.HeaderInfo
- org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
- org.biojava.nbio.structure.symmetry.core.Helix
- org.biojava.nbio.structure.symmetry.core.HelixExtender
- org.biojava.nbio.structure.symmetry.core.HelixLayers
- org.biojava.nbio.structure.symmetry.core.HelixSolver
- org.forester.development.Hello3d
- org.biojava.nbio.structure.align.gui.HelpDialog
- org.biojava.nbio.structure.HetatomImpl (implements org.biojava.nbio.structure.Group, java.io.Serializable)
  - org.biojava.nbio.structure.AminoAcidImpl (implements org.biojava.nbio.structure.AminoAcid, java.io.Serializable)
  - org.biojava.nbio.structure.NucleotideImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.Group, java.io.Serializable)
- org.biojava.nbio.core.search.io.Hit (implements java.lang.Iterable<T>)
- org.biojava.nbio.ws.hmmer.HmmerDomain (implements java.lang.Comparable<T>, java.io.Serializable)
- org.forester.development.HmmerRest
- org.biojava.nbio.ws.hmmer.HmmerResult (implements java.lang.Comparable<T>, java.io.Serializable)
- org.forester.io.parsers.HmmPfamOutputParser
- org.forester.io.parsers.HmmscanPerDomainTableParser
- org.biojava.nbio.core.search.io.Hsp<S,C>
- org.biojava.nbio.structure.align.util.HTTPConnectionTools
- org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
- org.biojava.nbio.structure.symmetry.geometry.Icosahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
- org.biojava.nbio.structure.Identifier
- org.forester.phylogeny.data.Identifier (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.IdentifierParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.align.helper.IdxComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader
- org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter
- org.forester.archaeopteryx.tools.ImageLoader (implements java.lang.Runnable)
- org.biojava.nbio.structure.align.helper.IndexPair (implements java.io.Serializable)
  - org.biojava.nbio.structure.align.helper.AligMatEl
- org.forester.archaeopteryx.tools.InferenceManager
- java.io.InputStream (implements java.io.Closeable)
  - java.io.FilterInputStream
    - org.biojava.nbio.core.util.UncompressInputStream
  - org.biojava.nbio.genome.parsers.twobit.TwoBitParser
- org.biojava.nbio.core.util.InputStreamProvider
- org.biojava.nbio.core.sequence.location.InsdcLocations
- org.biojava.nbio.core.sequence.location.InsdcParser<S,C>
- org.biojava.nbio.ontology.IntegerOntology (implements org.biojava.nbio.ontology.Ontology)
- org.biojava.nbio.ontology.IntegerOntology.IntTerm (implements org.biojava.nbio.ontology.Term)
- org.forester.datastructures.IntMatrix
- org.forester.applications.inverted_dcs
- org.biojava.nbio.core.sequence.io.util.IOUtils
- org.biojava.nbio.aaproperties.xml.Isotope
- org.biojava.nbio.core.sequence.io.IUPACParser
- org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable (implements org.biojava.nbio.core.sequence.transcription.Table)
- org.biojava.nbio.structure.align.client.JFatCatClient
- org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener)
- org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter (implements org.jmol.util.LoggerInterface)
- org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
  - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
  - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
    - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
    - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
    - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
    - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
    - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
    - org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
- org.biojava.nbio.structure.align.gui.jmol.JmolTools
- org.biojava.nbio.structure.gui.JmolViewerImpl (implements org.biojava.nbio.structure.gui.StructureViewer)
- org.biojava.nbio.structure.align.webstart.JNLPProxy
- org.biojava.nbio.core.sequence.storage.JoiningSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
- org.biojava.nbio.structure.align.helper.JointFragments
- org.biojava.nbio.structure.JournalArticle (implements java.io.Serializable)
- org.biojava.nbio.ronn.Jronn
- org.biojava.nbio.ronn.Jronn.Range
- java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
  - org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
  - org.biojava.nbio.structure.gui.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
- org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
- org.biojava.nbio.structure.secstruc.Ladder
- org.forester.phylogeny.iterators.LevelOrderTreeIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
- org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator (implements org.biojava.nbio.structure.gui.util.color.ColorInterpolator)
- org.biojava.nbio.structure.scop.server.ListStringWrapper (implements java.io.Serializable)
- org.biojava.nbio.structure.io.LocalPDBDirectory (implements org.biojava.nbio.structure.io.StructureIOFile)
  - org.biojava.nbio.structure.io.MMCIFFileReader
  - org.biojava.nbio.structure.io.PDBFileReader
- org.biojava.nbio.structure.domain.LocalProteinDomainParser
- org.biojava.nbio.genome.parsers.gff.Location (implements java.lang.Iterable<T>)
- org.biojava.nbio.core.sequence.location.template.Location.Tools
- org.biojava.nbio.core.sequence.location.LocationHelper
- org.biojava.nbio.genome.parsers.gff.LocIterator (implements java.util.Iterator<E>)
- org.biojava.nbio.structure.jama.LUDecomposition (implements java.io.Serializable)
- org.forester.applications.map_lengths
- org.forester.surfacing.MappingResults
- org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
- org.biojava.nbio.structure.jama.Maths
- org.biojava.nbio.structure.jama.Matrix (implements java.lang.Cloneable, java.io.Serializable)
- org.biojava.nbio.survival.cox.matrix.Matrix
- org.forester.application.mcc
- org.biojava.nbio.survival.cox.comparators.MeanModelComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer (implements org.biojava.nbio.survival.kaplanmeier.metadata.DiscreteQuantizerInterface)
- org.biojava.nbio.structure.align.gui.MenuCreator
- org.biojava.nbio.structure.gui.util.MenuCreator
- org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.core.exceptions.Messages
- org.forester.application.meta_ontologizer
- org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
- org.biojava.nbio.structure.io.mmcif.MetalBondConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
- org.biojava.nbio.structure.io.mmcif.chem.MetalBondDistance
- org.biojava.nbio.structure.io.mmcif.MetalBondParser
- org.forester.go.etc.MetaOntologizer
- org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
- org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
- org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider (implements org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider)
- org.forester.pccx.ModelingUtils
- org.biojava.nbio.structure.validation.ModelledSubgroup
- org.biojava.nbio.ronn.ModelLoader
- org.biojava.nbio.ronn.ModelLoader.Model
- org.biojava.nbio.ronn.ModelLoader.Threshold
- org.biojava.nbio.protmod.ModificationConditionImpl (implements org.biojava.nbio.protmod.ModificationCondition)
- org.biojava.nbio.protmod.ModificationLinkage
- org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>)
- org.biojava.nbio.protmod.structure.ModifiedCompoundImpl (implements java.lang.Comparable<T>, org.biojava.nbio.protmod.structure.ModifiedCompound, java.io.Serializable)
- org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
- org.biojava.nbio.structure.validation.MogAngleOutlier
- org.biojava.nbio.structure.validation.MogBondOutlier
- org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
- org.forester.application.msa_compactor
- org.forester.msa_compactor.MsaCompactor
- org.forester.msa.MsaInferrer
  - org.forester.msa.ClustalOmega
  - org.forester.msa.Mafft
- org.forester.msa.MsaMethods
- org.forester.msa_compactor.MsaProperties
- org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
- org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
- org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
- org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
- org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
- org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
- org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
- org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
- org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
- org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
- org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain (implements org.biojava.nbio.structure.align.MultipleStructureAligner)
- org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer (implements java.util.concurrent.Callable<V>)
- org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
- org.biojava.nbio.core.sequence.MultipleSequenceAlignment<S,C> (implements org.biojava.nbio.core.sequence.template.LightweightProfile<S,C>)
- org.biojava.nbio.structure.align.MultiThreadedDBSearch
- org.biojava.nbio.structure.Mutator
- org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.structure.align.gui.MyDistMaxListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.structure.align.gui.MyExportListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener (implements org.jmol.api.JmolStatusListener)
- org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.structure.align.gui.MySaveFileListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.aaproperties.xml.MyValidationEventHandler (implements javax.xml.bind.ValidationEventHandler)
- org.biojava.nbio.aaproperties.xml.Name2Count
- org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties (implements org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties)
- org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties (implements org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties)
- org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService (implements org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService)
- org.forester.evoinference.distance.NeighborJoining
- org.forester.evoinference.distance.NeighborJoiningF
- org.forester.evoinference.distance.NeighborJoiningR
- org.forester.development.neTest
- org.forester.development.neTest.DoublePointer
- org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser
- org.forester.io.parsers.nexus.NexusCharactersParser
- org.forester.io.parsers.nexus.NexusConstants
- org.forester.io.parsers.nexus.NexusPhylogeniesParser (implements org.forester.io.parsers.IteratingPhylogenyParser, org.forester.io.parsers.PhylogenyParser)
- org.forester.io.parsers.nhx.NHXParser (implements org.forester.io.parsers.IteratingPhylogenyParser, org.forester.io.parsers.PhylogenyParser)
- org.forester.io.parsers.nhx.NHXtags
- org.forester.application.nj
- org.forester.phylogeny.data.NodeData (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.phylogeny.data.NodeVisualData (implements org.forester.phylogeny.data.PhylogenyData)
- org.biojava.nbio.structure.validation.ObjectFactory
- org.forester.application.obo_tool
- org.biojava.nbio.ontology.obo.OboFileHandler (implements org.biojava.nbio.ontology.obo.OboFileEventListener)
- org.biojava.nbio.ontology.obo.OboFileParser
- org.biojava.nbio.ontology.obo.OboFileParser.SOPair
- org.biojava.nbio.ontology.io.OboParser
- org.forester.go.OBOparser
- org.biojava.nbio.structure.symmetry.geometry.Octahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
- org.forester.go.etc.OntologizerResult (implements java.lang.Comparable<T>)
- org.biojava.nbio.ontology.Ontology.Impl (implements org.biojava.nbio.ontology.Ontology, java.io.Serializable)
- org.biojava.nbio.ontology.OntologyTerm.Impl (implements org.biojava.nbio.ontology.OntologyTerm, java.io.Serializable)
- org.biojava.nbio.ontology.OntoTools
- org.biojava.nbio.structure.quaternary.OperatorResolver
- org.forester.archaeopteryx.Options
- org.biojava.nbio.structure.quaternary.OrderedPair<T>
- org.biojava.nbio.ronn.ORonn (implements java.util.concurrent.Callable<V>)
- org.biojava.nbio.ronn.ORonnModel
- org.biojava.nbio.genome.query.OutputHitsGFF
- java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
  - org.biojava.nbio.ronn.NullOutputStream
- org.biojava.nbio.structure.contact.Pair<T> (implements java.io.Serializable)
- org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
- org.forester.evoinference.distance.PairwiseDistanceCalculator
- org.forester.surfacing.PairwiseGenomeComparator
- org.jcolorbrewer.ui.PaletteIcon (implements javax.swing.Icon)
- org.forester.phylogeny.factories.ParserBasedPhylogenyFactory (implements org.forester.phylogeny.factories.PhylogenyFactory)
- org.forester.io.parsers.util.ParserUtils
- org.biojava.nbio.structure.PassthroughIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
- org.forester.io.parsers.nexus.PaupLogParser
- org.forester.application.pccx
- org.biojava.nbio.structure.io.PDBBioAssemblyParser
- org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
- org.biojava.nbio.structure.PDBCrystallographicInfo (implements java.io.Serializable)
- org.biojava.nbio.structure.domain.PDBDomainProvider (implements org.biojava.nbio.structure.domain.DomainProvider)
- org.biojava.nbio.structure.io.PDBFileParser
- org.biojava.nbio.structure.PDBHeader (implements org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
- org.biojava.nbio.structure.rcsb.PdbIdLists
- org.biojava.nbio.structure.align.client.PdbPair (implements java.lang.Comparable<T>)
- org.biojava.nbio.structure.align.xml.PdbPairsMessage
- org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
- org.biojava.nbio.structure.PDBStatus
- org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils
- org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
- org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
- org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
- org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
- org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
- org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly (implements java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen (implements java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
- org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
- org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList (implements java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
- org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
- org.biojava.nbio.structure.domain.PDPDomain (implements org.biojava.nbio.structure.StructureIdentifier)
- org.biojava.nbio.structure.domain.pdp.PDPParameters
- org.biojava.nbio.aaproperties.PeptideProperties
- org.biojava.nbio.aaproperties.PeptidePropertiesImpl (implements org.biojava.nbio.aaproperties.IPeptideProperties)
- org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
- org.biojava.nbio.structure.symmetry.core.PermutationGroup (implements java.lang.Iterable<T>)
- org.forester.application.pfam_go
- org.forester.application.pfam2go_extractor
- org.forester.application.pfamacc2go
- org.forester.application.pfamacc2pfamid
- org.forester.go.PfamToGoMapping (implements org.forester.go.Mapping)
- org.forester.go.PfamToGoParser
- org.forester.applications.phylo2coloredgraphics
- org.forester.applications.phylo2graphics
- org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
- org.forester.phylogeny.Phylogeny
- org.forester.phylogeny.PhylogenyBranch
- org.forester.phylogeny.data.PhylogenyDataUtil
- org.forester.tools.PhylogenyDecorator
- org.forester.phylogeny.PhylogenyMethods
- org.forester.phylogeny.PhylogenyNode (implements java.lang.Comparable<T>)
- org.forester.io.writers.PhylogenyWriter
- org.forester.application.phylostrip
- org.forester.application.phyloxml_converter
- org.forester.io.parsers.phyloxml.PhyloXmlMapping
- org.forester.io.writers.PhyloXmlNodeWriter
- org.forester.io.parsers.phyloxml.PhyloXmlParser (implements org.forester.io.parsers.PhylogenyParser)
- org.forester.io.parsers.phyloxml.PhyloXmlUtil
- org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
- org.forester.phylogeny.data.Point (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.PointParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.forester.phylogeny.data.Polygon (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.PolygonParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
- org.forester.phylogeny.iterators.PostOrderStackObject
- org.forester.phylogeny.iterators.PostorderTreeIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
- org.forester.phylogeny.iterators.PreorderTreeIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
- org.biojava.nbio.core.util.PrettyXMLWriter (implements org.biojava.nbio.core.util.XMLWriter)
- org.biojava.nbio.structure.symmetry.geometry.Prism (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
- org.forester.archaeopteryx.tools.ProcessPool
- org.forester.archaeopteryx.tools.ProcessRunning
- org.biojava.nbio.aaproperties.profeat.ProfeatProperties
- org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl (implements org.biojava.nbio.aaproperties.profeat.IProfeatProperties)
- org.biojava.nbio.structure.validation.Program
- org.biojava.nbio.structure.validation.Programs
- org.forester.phylogeny.data.PropertiesMap (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.phylogeny.data.Property (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.PropertyParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
- org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
- org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
- org.forester.phylogeny.data.ProteinDomain (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.ProteinDomainParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.forester.protein.ProteinId (implements java.lang.Comparable<T>)
- org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
- org.biojava.nbio.protmod.ProteinModificationImpl (implements java.lang.Comparable<T>, org.biojava.nbio.protmod.ProteinModification)
- org.biojava.nbio.protmod.ProteinModificationImpl.Builder
- org.biojava.nbio.protmod.ProteinModificationRegistry
- org.biojava.nbio.protmod.io.ProteinModificationXmlReader
- org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
- org.biojava.nbio.core.sequence.io.ProteinSequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  - org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
- org.biojava.nbio.structure.jama.QRDecomposition (implements java.io.Serializable)
- org.biojava.nbio.core.sequence.features.Qualifier
  - org.biojava.nbio.core.sequence.features.DBReferenceInfo
    - org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo<S,C> (implements org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>)
- org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer
- org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
- org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters (implements java.io.Serializable)
- org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
- org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
- org.forester.datastructures.Queue
- org.forester.development.RandomThing
- org.biojava.nbio.structure.rcsb.RCSBDescription
- org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
- org.biojava.nbio.structure.rcsb.RCSBLigand
- org.biojava.nbio.structure.rcsb.RCSBLigands
- org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
- org.biojava.nbio.structure.rcsb.RCSBMacromolecule
- org.biojava.nbio.structure.rcsb.RCSBPolymer
- org.biojava.nbio.structure.rcsb.RCSBTaxonomy
- org.biojava.nbio.structure.rcsb.RCSBUpdates
- java.io.Reader (implements java.io.Closeable, java.lang.Readable)
  - org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
- org.biojava.nbio.structure.rcsb.ReadUtils
- org.biojava.nbio.structure.symmetry.geometry.RectangularPrism (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
- org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)
- java.lang.ref.Reference<T>
  - java.lang.ref.WeakReference<T>
    - org.biojava.nbio.ontology.utils.KeyedWeakReference
- org.forester.phylogeny.data.Reference (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.ReferenceParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer (implements org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer)
- org.biojava.nbio.structure.io.mmcif.model.Refine
- org.forester.applications.reinv_count
- org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
- org.biojava.nbio.ws.hmmer.RemoteHmmerScan (implements org.biojava.nbio.ws.hmmer.HmmerScan)
- org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider)
- org.biojava.nbio.structure.scop.RemoteScopInstallation (implements org.biojava.nbio.structure.scop.ScopDatabase)
- org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence (implements org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData)
- org.forester.archaeopteryx.phylogeny.data.RenderableVector (implements org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData)
- org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter
- org.biojava.nbio.survival.cox.ResidualsCoxph
- org.biojava.nbio.structure.symmetry.internal.ResidueGroup
- org.biojava.nbio.structure.ResidueNumber (implements java.lang.Comparable<T>, java.io.Serializable)
- org.biojava.nbio.structure.ResidueRange
  - org.biojava.nbio.structure.ResidueRangeAndLength
    - org.biojava.nbio.structure.AugmentedResidueRange
- org.biojava.nbio.structure.align.util.ResourceManager
- org.forester.ws.wabi.RestUtil
- org.biojava.nbio.core.search.io.Result (implements java.lang.Iterable<T>)
  - org.biojava.nbio.core.search.io.blast.BlastResult
- org.forester.application.rio
- org.forester.rio.RIO
- org.biojava.nbio.survival.cox.RiskInfo
- org.biojava.nbio.core.sequence.io.RNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
- org.biojava.nbio.ronn.RonnConstraint
- org.biojava.nbio.structure.symmetry.core.Rotation
- org.biojava.nbio.structure.align.util.RotationAxis
- org.biojava.nbio.structure.symmetry.core.RotationGroup (implements java.lang.Iterable<T>)
- org.biojava.nbio.structure.symmetry.core.RotationSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
- javax.swing.RowSorter<M>
  - javax.swing.DefaultRowSorter<M,I>
    - javax.swing.table.TableRowSorter<M>
      - org.biojava.nbio.structure.align.gui.MyTableRowSorter
- org.forester.archaeopteryx.tools.RunnableProcess (implements java.lang.Runnable)
  - org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer
  - org.forester.archaeopteryx.tools.PhylogeneticInferrer
  - org.forester.archaeopteryx.tools.SequenceDataRetriver
  - org.forester.analysis.TaxonomyDataManager
- org.biojava.nbio.structure.io.SandboxStyleStructureProvider (implements org.biojava.nbio.structure.io.StructureProvider)
- org.biojava.nbio.sequencing.io.fastq.SangerFastqReader
- org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter
- org.forester.evoinference.parsimony.SankoffParsimony<STATE_TYPE>
- org.forester.evoinference.distance.Sarray
- org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix (implements org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>)
- org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry (implements java.lang.Runnable)
- javax.xml.bind.SchemaOutputResolver
  - org.biojava.nbio.aaproperties.xml.SchemaGenerator
- org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider (implements org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider)
- org.biojava.nbio.structure.scop.ScopDescription (implements java.lang.Cloneable, java.io.Serializable)
- org.biojava.nbio.structure.scop.server.ScopDescriptions (implements java.io.Serializable)
- org.biojava.nbio.structure.scop.ScopDomain (implements java.lang.Cloneable, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
- org.biojava.nbio.structure.scop.server.ScopDomains (implements java.io.Serializable)
- org.biojava.nbio.structure.scop.ScopFactory
- org.biojava.nbio.structure.scop.ScopInstallation (implements org.biojava.nbio.structure.scop.LocalScopDatabase)
  - org.biojava.nbio.structure.scop.BerkeleyScopInstallation
- org.biojava.nbio.structure.gui.util.ScopInstallationInstance
- org.biojava.nbio.structure.scop.ScopMirror
- org.biojava.nbio.structure.scop.ScopNode (implements java.io.Serializable)
- org.biojava.nbio.structure.scop.server.ScopNodes (implements java.io.Serializable)
- org.forester.sdi.SDI
- org.forester.sdi.SDIR
- org.forester.sdi.SDIutil
- org.biojava.nbio.core.search.io.SearchIO (implements java.lang.Iterable<T>)
- org.biojava.nbio.structure.secstruc.SecStrucCalc
- org.biojava.nbio.structure.secstruc.SecStrucElement
- org.biojava.nbio.structure.secstruc.SecStrucInfo
  - org.biojava.nbio.structure.secstruc.SecStrucState
- org.biojava.nbio.structure.secstruc.SecStrucTools
- org.biojava.nbio.structure.domain.pdp.Segment (implements java.lang.Comparable<T>, java.io.Serializable)
- org.biojava.nbio.structure.domain.pdp.SegmentComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.structure.gui.SelectionImpl (implements org.biojava.nbio.structure.gui.Selection)
- org.biojava.nbio.structure.SeqMisMatchImpl (implements org.biojava.nbio.structure.SeqMisMatch, java.io.Serializable)
- org.biojava.nbio.structure.io.SeqRes2AtomAligner
- org.forester.phylogeny.data.Sequence (implements java.lang.Comparable<T>, org.forester.phylogeny.data.MultipleUris, org.forester.phylogeny.data.PhylogenyData)
- org.forester.util.SequenceAccessionTools
- org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster (implements java.lang.Cloneable)
- org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper<C>
- org.biojava.nbio.core.sequence.SequenceComparator (implements java.util.Comparator<T>)
- org.forester.ws.seqdb.SequenceDbWsTools
- org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
- org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
- org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner (implements org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner)
- org.biojava.nbio.core.sequence.template.SequenceMixin
- org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator<C> (implements java.util.Iterator<E>)
- org.biojava.nbio.structure.gui.util.SequenceMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
- org.biojava.nbio.core.sequence.SequenceOptimizationHints
- org.forester.io.parsers.phyloxml.data.SequenceParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.core.sequence.template.SequenceProxyView<C> (implements org.biojava.nbio.core.sequence.template.SequenceView<C>)
  - org.biojava.nbio.core.sequence.views.ComplementSequenceView<C>
  - org.biojava.nbio.core.sequence.views.ReversedSequenceView<C>
  - org.biojava.nbio.core.sequence.views.RnaSequenceView (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
- org.forester.phylogeny.data.SequenceRelation (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.SequenceRelationParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.core.util.SequenceTools
- org.biojava.nbio.data.sequence.SequenceUtil
- org.forester.io.writers.SequenceWriter
- org.biojava.nbio.structure.domain.SerializableCache<K,V>
  - org.biojava.nbio.structure.scop.CachedRemoteScopInstallation (implements org.biojava.nbio.structure.scop.ScopDatabase)
  - org.biojava.nbio.structure.domain.RemoteDomainProvider (implements org.biojava.nbio.structure.domain.DomainProvider)
  - org.biojava.nbio.structure.domain.RemotePDPProvider (implements org.biojava.nbio.structure.domain.PDPProvider)
- org.forester.applications.set_comparator
- org.forester.applications.shared_chars_in_ext_nodes
- org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
- org.biojava.nbio.structure.align.gui.ShowPDBIDListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.structure.io.sifts.SiftsChainEntry
- org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
- org.biojava.nbio.structure.io.sifts.SiftsEntity (implements java.io.Serializable)
- org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
- org.biojava.nbio.structure.io.sifts.SiftsResidue (implements java.io.Serializable)
- org.biojava.nbio.structure.io.sifts.SiftsSegment (implements java.io.Serializable)
- org.biojava.nbio.structure.io.sifts.SiftsXMLParser
- org.biojava.nbio.structure.align.fatcat.calc.SigEva
- org.forester.applications.simple_node_processor
- org.biojava.nbio.core.alignment.SimpleAlignedSequence<S,C> (implements org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>, java.io.Serializable)
- org.forester.surfacing.SimpleDomain (implements org.forester.protein.Domain)
- org.biojava.nbio.alignment.SimpleGapPenalty (implements org.biojava.nbio.alignment.template.GapPenalty, java.io.Serializable)
- org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
- org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser (implements org.biojava.nbio.structure.io.mmcif.MMcifParser)
- org.biojava.nbio.core.sequence.location.SimplePoint (implements org.biojava.nbio.core.sequence.location.template.Point, java.io.Serializable)
  - org.biojava.nbio.core.sequence.location.FuzzyPoint
- org.biojava.nbio.core.alignment.SimpleProfile<S,C> (implements org.biojava.nbio.core.alignment.template.Profile<S,C>, java.io.Serializable)
  - org.biojava.nbio.core.alignment.SimpleProfilePair<S,C> (implements org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
  - org.biojava.nbio.core.alignment.SimpleSequencePair<S,C> (implements org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
- org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix<C> (implements java.io.Serializable, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>)
- org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
- org.biojava.nbio.core.util.SingleLinkageClusterer
- org.biojava.nbio.structure.jama.SingularValueDecomposition (implements java.io.Serializable)
- org.biojava.nbio.phosphosite.Site
- org.biojava.nbio.structure.Site (implements java.lang.Comparable<T>, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
- org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
- org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader
- org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter
- org.biojava.nbio.structure.xtal.SpaceGroup (implements java.io.Serializable)
- org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
- org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
- org.biojava.nbio.structure.math.SparseSquareMatrix (implements java.io.Serializable)
- org.biojava.nbio.structure.math.SparseVector (implements java.io.Serializable)
- org.biojava.nbio.structure.symmetry.geometry.SphereSampler
- org.biojava.nbio.genome.util.SplitFasta
- org.biojava.nbio.structure.io.SSBondImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
- org.forester.evoinference.distance.Sset
- org.biojava.nbio.structure.StandardAminoAcid
- org.biojava.nbio.structure.align.ce.StartupParameters
  - org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
    - org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
  - org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
  - org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
- org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder (implements java.io.Serializable)
- org.biojava.nbio.survival.cox.matrix.StdArrayIO
- org.biojava.nbio.alignment.io.StockholmFileAnnotation
- org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
- org.biojava.nbio.alignment.io.StockholmFileParser
- org.biojava.nbio.alignment.io.StockholmStructure
- org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
- org.biojava.nbio.survival.cox.StrataInfo
- org.biojava.nbio.structure.align.pairwise.StrCompAlignment (implements org.biojava.nbio.structure.align.pairwise.Alignable)
- org.forester.util.StringInt
- org.forester.util.StringInt.DescendingIntComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.core.util.StringManipulationHelper
- org.biojava.nbio.core.sequence.loader.StringProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  - org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface, org.biojava.nbio.core.sequence.features.FeatureRetriever, org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface)
- org.biojava.nbio.structure.align.StrucAligParameters
- org.biojava.nbio.structure.io.mmcif.model.Struct
- org.biojava.nbio.structure.io.mmcif.model.StructKeywords
- org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
- org.biojava.nbio.structure.io.mmcif.model.StructSite
- org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
- org.biojava.nbio.structure.align.StructureAlignmentFactory
- org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
- org.biojava.nbio.protmod.structure.StructureAtom
- org.biojava.nbio.protmod.structure.StructureAtomLinkage
- org.biojava.nbio.protmod.io.StructureAtomXMLConverter
- org.biojava.nbio.protmod.structure.StructureGroup (implements java.lang.Comparable<T>)
- org.biojava.nbio.protmod.io.StructureGroupXMLConverter
- org.biojava.nbio.structure.StructureImpl (implements java.io.Serializable, org.biojava.nbio.structure.Structure)
- org.biojava.nbio.structure.contact.StructureInterface (implements java.lang.Comparable<T>, java.io.Serializable)
- org.biojava.nbio.structure.contact.StructureInterfaceCluster (implements java.io.Serializable)
- org.biojava.nbio.structure.contact.StructureInterfaceList (implements java.lang.Iterable<T>, java.io.Serializable)
- org.biojava.nbio.structure.StructureIO
- org.biojava.nbio.structure.align.client.StructureName (implements java.lang.Comparable<T>, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
- org.biojava.nbio.structure.align.StructurePairAligner
- org.biojava.nbio.structure.io.StructureSequenceMatcher
- org.biojava.nbio.structure.StructureTools
- org.biojava.nbio.protmod.structure.StructureUtil
- org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper (implements java.io.Serializable)
- org.biojava.nbio.structure.SubstructureIdentifier (implements java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
- org.forester.applications.subtree_feature_count
- org.biojava.nbio.structure.symmetry.core.SubunitGraph
- org.biojava.nbio.structure.symmetry.core.Subunits
- org.biojava.nbio.structure.symmetry.geometry.SuperPosition
- org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
- org.forester.application.support_statistics
- org.forester.application.support_transfer
- org.forester.tools.SupportCount
- org.forester.application.surfacing
- org.forester.surfacing.SurfacingConstants
- org.forester.surfacing.SurfacingUtil
- org.biojava.nbio.survival.cox.SurvFitInfo
- org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
- org.biojava.nbio.survival.cox.SurvivalInfo (implements java.lang.Comparable<T>)
- org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.survival.cox.SurvivalInfoHelper
- org.biojava.nbio.survival.cox.SurvivalInfoIndex (implements java.lang.Comparable<T>)
- org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator (implements java.util.Comparator<T>)
- org.biojava.nbio.structure.SVDSuperimposer
- javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
  - org.biojava.nbio.structure.align.gui.StructureLoaderThread
- org.biojava.nbio.structure.math.SymbolTable<Key,Value> (implements java.lang.Iterable<T>, java.io.Serializable)
- org.biojava.nbio.structure.validation.SymmClash
- org.forester.io.parsers.SymmetricalDistanceMatrixParser
- org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
- org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
- org.biojava.nbio.structure.symmetry.gui.SymmetryCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
- org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
- org.biojava.nbio.structure.symmetry.gui.SymmetryListener (implements java.awt.event.ActionListener)
- org.biojava.nbio.structure.symmetry.utils.SymmetryTools
- org.biojava.nbio.structure.symmetry.internal.SymmOptimizer
- org.biojava.nbio.structure.xtal.SymoplibParser
- org.biojava.nbio.structure.align.util.SynchronizedOutFile
- org.biojava.nbio.ontology.Synonym (implements java.lang.Comparable<T>)
- org.biojava.nbio.structure.symmetry.core.SystematicSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
- org.forester.util.SystemCommandExecutor
- org.biojava.nbio.structure.align.gui.SystemInfo
- org.biojava.nbio.ontology.io.TabDelimParser
- org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
- org.biojava.nbio.core.sequence.transcription.Table.Codon (implements org.biojava.nbio.core.sequence.template.Compound)
- org.forester.application.table2fasta
- org.forester.applications.tax_code_cleaner
- org.forester.phylogeny.data.Taxonomy (implements java.lang.Comparable<T>, org.forester.phylogeny.data.MultipleUris, org.forester.phylogeny.data.PhylogenyData)
- org.forester.util.TaxonomyColors
- org.biojava.nbio.core.sequence.TaxonomyID
- org.forester.io.parsers.phyloxml.data.TaxonomyParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.forester.util.TaxonomyUtil
- org.forester.development.Test
- org.forester.test.Test
- org.forester.ws.hmmer.Test
- org.forester.go.TestGo
- org.forester.sdi.TestGSDI
- org.forester.pccx.TestPccx
- org.forester.evoinference.TestPhylogenyReconstruction
- org.forester.rio.TestRIO
- org.forester.surfacing.TestSurfacing
- org.biojava.nbio.structure.symmetry.geometry.Tetrahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
- java.lang.Throwable (implements java.io.Serializable)
  - java.lang.Error
    - java.lang.AssertionError
      - org.biojava.nbio.ontology.utils.AssertionFailure
  - java.lang.Exception
    - org.forester.analysis.AncestralTaxonomyInferenceException
    - org.biojava.nbio.core.exceptions.CompoundNotFoundException
    - org.biojava.nbio.structure.align.util.ConfigurationException
    - java.io.IOException
      - org.forester.msa.MsaFormatException
      - org.forester.io.parsers.nexus.NexusFormatException
      - org.forester.io.parsers.nhx.NHXFormatException
      - org.forester.io.parsers.util.PhylogenyParserException
      - org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException
    - org.biojava.nbio.structure.align.client.JobKillException
    - org.biojava.nbio.ontology.OntologyException
      - org.biojava.nbio.ontology.AlreadyExistsException
      - org.biojava.nbio.ontology.InvalidTermException
    - org.biojava.nbio.structure.io.PDBParseException
    - org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
    - org.forester.rio.RIOException
    - java.lang.RuntimeException
      - org.forester.util.FailedConditionCheckException
      - java.lang.IllegalArgumentException
        
        org.forester.util.IllegalFormatUseException
      - org.biojava.nbio.core.exceptions.ParserException
      - org.forester.io.parsers.phyloxml.PhyloXmlException
      - org.biojava.nbio.structure.scop.ScopIOException
      - org.biojava.nbio.core.exceptions.TranslationException
    - org.forester.sdi.SDIException
    - org.biojava.nbio.structure.StructureException
- org.forester.development.Time
- org.biojava.nbio.ronn.Timer
- org.forester.io.parsers.tol.TolParser (implements org.forester.io.parsers.PhylogenyParser)
- org.forester.io.parsers.tol.TolXmlMapping
- org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
- org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
- org.forester.archaeopteryx.TreeColorSet
- org.biojava.nbio.phylo.TreeConstructor
- org.forester.archaeopteryx.TreeFontSet
- org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper (implements java.io.Serializable)
- org.forester.archaeopteryx.TreePanelUtil
- org.biojava.nbio.structure.scop.server.TreeSetStringWrapper (implements java.io.Serializable)
- org.forester.tools.TreeSplitMatrix
- org.biojava.nbio.ontology.Triple.Impl (implements java.io.Serializable, org.biojava.nbio.ontology.Triple)
- org.forester.ws.wabi.TxSearch
- org.forester.ws.seqdb.UniProtEntry (implements org.forester.ws.seqdb.SequenceDatabaseEntry)
- org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface, org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface, org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
- org.forester.ws.seqdb.UniProtTaxonomy
- org.biojava.nbio.genome.uniprot.UniprotToFasta
- org.biojava.nbio.structure.symmetry.core.UniqueSequenceList (implements java.lang.Cloneable)
- org.biojava.nbio.structure.xtal.UnitCellBoundingBox
- org.forester.phylogeny.data.Uri (implements org.forester.phylogeny.data.PhylogenyData)
- org.forester.io.parsers.phyloxml.data.UriParser (implements org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser)
- org.biojava.nbio.structure.URLIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
- org.forester.archaeopteryx.UrlTreeReader (implements java.lang.Runnable)
- org.biojava.nbio.structure.align.util.UserConfiguration
- org.biojava.nbio.aaproperties.Utils
- org.forester.ws.wabi.WabiTools
- org.biojava.nbio.survival.cox.WaldTest
- org.biojava.nbio.survival.cox.WaldTestInfo
- org.forester.archaeopteryx.webservices.WebservicesManager
- org.forester.archaeopteryx.webservices.WebserviceUtil
- org.biojava.nbio.structure.align.webstart.WebStartDBSearch
- org.biojava.nbio.structure.align.webstart.WebStartDBSearchResults
- org.biojava.nbio.structure.align.webstart.WebStartMain
- org.forester.applications.wiki_examples
- org.biojava.nbio.core.sequence.views.WindowedSequence<C> (implements java.lang.Iterable<T>)
- org.forester.util.WindowsUtils
- org.biojava.nbio.survival.data.WorkSheet
- java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
  - java.io.BufferedWriter
    - org.forester.util.EasyWriter
- org.biojava.nbio.structure.validation.WwPDBValidationInformation (implements java.io.Serializable)
- javax.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
  - org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
- org.forester.io.parsers.phyloxml.XmlElement
- org.biojava.nbio.core.util.XMLHelper
- org.biojava.nbio.structure.scop.server.XMLUtil
- org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)

Interface Hierarchy

org.biojava.nbio.core.alignment.matrices.AAIndexProvider
org.biojava.nbio.core.sequence.template.Accessioned
- org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.location.template.Location)
- org.biojava.nbio.core.sequence.location.template.Location (also extends java.lang.Iterable<T>)
  - org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.template.Accessioned)
- org.biojava.nbio.core.sequence.template.Sequence<C> (also extends java.lang.Iterable<T>)
  - org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
    - org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
  - org.biojava.nbio.core.sequence.template.SequenceReader<C>
    - org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
  - org.biojava.nbio.core.sequence.template.SequenceView<C>
org.biojava.nbio.structure.align.pairwise.Alignable
org.biojava.nbio.structure.gui.events.AlignmentPositionListener
org.biojava.nbio.structure.align.events.AlignmentProgressListener
org.biojava.nbio.ontology.utils.Annotatable
- org.biojava.nbio.ontology.Term
  - org.biojava.nbio.ontology.OntologyTerm
  - org.biojava.nbio.ontology.RemoteTerm
  - org.biojava.nbio.ontology.Triple
  - org.biojava.nbio.ontology.Variable
org.biojava.nbio.ontology.utils.Annotation
org.biojava.nbio.structure.AtomPositionMap.GroupMatcher
org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
org.biojava.nbio.structure.Bond
org.biojava.nbio.structure.cath.CathDatabase
org.biojava.nbio.survival.kaplanmeier.figure.CensorStatusSelect
org.biojava.nbio.structure.Chain
org.biojava.nbio.survival.data.ChangeValue
org.forester.evoinference.matrix.character.CharacterStateMatrix<S>
org.biojava.nbio.structure.io.mmcif.ChemCompProvider
java.lang.Cloneable
- org.biojava.nbio.structure.Atom (also extends org.biojava.nbio.structure.PDBRecord)
- org.biojava.nbio.structure.Structure
org.biojava.nbio.structure.gui.util.color.ColorInterpolator
org.forester.surfacing.CombinableDomains
java.lang.Comparable<T>
- org.forester.protein.BinaryDomainCombination
- org.forester.protein.Domain
- org.forester.go.GoRelationship
- org.forester.go.GoSubset
- org.forester.go.GoTerm (also extends org.forester.phylogeny.data.PhylogenyData)
- org.forester.go.GoXRef
- org.forester.go.Mapping
- org.biojava.nbio.core.sequence.location.template.Point
- org.forester.species.Species
java.util.Comparator<T>
- org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
org.biojava.nbio.core.sequence.template.Compound
- org.biojava.nbio.core.sequence.template.ComplementCompound
org.biojava.nbio.core.sequence.template.CompoundSet<C>
org.biojava.nbio.core.sequence.template.CompoundTranslator<F,T>
org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
org.forester.pccx.Coverage
org.forester.pccx.CoverageCalculationMethod
org.forester.pccx.CoverageCalculationOptions
org.forester.pccx.CoverageExtender
org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface
org.forester.util.DescriptiveStatistics
org.biojava.nbio.survival.kaplanmeier.metadata.DiscreteQuantizerInterface
org.forester.evoinference.matrix.distance.DistanceMatrix
org.biojava.nbio.structure.domain.DomainProvider
org.forester.surfacing.DomainSimilarityCalculator
org.biojava.nbio.structure.ecod.EcodDatabase
org.biojava.nbio.core.sequence.edits.Edit<C>
org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface<S,C>
org.biojava.nbio.sequencing.io.fastq.FastqReader
org.biojava.nbio.sequencing.io.fastq.FastqWriter
org.biojava.nbio.genome.parsers.gff.FeatureI
org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>
org.biojava.nbio.core.sequence.features.FeatureRetriever
org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface
org.biojava.nbio.alignment.template.GapPenalty
org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S,C>
org.forester.surfacing.GenomeWideCombinableDomains
org.biojava.nbio.structure.Group
- org.biojava.nbio.structure.AminoAcid
org.forester.sdi.GSDII
org.biojava.nbio.alignment.template.HierarchicalClusterer<S,C>
org.biojava.nbio.ws.hmmer.HmmerScan
org.biojava.nbio.core.sequence.io.util.IOUtils.ReaderProcessor
org.biojava.nbio.aaproperties.IPeptideProperties
org.biojava.nbio.aaproperties.profeat.IProfeatProperties
java.lang.Iterable<T>
- org.biojava.nbio.core.sequence.location.template.Location (also extends org.biojava.nbio.core.sequence.template.Accessioned)
  - org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.template.Accessioned)
- org.biojava.nbio.core.alignment.template.Profile<S,C>
  - org.biojava.nbio.core.alignment.template.MutableProfile<S,C>
    - org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
    - org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
  - org.biojava.nbio.core.alignment.template.ProfilePair<S,C>
    - org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
  - org.biojava.nbio.core.alignment.template.ProfileView<S,C>
  - org.biojava.nbio.core.alignment.template.SequencePair<S,C>
    - org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
- org.biojava.nbio.core.sequence.template.Sequence<C> (also extends org.biojava.nbio.core.sequence.template.Accessioned)
  - org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
    - org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
  - org.biojava.nbio.core.sequence.template.SequenceReader<C>
    - org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
  - org.biojava.nbio.core.sequence.template.SequenceView<C>
org.forester.io.parsers.IteratingPhylogenyParser
java.util.Iterator<E>
- org.forester.phylogeny.iterators.PhylogenyNodeIterator
org.biojava.nbio.core.sequence.template.LightweightProfile<S,C>
org.biojava.nbio.structure.align.ce.MatrixListener
org.biojava.nbio.structure.io.mmcif.MMcifConsumer
org.biojava.nbio.structure.io.mmcif.MMcifParser
org.biojava.nbio.protmod.ModificationCondition
org.biojava.nbio.protmod.structure.ModifiedCompound
org.forester.sequence.MolecularSequence
org.forester.msa.Msa
org.biojava.nbio.structure.align.MultipleStructureAligner
org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer
org.forester.phylogeny.data.MultipleUris
org.biojava.nbio.ontology.obo.OboFileEventListener
org.biojava.nbio.ontology.Ontology
org.biojava.nbio.ontology.OntologyFactory
org.biojava.nbio.ontology.OntologyOps
org.biojava.nbio.structure.symmetry.internal.OrderDetector
org.forester.surfacing.PairwiseDomainSimilarity
org.forester.surfacing.PairwiseDomainSimilarityCalculator
org.biojava.nbio.sequencing.io.fastq.ParseListener
org.biojava.nbio.structure.PDBRecord
- org.biojava.nbio.structure.Atom (also extends java.lang.Cloneable)
org.biojava.nbio.structure.domain.PDPProvider
org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
org.forester.phylogeny.data.PhylogenyData
- org.forester.go.GoTerm (also extends java.lang.Comparable<T>)
- org.forester.archaeopteryx.phylogeny.data.RenderablePhylogenyData
org.forester.io.parsers.phyloxml.data.PhylogenyDataPhyloXmlParser
org.forester.phylogeny.factories.PhylogenyFactory
org.forester.io.parsers.PhylogenyParser
org.biojava.nbio.core.sequence.location.template.Point.Resolver<T>
org.biojava.nbio.structure.symmetry.geometry.Polyhedron
org.forester.protein.Protein
org.biojava.nbio.protmod.ProteinModification
org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
org.biojava.nbio.core.search.io.ResultFactory
java.lang.Runnable
- org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
org.biojava.nbio.structure.scop.ScopDatabase
- org.biojava.nbio.structure.scop.LocalScopDatabase
org.biojava.nbio.alignment.template.Scorer
- org.biojava.nbio.alignment.template.Aligner<S,C>
  - org.biojava.nbio.alignment.template.MatrixAligner<S,C>
  - org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
  - org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
  - org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
  - org.biojava.nbio.alignment.template.RescoreRefiner<S,C>
- org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>
  - org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>
  - org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
- org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>
  - org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
  - org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
org.biojava.nbio.structure.align.multiple.ScoresCache
- org.biojava.nbio.structure.align.multiple.Block
- org.biojava.nbio.structure.align.multiple.BlockSet
- org.biojava.nbio.structure.align.multiple.MultipleAlignment
- org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
org.forester.pccx.ScoringMethodForExternalNode
org.biojava.nbio.structure.gui.Selection
org.biojava.nbio.structure.SeqMisMatch
org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>
org.forester.ws.seqdb.SequenceDatabaseEntry
org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>
org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
java.io.Serializable
- org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
- org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
org.biojava.nbio.sequencing.io.fastq.StreamListener
org.biojava.nbio.structure.align.StructureAlignment
org.biojava.nbio.structure.StructureIdentifier
org.biojava.nbio.structure.gui.util.StructurePairSelector
org.biojava.nbio.structure.io.StructureProvider
- org.biojava.nbio.structure.io.StructureIOFile
org.biojava.nbio.structure.gui.StructureViewer
org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>
org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner
org.biojava.nbio.core.sequence.transcription.Table
javax.swing.tree.TreeNode
- org.biojava.nbio.alignment.template.GuideTreeNode<S,C>
org.biojava.nbio.structure.align.ce.UserArgumentProcessor
org.biojava.nbio.core.util.XMLWriter

Annotation Interface Hierarchy

org.biojava.nbio.structure.io.mmcif.model.CIFLabel (implements java.lang.annotation.Annotation)
org.biojava.nbio.structure.io.mmcif.model.IgnoreField (implements java.lang.annotation.Annotation)

Enum Class Hierarchy

java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
  - org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
  - org.forester.phylogeny.data.Accession.Source
  - org.biojava.nbio.core.alignment.template.AlignedSequence.Step
  - org.biojava.nbio.alignment.routines.AlignerHelper.Last
  - org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
  - org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
  - org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
  - org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
  - org.biojava.nbio.alignment.Alignments.RefinerType
  - org.forester.archaeopteryx.AptxUtil.GraphicsExportType
  - org.biojava.nbio.structure.scop.Astral.AstralSet
  - org.forester.protein.BinaryDomainCombination.DomainCombinationType
  - org.forester.protein.BinaryDomainCombination.OutputFormat
  - org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
  - org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
  - org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
  - org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
  - org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
  - org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
  - org.biojava.nbio.structure.BondType
  - org.biojava.nbio.structure.xtal.BravaisLattice
  - org.biojava.nbio.structure.secstruc.BridgeType
  - org.biojava.nbio.structure.cath.CathCategory
  - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
  - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
  - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
  - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
  - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
  - org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates
  - org.forester.evoinference.matrix.character.CharacterStateMatrix.Format
  - org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates
  - org.forester.evoinference.matrix.character.CharacterStateMatrix.NucleotideStates
  - org.jcolorbrewer.ColorBrewer
  - org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
  - org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON
  - org.forester.archaeopteryx.Configuration.UI
  - org.biojava.nbio.survival.cox.CoxMethod
  - org.biojava.nbio.core.sequence.DataSource
  - org.forester.evoinference.matrix.distance.DistanceMatrix.Format
  - org.biojava.nbio.core.sequence.DNASequence.DNAType
  - org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
  - org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
  - org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField
  - org.forester.surfacing.DomainSimilarity.PRINT_OPTION
  - org.forester.surfacing.DomainSimilarityCalculator.Detailedness
  - org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput
  - org.biojava.nbio.structure.Element (implements java.io.Serializable)
  - org.biojava.nbio.structure.ElementType (implements java.io.Serializable)
  - org.forester.phylogeny.data.Event.EventType
  - org.biojava.nbio.structure.ExperimentalTechnique
  - org.biojava.nbio.sequencing.io.fastq.FastqVariant
  - org.forester.util.ForesterConstants.PhylogeneticTreeFormats
  - org.biojava.nbio.core.sequence.transcription.Frame
  - org.biojava.nbio.alignment.template.GapPenalty.Type
  - org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
  - org.forester.go.GoNameSpace.GoNamespaceType
  - org.forester.go.GoRelationship.Type
  - org.forester.go.GoSubset.Type
  - org.forester.go.GoXRef.Type
  - org.biojava.nbio.structure.GroupType
  - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
  - org.forester.io.parsers.HmmPfamOutputParser.FilterType
  - org.forester.io.parsers.HmmPfamOutputParser.ReturnType
  - org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType
  - org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
  - org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType
  - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
  - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
  - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
  - org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
  - org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
  - org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
  - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
  - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
  - org.biojava.nbio.protmod.ModificationCategory
  - org.biojava.nbio.protmod.ModificationOccurrenceType
  - org.forester.sequence.MolecularSequence.TYPE
  - org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass
  - org.forester.msa.Msa.MSA_FORMAT
  - org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION
  - org.forester.phylogeny.data.NodeDataField
  - org.forester.phylogeny.data.NodeVisualData.FontType
  - org.forester.phylogeny.data.NodeVisualData.NodeFill
  - org.forester.phylogeny.data.NodeVisualData.NodeShape
  - org.forester.go.OBOparser.ReturnType
  - org.forester.go.etc.OntologizerResult.TYPE
  - org.forester.archaeopteryx.Options.CLADOGRAM_TYPE
  - org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION
  - org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE
  - org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
  - org.biojava.nbio.structure.PDBStatus.Status
  - org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
  - org.forester.archaeopteryx.tools.PhylogeneticInferrer.MSA_PRG
  - org.forester.tools.PhylogenyDecorator.FIELD
  - org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY
  - org.forester.phylogeny.PhylogenyMethods.PhylogenyNodeField
  - org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE
  - org.forester.io.writers.PhylogenyWriter.FORMAT
  - org.biojava.nbio.structure.io.mmcif.chem.PolymerType (implements java.io.Serializable)
  - org.biojava.nbio.core.alignment.template.Profile.StringFormat
  - org.forester.phylogeny.data.Property.AppliesTo
  - org.biojava.nbio.structure.gui.RenderStyle
  - org.biojava.nbio.survival.cox.ResidualsCoxph.Type
  - org.biojava.nbio.structure.io.mmcif.chem.ResidueType (implements java.io.Serializable)
  - org.forester.rio.RIO.REROOTING
  - org.biojava.nbio.ronn.RonnConstraint.Threshold
  - org.biojava.nbio.structure.scop.ScopCategory (implements java.io.Serializable)
  - org.forester.sdi.SDIutil.ALGORITHM
  - org.forester.sdi.SDIutil.TaxonomyComparisonBase
  - org.biojava.nbio.structure.secstruc.SecStrucType
  - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
  - org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
  - org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE
  - org.forester.io.writers.SequenceWriter.SEQ_FORMAT
  - org.biojava.nbio.genome.parsers.cytoband.StainType (implements java.io.Serializable)
  - org.biojava.nbio.core.sequence.Strand
  - org.biojava.nbio.structure.StructureIO.StructureFiletype
  - org.biojava.nbio.structure.align.client.StructureName.Source
  - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
  - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
  - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
  - org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
  - org.forester.io.parsers.SymmetricalDistanceMatrixParser.InputMatrixType
  - org.biojava.nbio.structure.xtal.TransformType
  - org.biojava.nbio.phylo.TreeConstructorType
  - org.biojava.nbio.phylo.TreeType
  - org.forester.ws.wabi.TxSearch.RANKS
  - org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS
  - org.forester.ws.wabi.TxSearch.TAX_RANK
  - org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat

Hierarchy For All Packages

Class Hierarchy

Interface Hierarchy

Annotation Interface Hierarchy

Enum Class Hierarchy