Hierarchy For All Packages

Package Hierarchies:

org.biojava.bio.structure, org.biojava.bio.structure.align, org.biojava.bio.structure.align.ce, org.biojava.bio.structure.align.client, org.biojava.bio.structure.align.events, org.biojava.bio.structure.align.fatcat, org.biojava.bio.structure.align.fatcat.calc, org.biojava.bio.structure.align.gui, org.biojava.bio.structure.align.gui.aligpanel, org.biojava.bio.structure.align.gui.autosuggest, org.biojava.bio.structure.align.gui.jmol, org.biojava.bio.structure.align.helper, org.biojava.bio.structure.align.model, org.biojava.bio.structure.align.pairwise, org.biojava.bio.structure.align.seq, org.biojava.bio.structure.align.util, org.biojava.bio.structure.align.webstart, org.biojava.bio.structure.align.xml, org.biojava.bio.structure.domain, org.biojava.bio.structure.domain.pdp, org.biojava.bio.structure.gui, org.biojava.bio.structure.gui.events, org.biojava.bio.structure.gui.util, org.biojava.bio.structure.gui.util.color, org.biojava.bio.structure.io, org.biojava.bio.structure.io.mmcif, org.biojava.bio.structure.io.mmcif.chem, org.biojava.bio.structure.io.mmcif.model, org.biojava.bio.structure.io.sifts, org.biojava.bio.structure.io.util, org.biojava.bio.structure.jama, org.biojava.bio.structure.scop, org.biojava.bio.structure.scop.server, org.biojava.bio.structure.secstruc, org.biojava.bio.structure.server, org.biojava3.aaproperties, org.biojava3.aaproperties.profeat, org.biojava3.aaproperties.profeat.convertor, org.biojava3.aaproperties.xml, org.biojava3.alignment, org.biojava3.alignment.aaindex, org.biojava3.alignment.routines, org.biojava3.alignment.template, org.biojava3.core.exceptions, org.biojava3.core.sequence, org.biojava3.core.sequence.compound, org.biojava3.core.sequence.edits, org.biojava3.core.sequence.features, org.biojava3.core.sequence.io, org.biojava3.core.sequence.io.template, org.biojava3.core.sequence.io.util, org.biojava3.core.sequence.loader, org.biojava3.core.sequence.location, org.biojava3.core.sequence.location.template, org.biojava3.core.sequence.storage, org.biojava3.core.sequence.template, org.biojava3.core.sequence.transcription, org.biojava3.core.sequence.views, org.biojava3.core.util, org.biojava3.data.sequence, org.biojava3.genome, org.biojava3.genome.homology, org.biojava3.genome.parsers.geneid, org.biojava3.genome.parsers.gff, org.biojava3.genome.query, org.biojava3.genome.uniprot, org.biojava3.genome.util, org.biojava3.phylo, org.biojava3.protmod, org.biojava3.protmod.io, org.biojava3.protmod.structure, org.biojava3.ronn, org.biojava3.sequencing.io.fastq, org.biojava3.structure.gui, org.biojava3.ws.alignment, org.biojava3.ws.alignment.qblast, org.biojava3.ws.hmmer, org.forester.application, org.forester.archaeopteryx, org.forester.archaeopteryx.phylogeny.data, org.forester.archaeopteryx.webservices, org.forester.datastructures, org.forester.development, org.forester.go, org.forester.go.etc, org.forester.io.parsers, org.forester.io.parsers.nexus, org.forester.io.parsers.nhx, org.forester.io.parsers.phyloxml, org.forester.io.parsers.phyloxml.phylogenydata, org.forester.io.parsers.tol, org.forester.io.writers, org.forester.pccx, org.forester.phylogeny, org.forester.phylogeny.data, org.forester.phylogeny.factories, org.forester.phylogeny.iterators, org.forester.phylogenyinference, org.forester.sdi, org.forester.surfacing, org.forester.test, org.forester.tools, org.forester.util

Class Hierarchy

• java.lang.Object
  • org.biojava3.alignment.aaindex.AAindexFactory
  • org.biojava3.alignment.aaindex.AAIndexFileParser
  • org.biojava.bio.structure.align.gui.AboutDialog
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • org.biojava.bio.structure.align.gui.ChooseDirAction
  • org.biojava.bio.structure.io.mmcif.model.AbstractBean
    • org.biojava.bio.structure.io.mmcif.model.AtomSite
    • org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
    • org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
    • org.biojava.bio.structure.io.mmcif.model.Exptl
    • org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
    • org.biojava.bio.structure.io.mmcif.model.StructAsym
    • org.biojava.bio.structure.io.mmcif.model.StructRef
    • org.biojava.bio.structure.io.mmcif.model.StructRefSeq
  • 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.biojava3.genome.parsers.gff.FeatureList
  • org.biojava3.core.sequence.template.AbstractCompound (implements org.biojava3.core.sequence.template.Compound)
    • org.biojava3.core.sequence.compound.AminoAcidCompound
    • org.biojava3.core.sequence.compound.CodonCompound
    • org.biojava3.core.sequence.compound.NucleotideCompound (implements org.biojava3.core.sequence.template.ComplementCompound)
  • org.biojava3.core.sequence.template.AbstractCompoundSet<C> (implements org.biojava3.core.sequence.template.CompoundSet<C>)
    • org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet<C>
      • org.biojava3.core.sequence.compound.DNACompoundSet
        • org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
      • org.biojava3.core.sequence.compound.RNACompoundSet
        • org.biojava3.core.sequence.compound.AmbiguityRNACompoundSet
  • org.biojava3.core.sequence.template.AbstractCompoundTranslator<F,T> (implements org.biojava3.core.sequence.template.CompoundTranslator<F,T>)
    • org.biojava3.core.sequence.transcription.DNAToRNATranslator
    • org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator
  • org.biojava3.core.sequence.features.AbstractFeature<S,C> (implements org.biojava3.core.sequence.features.FeatureInterface<S,C>)
    • org.biojava3.core.sequence.features.QualityFeature<S,C>
    • org.biojava3.core.sequence.features.QuantityFeature<S,C>
    • org.biojava3.core.sequence.features.TextFeature<S,C>
  • org.biojava3.core.sequence.location.template.AbstractLocation (implements org.biojava3.core.sequence.location.template.Location)
    • org.biojava3.core.sequence.location.InsdcLocations.BondLocation
    • org.biojava3.core.sequence.location.InsdcLocations.OneOfLocation
    • org.biojava3.core.sequence.location.SimpleLocation
      • org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
      • org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
      • org.biojava3.core.sequence.location.SequenceLocation<S,C>
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • org.biojava.bio.structure.align.util.AlignmentTools.IdentityMap<K>
    • org.biojava3.core.util.SoftHashMap<K,V>
  • org.biojava3.alignment.template.AbstractScorer (implements org.biojava3.alignment.template.Scorer)
    • org.biojava3.alignment.template.AbstractMatrixAligner<S,C> (implements org.biojava3.alignment.template.MatrixAligner<S,C>)
      • org.biojava3.alignment.template.AbstractPairwiseSequenceAligner<S,C> (implements org.biojava3.alignment.template.PairwiseSequenceAligner<S,C>)
        • org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>
          • org.biojava3.alignment.routines.GuanUberbacher<S,C>
        • org.biojava3.alignment.NeedlemanWunsch<S,C>
        • org.biojava3.alignment.SmithWaterman<S,C>
      • org.biojava3.alignment.template.AbstractProfileProfileAligner<S,C> (implements org.biojava3.alignment.template.ProfileProfileAligner<S,C>)
        • org.biojava3.alignment.SimpleProfileProfileAligner<S,C>
    • org.biojava3.alignment.FractionalIdentityScorer<S,C> (implements org.biojava3.alignment.template.PairwiseSequenceScorer<S,C>)
      • org.biojava3.alignment.FractionalIdentityInProfileScorer<S,C> (implements org.biojava3.alignment.template.PairInProfileScorer<S,C>)
    • org.biojava3.alignment.FractionalSimilarityScorer<S,C> (implements org.biojava3.alignment.template.PairwiseSequenceScorer<S,C>)
      • org.biojava3.alignment.FractionalSimilarityInProfileScorer<S,C> (implements org.biojava3.alignment.template.PairInProfileScorer<S,C>)
    • org.biojava3.alignment.StandardRescoreRefiner<S,C> (implements org.biojava3.alignment.template.RescoreRefiner<S,C>)
  • org.biojava3.core.sequence.template.AbstractSequence<C> (implements org.biojava3.core.sequence.template.Sequence<C>)
    • org.biojava3.core.sequence.BasicSequence<C>
    • org.biojava3.core.sequence.DNASequence
      • org.biojava3.core.sequence.CDSSequence
      • org.biojava3.core.sequence.ChromosomeSequence
      • org.biojava3.core.sequence.ExonSequence
      • org.biojava3.core.sequence.GeneSequence
      • org.biojava3.core.sequence.IntronSequence
      • org.biojava3.core.sequence.StartCodonSequence
      • org.biojava3.core.sequence.StopCodonSequence
      • org.biojava3.core.sequence.TranscriptSequence
    • org.biojava3.core.sequence.ProteinSequence
    • org.biojava3.core.sequence.RNASequence
  • org.biojava.bio.structure.align.AbstractStructureAlignment (implements org.biojava.bio.structure.align.StructureAlignment)
    • org.biojava.bio.structure.align.ce.CeMain (implements org.biojava.bio.structure.align.StructureAlignment)
      • org.biojava.bio.structure.align.ce.CeCPMain
      • org.biojava.bio.structure.align.ce.CeSideChainMain (implements org.biojava.bio.structure.align.StructureAlignment)
      • org.biojava.bio.structure.align.ce.OptimalCECPMain
    • org.biojava.bio.structure.align.seq.SmithWaterman3Daligner (implements org.biojava.bio.structure.align.StructureAlignment)
  • org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor (implements org.biojava.bio.structure.align.ce.UserArgumentProcessor)
    • org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor
    • org.biojava.bio.structure.align.ce.CeUserArgumentProcessor
      • org.biojava.bio.structure.align.ce.CeCPUserArgumentProcessor
    • org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor
    • org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor
  • org.forester.phylogeny.data.Accession (implements org.forester.phylogeny.data.PhylogenyData)
  • org.biojava3.core.sequence.AccessionID
  • org.forester.io.parsers.phyloxml.phylogenydata.AccessionParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava.bio.structure.align.model.AFP (implements java.io.Serializable)
  • org.biojava.bio.structure.align.util.AFPAlignmentDisplay
  • org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
  • org.biojava.bio.structure.align.model.AFPChain (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
  • org.biojava.bio.structure.align.fatcat.calc.AFPChainer
  • org.biojava.bio.structure.align.xml.AFPChainFlipper
  • org.biojava.bio.structure.align.util.AFPChainScorer
  • org.biojava.bio.structure.align.model.AfpChainWriter
  • org.biojava.bio.structure.align.xml.AFPChainXMLConverter
  • org.biojava.bio.structure.align.xml.AFPChainXMLParser
  • org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
  • org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor
  • org.biojava.bio.structure.align.AFPTwister
  • org.biojava.bio.structure.gui.util.AlignedPosition
  • org.biojava3.alignment.routines.AlignerHelper
  • org.biojava3.alignment.routines.AlignerHelper.Cut
  • org.biojava.bio.structure.align.gui.AlignmentCalc (implements org.biojava.bio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.bio.structure.gui.util.AlignmentCalc (implements java.lang.Runnable)
  • org.biojava.bio.structure.align.gui.AlignmentCalcDB (implements org.biojava.bio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.bio.structure.align.pairwise.AlignmentProgressListener
  • org.biojava.bio.structure.align.pairwise.AlignmentResult (implements java.io.Serializable)
  • org.biojava3.alignment.Alignments
  • org.biojava.bio.structure.align.util.AlignmentTools
  • org.biojava.bio.structure.align.pairwise.AligNPE
  • org.biojava.bio.structure.align.helper.AlignTools
  • org.biojava.bio.structure.align.gui.aligpanel.AligPanelMouseMotionListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava.bio.structure.align.webstart.AligUIManager
  • org.biojava.bio.structure.io.mmcif.AllChemCompProvider (implements org.biojava.bio.structure.io.mmcif.ChemCompProvider, java.lang.Runnable)
  • org.biojava.bio.structure.align.pairwise.AltAligComparator (implements java.util.Comparator<T>)
  • org.biojava.bio.structure.align.pairwise.AlternativeAlignment (implements java.io.Serializable)
  • org.forester.development.AminoAcid
  • org.biojava3.aaproperties.xml.AminoAcidComposition
  • org.biojava3.aaproperties.xml.AminoAcidCompositionTable
  • org.biojava3.core.sequence.compound.AminoAcidCompoundSet (implements org.biojava3.core.sequence.template.CompoundSet<C>)
  • org.forester.development.AminoAcidSequence (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.phylogeny.data.Annotation (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.AnnotationParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava3.genome.App
  • org.biojava3.phylo.App
  • org.forester.archaeopteryx.Archaeopteryx
  • org.biojava3.core.sequence.storage.ArrayListSequenceReader<C> (implements org.biojava3.core.sequence.template.SequenceReader<C>)
    • org.biojava3.core.sequence.loader.ArrayListProxySequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.forester.util.AsciiHistogram
  • org.biojava.bio.structure.domain.AssignmentXMLSerializer
  • org.biojava.bio.structure.align.util.AtomCache
  • org.biojava.bio.structure.AtomImpl (implements org.biojava.bio.structure.Atom, org.biojava.bio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.bio.structure.align.gui.jmol.AtomInfo
  • org.biojava.bio.structure.align.gui.jmol.AtomInfoParser
  • org.biojava.bio.structure.AtomIterator (implements java.util.Iterator<E>)
  • org.biojava.bio.structure.io.mmcif.model.AuditAuthor
  • org.biojava.bio.structure.Author (implements java.io.Serializable)
  • org.forester.surfacing.BasicBinaryDomainCombination (implements org.forester.surfacing.BinaryDomainCombination)
    • org.forester.surfacing.AdjactantDirectedBinaryDomainCombination
    • org.forester.surfacing.DirectedBinaryDomainCombination
  • org.forester.phylogenyinference.BasicCharacterStateMatrix<S> (implements org.forester.phylogenyinference.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.surfacing.BasicDomain (implements org.forester.surfacing.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.development.BasicMsa (implements org.forester.development.Msa)
  • org.forester.archaeopteryx.webservices.BasicPhylogeniesWebserviceClient (implements org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient)
  • org.forester.phylogeny.factories.BasicPhylogenyFactory (implements org.forester.phylogeny.factories.PhylogenyFactory)
    • org.forester.phylogeny.factories.ParserBasedPhylogenyFactory
  • org.forester.surfacing.BasicProtein (implements org.forester.surfacing.Protein)
  • org.forester.surfacing.BasicSpecies (implements org.forester.surfacing.Species)
  • org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix (implements org.forester.phylogenyinference.DistanceMatrix)
  • org.forester.util.BasicTable<E>
  • org.forester.util.BasicTableParser
  • org.biojava.bio.structure.secstruc.BigSqrt
  • org.forester.phylogeny.data.BinaryCharacters (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.BinaryCharactersParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava.bio.structure.gui.BiojavaJmol
  • org.biojava.bio.structure.align.BioJavaStructureAlignment (implements org.biojava.bio.structure.align.StructureAlignment)
  • org.biojava3.core.sequence.storage.BitSequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
    • org.biojava3.core.sequence.storage.FourBitSequenceReader<C>
    • org.biojava3.core.sequence.storage.TwoBitSequenceReader<C>
  • org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
    • org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker<C>
    • org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker<C>
  • org.forester.archaeopteryx.Blast
  • org.biojava3.genome.homology.BlastHomologyHits
  • org.biojava3.ws.alignment.qblast.BlastJob
  • org.biojava3.genome.query.BlastXMLQuery
  • org.biojava.bio.structure.Bond
  • 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.phylogenydata.BranchWidthParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava.bio.structure.align.webstart.BrowserOpener
  • org.biojava.bio.structure.align.util.CacheFactory
  • org.biojava.bio.structure.io.CAConverter
  • org.biojava.bio.structure.Calc
  • org.biojava3.alignment.template.CallablePairwiseSequenceAligner<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava3.alignment.template.CallablePairwiseSequenceScorer<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava3.alignment.template.CallableProfileProfileAligner<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava.bio.structure.align.CallableStructureAlignment (implements java.util.concurrent.Callable<V>)
  • org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet (implements org.biojava3.core.sequence.template.CompoundSet<C>)
  • org.biojava3.core.sequence.transcription.CaseInsensitiveCompound (implements org.biojava3.core.sequence.template.Compound)
  • org.biojava3.core.sequence.CDSComparator (implements java.util.Comparator<T>)
  • org.biojava.bio.structure.align.ce.CECalculator
  • org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
  • org.biojava.bio.structure.align.ce.CeCPMain.CPRange
  • org.biojava.bio.structure.align.ce.CeParameters (implements org.biojava.bio.structure.align.ce.ConfigStrucAligParams)
    • org.biojava.bio.structure.align.ce.OptimalCECPParameters
  • org.biojava.bio.structure.ChainImpl (implements org.biojava.bio.structure.Chain, java.io.Serializable)
  • org.biojava3.phylo.CheckTreeAccuracy
  • org.forester.application.CheckTreeAccuracy
  • org.biojava.bio.structure.io.mmcif.model.ChemComp (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.bio.structure.io.mmcif.ChemCompConsumer (implements org.biojava.bio.structure.io.mmcif.MMcifConsumer)
  • org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor (implements java.io.Serializable)
  • org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory
  • org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
  • org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
  • org.forester.phylogeny.iterators.ChildNodeIteratorForward (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
  • org.biojava.bio.structure.jama.CholeskyDecomposition (implements java.io.Serializable)
  • org.biojava3.core.sequence.io.util.ClasspathResource
  • org.biojava.bio.structure.align.util.CliTools
  • org.biojava.bio.structure.align.ClusterAltAligs
  • org.biojava.bio.structure.domain.pdp.ClusterDomains
  • org.biojava.bio.structure.align.util.CollectionTools
  • org.forester.io.parsers.phyloxml.phylogenydata.ColorParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • java.awt.color.ColorSpace (implements java.io.Serializable)
    • org.biojava.bio.structure.gui.util.color.HSVColorSpace
  • org.biojava.bio.structure.gui.util.color.ColorUtils
  • org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarity (implements org.forester.surfacing.PairwiseDomainSimilarity)
  • org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
  • org.forester.util.CommandLineArguments
  • org.biojava3.aaproperties.CommandPrompt
  • org.biojava3.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)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
          • org.biojava.bio.structure.align.gui.DBSearchGUI
          • org.biojava.bio.structure.gui.util.color.GradientPanel
          • org.biojava.bio.structure.align.gui.GUIAlignmentProgressListener (implements java.awt.event.ActionListener, org.biojava.bio.structure.align.events.AlignmentProgressListener)
          • org.biojava.bio.structure.gui.JMatrixPanel
          • org.biojava.bio.structure.align.gui.JPrintPanel (implements java.awt.event.ActionListener, java.awt.print.Printable)
            • org.biojava.bio.structure.align.gui.AlignmentTextPanel
            • org.biojava.bio.structure.align.gui.aligpanel.AligPanel (implements java.awt.event.ActionListener, org.biojava.bio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
            • org.biojava.bio.structure.align.gui.jmol.JmolPanel (implements java.awt.event.ActionListener)
          • org.forester.archaeopteryx.MainPanel (implements java.awt.event.ComponentListener)
          • org.biojava.bio.structure.gui.util.PDBDirPanel (implements org.biojava.bio.structure.gui.util.StructurePairSelector)
          • org.biojava.bio.structure.gui.util.PDBServerPanel (implements org.biojava.bio.structure.gui.util.StructurePairSelector)
          • org.biojava.bio.structure.gui.util.PDBUploadPanel (implements org.biojava.bio.structure.gui.util.StructurePairSelector)
          • org.biojava.bio.structure.gui.ScaleableMatrixPanel (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener)
            • org.biojava.bio.structure.align.gui.DotPlotPanel
          • org.biojava.bio.structure.gui.ScaleableMatrixPanel.GradientRenderer (implements javax.swing.ListCellRenderer)
          • org.biojava.bio.structure.gui.util.ScopSelectPanel (implements org.biojava.bio.structure.gui.util.StructurePairSelector)
          • org.biojava.bio.structure.align.gui.SelectPDBPanel (implements org.biojava.bio.structure.gui.util.StructurePairSelector)
          • org.biojava.bio.structure.gui.SequenceDisplay (implements javax.swing.event.ChangeListener)
          • org.biojava.bio.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.bio.structure.align.gui.autosuggest.JAutoSuggest
            • org.biojava.bio.structure.align.gui.aligpanel.StatusDisplay (implements org.biojava.bio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
      • 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.archaeopteryx.FontChooser (implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.biojava.bio.structure.align.gui.AlignmentGui
            • org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
            • org.forester.archaeopteryx.MainFrame (implements java.awt.event.ActionListener)
              • org.forester.archaeopteryx.MainFrameApplet
              • org.forester.archaeopteryx.MainFrameApplication
            • org.biojava.bio.structure.align.gui.ParameterGUI
  • org.biojava3.protmod.Component
  • org.biojava3.protmod.io.ComponentXMLConverter
  • org.biojava.bio.structure.Compound (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava3.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.phylogenydata.ConfidenceParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.forester.archaeopteryx.Constants
  • org.biojava3.aaproperties.Constraints
  • org.biojava.bio.structure.gui.util.color.ContinuousColorMapperTransform (implements org.biojava.bio.structure.gui.util.color.ContinuousColorMapper)
    • org.biojava.bio.structure.gui.util.color.LogColorMapper
    • org.biojava.bio.structure.gui.util.color.SqrtColorMapper
  • org.biojava3.aaproperties.profeat.convertor.Convertor
    • org.biojava3.aaproperties.profeat.convertor.Convert2Charge
    • org.biojava3.aaproperties.profeat.convertor.Convert2Hydrophobicity
    • org.biojava3.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
    • org.biojava3.aaproperties.profeat.convertor.Convert2Polarity
    • org.biojava3.aaproperties.profeat.convertor.Convert2Polarizability
    • org.biojava3.aaproperties.profeat.convertor.Convert2SecondaryStructure
    • org.biojava3.aaproperties.profeat.convertor.Convert2SolventAccessibility
  • org.biojava.bio.structure.gui.util.CoordManager
  • org.forester.application.count_support
  • org.biojava.bio.structure.align.client.CountProgressListener (implements org.biojava.bio.structure.align.events.AlignmentProgressListener)
  • org.forester.surfacing.CountsBasedPairwiseDomainSimilarity (implements org.forester.surfacing.PairwiseDomainSimilarity)
  • org.forester.pccx.CoverageCalculator
  • org.biojava3.core.util.CRC64Checksum (implements java.util.zip.Checksum)
  • org.biojava.bio.structure.domain.pdp.Cut
  • org.biojava.bio.structure.domain.pdp.CutDomain
  • org.biojava.bio.structure.domain.pdp.CutSites
  • org.biojava.bio.structure.domain.pdp.CutValues
  • org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
  • org.forester.phylogeny.data.Date (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.DateParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava.bio.structure.DBRef (implements org.biojava.bio.structure.PDBRecord, java.io.Serializable)
  • org.biojava3.core.sequence.features.DBReferenceInfo
  • org.biojava.bio.structure.align.gui.DBResultTable (implements java.awt.event.ActionListener)
  • org.forester.application.decorator
  • org.biojava3.alignment.aaindex.DefaultAAIndexProvider (implements org.biojava3.alignment.aaindex.AAIndexProvider)
  • org.biojava.bio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider (implements org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider)
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • org.biojava.bio.structure.align.webstart.ConfigXMLHandler
    • org.forester.io.parsers.phyloxml.PhyloXmlHandler
    • org.forester.io.parsers.tol.TolXmlHandler
  • org.biojava.bio.structure.gui.util.color.DefaultMatrixMapper (implements org.biojava.bio.structure.gui.util.color.ContinuousColorMapper)
  • org.forester.development.DevelopmentTools
  • org.forester.phylogenyinference.DiscreteState (implements java.lang.Comparable<T>)
  • org.biojava.bio.structure.align.gui.DisplayAFP
  • org.forester.sdi.DistanceCalculator
  • org.biojava.bio.structure.secstruc.DistEn
  • org.forester.phylogeny.data.Distribution (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.DistributionParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava3.core.sequence.io.DNASequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.forester.phylogenyinference.DolloParsimony
  • org.biojava.bio.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.phylogenydata.DomainArchitectureParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator (implements org.forester.surfacing.PairwiseDomainSimilarityCalculator)
  • org.forester.surfacing.DomainCountsDifferenceUtil
  • org.forester.surfacing.DomainId (implements java.lang.Comparable<T>)
  • org.forester.surfacing.DomainLengths
  • org.forester.surfacing.DomainLengthsTable
  • org.forester.surfacing.DomainParsimonyCalculator
  • org.biojava.bio.structure.domain.DomainProviderFactory
  • org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider (implements org.biojava.bio.structure.io.mmcif.ChemCompProvider)
  • org.biojava3.core.sequence.edits.Edit.AbstractEdit<C> (implements org.biojava3.core.sequence.edits.Edit<C>)
    • org.biojava3.core.sequence.edits.Edit.Delete<C>
    • org.biojava3.core.sequence.edits.Edit.Insert<C>
    • org.biojava3.core.sequence.edits.Edit.Substitute<C>
  • org.biojava.bio.structure.jama.EigenvalueDecomposition (implements java.io.Serializable)
  • org.biojava3.aaproperties.xml.Element
  • org.biojava3.aaproperties.xml.ElementTable
  • org.biojava.bio.structure.io.mmcif.model.Entity
  • org.biojava3.core.util.Equals
  • org.forester.phylogeny.data.Event (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.EventParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava3.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.biojava.bio.structure.align.FarmJob (implements java.lang.Runnable)
  • org.biojava.bio.structure.align.client.FarmJobParameters
  • org.biojava.bio.structure.align.client.FarmJobRunnable (implements java.lang.Runnable)
  • org.biojava3.core.sequence.io.FastaGeneWriter
  • org.biojava3.core.sequence.io.FastaReader<S,C>
  • org.biojava3.core.sequence.io.FastaReaderHelper
  • org.biojava3.data.sequence.FastaSequence (implements java.lang.Comparable<T>)
  • org.biojava3.core.sequence.io.FastaSequenceParser (implements org.biojava3.core.sequence.io.template.SequenceParserInterface)
  • org.biojava.bio.structure.io.FastaStructureParser
  • org.biojava3.core.sequence.io.FastaWriter<S,C>
  • org.biojava3.core.sequence.io.FastaWriterHelper
  • org.biojava3.sequencing.io.fastq.Fastq
  • org.biojava3.sequencing.io.fastq.FastqBuilder
  • org.biojava3.sequencing.io.fastq.FastqTools
  • org.biojava.bio.structure.align.fatcat.FatCat
    • org.biojava.bio.structure.align.fatcat.FatCatFlexible (implements org.biojava.bio.structure.align.StructureAlignment)
    • org.biojava.bio.structure.align.fatcat.FatCatRigid (implements org.biojava.bio.structure.align.StructureAlignment)
  • org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
  • org.biojava.bio.structure.align.fatcat.calc.FatCatParameters (implements org.biojava.bio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava.bio.structure.align.fatcat.calc.FCAlignHelper
  • org.biojava3.genome.parsers.gff.Feature (implements org.biojava3.genome.parsers.gff.FeatureI)
  • org.biojava3.genome.parsers.gff.FeatureHelper
  • org.biojava.bio.structure.io.FileConvert
  • org.biojava.bio.structure.io.util.FileDownloadUtils
  • org.biojava.bio.structure.io.FileParsingParameters (implements java.io.Serializable)
  • org.biojava3.core.sequence.io.FileProxyDNASequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.forester.phylogenyinference.FitchParsimony<STATE_TYPE>
  • org.biojava3.core.util.FlatFileCache
  • org.biojava.bio.structure.server.FlatFileInstallation (implements org.biojava.bio.structure.server.PDBInstallation)
  • org.forester.util.ForesterConstants
  • org.forester.util.ForesterUtil
  • org.biojava.bio.structure.align.pairwise.FragmentJoiner
  • org.biojava.bio.structure.align.pairwise.FragmentPair
  • org.biojava.bio.structure.align.helper.GapArray
  • org.biojava3.genome.parsers.gff.GCStats
  • org.biojava3.genome.GeneFeatureHelper
  • org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
  • org.biojava3.genome.parsers.geneid.GeneIDXMLReader
  • org.biojava3.genome.parsers.gff.GeneMarkGTFReader
  • org.forester.util.GeneralTable<IDENTIFIER_TYPE,VALUE_TYPE>
  • org.biojava3.core.sequence.io.GenericFastaHeaderFormat<S,C> (implements org.biojava3.core.sequence.io.template.FastaHeaderFormatInterface<S,C>)
  • org.biojava3.core.sequence.io.GenericFastaHeaderParser<S,C> (implements org.biojava3.core.sequence.io.template.FastaHeaderParserInterface<S,C>)
  • org.forester.application.get_distances
  • org.biojava.bio.structure.domain.pdp.GetDistanceMatrix
  • org.biojava3.genome.homology.GFF3FromUniprotBlastHits
  • org.biojava3.genome.parsers.gff.GFF3Reader
  • org.biojava3.genome.parsers.gff.GFF3Writer
  • org.forester.application.goac
  • org.forester.go.GoId (implements java.lang.Comparable<T>)
  • org.forester.go.GoNameSpace
  • org.biojava.bio.structure.align.pairwise.Gotoh
  • org.forester.go.GoUtils
  • org.biojava.bio.structure.gui.util.color.GradientMapper (implements org.biojava.bio.structure.gui.util.color.ContinuousColorMapper, java.util.Map<K,V>)
  • org.biojava.bio.structure.GroupIterator (implements java.util.Iterator<E>)
  • org.biojava.bio.structure.GroupType
  • org.biojava3.alignment.GuideTree<S,C> (implements java.lang.Iterable<T>)
  • org.biojava3.alignment.GuideTree.Node (implements org.biojava3.alignment.template.GuideTreeNode<S,C>)
  • org.biojava.bio.structure.align.gui.GUIFarmJobRunnable (implements java.lang.Runnable)
  • org.biojava.bio.structure.align.ce.GuiWrapper
  • org.biojava3.core.util.Hashcoder
  • org.biojava.bio.structure.align.xml.HasResultXMLConverter
  • org.biojava.bio.structure.secstruc.HBond
  • org.biojava.bio.structure.align.gui.HelpDialog
  • org.biojava.bio.structure.HetatomImpl (implements org.biojava.bio.structure.Group, java.io.Serializable)
    • org.biojava.bio.structure.AminoAcidImpl (implements org.biojava.bio.structure.AminoAcid, java.io.Serializable)
    • org.biojava.bio.structure.NucleotideImpl (implements org.biojava.bio.structure.Group, java.io.Serializable)
    • org.biojava.bio.structure.secstruc.SecStrucGroup (implements org.biojava.bio.structure.Group)
  • org.biojava3.ws.hmmer.HmmerDomain (implements java.lang.Comparable<T>)
  • org.biojava3.ws.hmmer.HmmerResult (implements java.lang.Comparable<T>)
  • org.forester.io.parsers.HmmPfamOutputParser
  • org.forester.io.parsers.HmmscanPerDomainTableParser
  • org.biojava.bio.structure.align.util.HTTPConnectionTools
  • org.forester.phylogeny.data.Identifier (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.IdentifierParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava.bio.structure.align.helper.IdxComparator (implements java.util.Comparator<T>)
  • org.biojava3.sequencing.io.fastq.IlluminaFastqReader
  • org.biojava3.sequencing.io.fastq.IlluminaFastqWriter
  • org.biojava.bio.structure.align.helper.IndexPair (implements java.io.Serializable)
    • org.biojava.bio.structure.align.helper.AligMatEl
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • org.biojava3.core.util.UncompressInputStream
  • org.biojava3.core.util.InputStreamProvider
  • org.biojava3.core.sequence.location.InsdcLocations
  • org.biojava3.core.sequence.location.InsdcParser
  • org.biojava3.core.sequence.io.util.IOUtils
  • org.biojava3.aaproperties.xml.Isotope
  • org.biojava3.core.sequence.io.IUPACParser
  • org.biojava3.core.sequence.io.IUPACParser.IUPACTable (implements org.biojava3.core.sequence.transcription.Table)
  • org.biojava.bio.structure.align.client.JFatCatClient
  • org.biojava.bio.structure.gui.events.JmolAlignedPositionListener (implements org.biojava.bio.structure.gui.events.AlignmentPositionListener)
  • org.biojava.bio.structure.align.gui.jmol.JmolTools
  • org.biojava3.structure.gui.JmolViewerImpl (implements org.biojava3.structure.gui.StructureViewer)
  • org.biojava.bio.structure.align.webstart.JNLPProxy
  • org.biojava3.core.sequence.storage.JoiningSequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.bio.structure.align.helper.JointFragments
  • org.biojava.bio.structure.JournalArticle (implements java.io.Serializable)
  • org.biojava3.ronn.Jronn
  • org.biojava3.ronn.Jronn.Range
  • java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    • org.biojava.bio.structure.align.gui.jmol.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
    • org.biojava.bio.structure.gui.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
  • org.forester.phylogeny.iterators.LevelOrderTreeIterator (implements org.forester.phylogeny.iterators.PhylogenyNodeIterator)
  • org.biojava.bio.structure.gui.util.color.LinearColorInterpolator (implements org.biojava.bio.structure.gui.util.color.ColorInterpolator)
  • org.biojava.bio.structure.io.LocalCacheStructureProvider (implements org.biojava.bio.structure.io.StructureProvider)
  • org.biojava.bio.structure.domain.LocalProteinDomainParser
  • org.biojava3.genome.parsers.gff.Location (implements java.lang.Iterable<T>)
  • org.biojava3.core.sequence.location.template.Location.Tools
  • org.biojava3.core.sequence.location.LocationHelper
  • org.biojava3.genome.parsers.gff.LocIterator (implements java.util.Iterator<E>)
  • org.biojava.bio.structure.jama.LUDecomposition (implements java.io.Serializable)
  • org.forester.surfacing.MappingResults
  • org.biojava3.ws.alignment.qblast.MapToStringTransformer
  • org.biojava.bio.structure.jama.Maths
  • org.biojava.bio.structure.jama.Matrix (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.bio.structure.align.gui.MenuCreator
  • org.biojava.bio.structure.gui.util.MenuCreator
  • org.forester.application.meta_ontologizer
  • org.forester.go.etc.MetaOntologizer
  • org.biojava.bio.structure.server.MMCIFFileInstallation (implements org.biojava.bio.structure.server.PDBInstallation)
  • org.biojava.bio.structure.io.MMCIFFileReader (implements org.biojava.bio.structure.io.StructureIOFile)
  • org.forester.pccx.ModelingUtils
  • org.biojava3.ronn.ModelLoader
  • org.biojava3.ronn.ModelLoader.Model
  • org.biojava3.ronn.ModelLoader.Threshold
  • org.biojava3.protmod.ModificationConditionImpl (implements org.biojava3.protmod.ModificationCondition)
  • org.biojava3.protmod.ModificationLinkage
  • org.biojava3.aaproperties.xml.ModifiedAminoAcidCompoundSet (implements org.biojava3.core.sequence.template.CompoundSet<C>)
  • org.biojava3.protmod.structure.ModifiedCompoundImpl (implements java.lang.Comparable<T>, org.biojava3.protmod.structure.ModifiedCompound, java.io.Serializable)
  • org.biojava3.protmod.io.ModifiedCompoundXMLConverter
  • org.biojava3.core.sequence.MultipleSequenceAlignment<S,C> (implements org.biojava3.core.sequence.template.LightweightProfile<S,C>)
  • org.biojava.bio.structure.Mutator
  • org.biojava.bio.structure.align.gui.MyAlignmentLoadListener (implements java.awt.event.ActionListener)
  • org.biojava.bio.structure.align.gui.MyDistMaxListener (implements java.awt.event.ActionListener)
  • org.biojava.bio.structure.align.gui.MyExportListener (implements java.awt.event.ActionListener)
  • org.biojava.bio.structure.align.gui.jmol.MyJmolStatusListener
  • org.biojava.bio.structure.align.gui.MyOpenPdbFileListener (implements java.awt.event.ActionListener)
  • org.biojava.bio.structure.align.gui.MySaveFileListener (implements java.awt.event.ActionListener)
  • org.biojava3.aaproperties.xml.MyValidationEventHandler (implements javax.xml.bind.ValidationEventHandler)
  • org.biojava3.aaproperties.xml.Name2Count
  • org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties (implements org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties)
  • org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties (implements org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties)
  • org.biojava3.ws.alignment.qblast.NCBIQBlastService (implements org.biojava3.ws.alignment.RemotePairwiseAlignmentService)
  • org.forester.phylogenyinference.NeighborJoining
  • 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.PhylogenyParser)
  • org.forester.application.nhx_too
  • org.forester.io.parsers.nhx.NHXParser (implements 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.application.obo_tool
  • org.forester.go.OBOparser
  • org.forester.go.etc.OntologizerResult (implements java.lang.Comparable<T>)
  • org.forester.sdi.ORcount
  • org.biojava3.ronn.ORonn (implements java.util.concurrent.Callable<V>)
  • org.biojava3.ronn.ORonnModel
  • org.biojava3.genome.query.OutputHitsGFF
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • org.biojava3.ronn.NullOutputStream
  • org.forester.surfacing.PairwiseGenomeComparator
  • org.forester.io.parsers.ParserUtils
  • org.forester.io.parsers.nexus.PaupLogParser
  • org.forester.application.pccx
  • org.biojava.bio.structure.PDBCrystallographicInfo (implements java.io.Serializable)
  • org.biojava.bio.structure.io.PDBFileParser
  • org.biojava.bio.structure.io.PDBFileReader (implements org.biojava.bio.structure.io.StructureIOFile)
  • org.biojava.bio.structure.PDBHeader (implements org.biojava.bio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.bio.structure.align.client.PdbPair (implements java.lang.Comparable<T>)
  • org.biojava.bio.structure.align.xml.PdbPairsMessage
  • org.biojava.bio.structure.align.xml.PdbPairXMLConverter
  • org.biojava.bio.structure.io.PDBSRSReader (implements org.biojava.bio.structure.io.StructureIO)
  • org.biojava.bio.structure.PDBStatus
  • org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
  • org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
  • org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix
  • org.biojava.bio.structure.domain.pdp.PDPParameters
  • org.biojava3.aaproperties.PeptideProperties
  • org.biojava3.aaproperties.PeptidePropertiesImpl (implements org.biojava3.aaproperties.IPeptideProperties)
  • org.forester.application.perfume
  • org.biojava.bio.structure.align.webstart.PersistentConfig
  • org.forester.application.pfam_go
  • org.forester.application.pfam2go_extractor
  • org.forester.go.PfamToGoMapping (implements org.forester.go.Mapping)
  • org.forester.go.PfamToGoParser
  • org.forester.phylogeny.Phylogeny
  • org.forester.phylogeny.PhylogenyBranch (implements org.forester.phylogeny.Edge)
  • org.forester.phylogeny.data.PhylogenyDataUtil
  • org.forester.tools.PhylogenyDecorator
  • org.forester.phylogeny.PhylogenyMethods
  • org.forester.phylogeny.PhylogenyNode (implements java.lang.Comparable<T>, org.forester.phylogeny.PhylogenyNodeI)
  • org.forester.io.writers.PhylogenyWriter
  • 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.forester.phylogeny.data.Point (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.PointParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava.bio.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.bio.structure.server.PrepareIndexFile
    • org.biojava.bio.structure.server.PrepareMMcifIndexFile
  • org.biojava3.core.util.PrettyXMLWriter (implements org.biojava3.core.util.XMLWriter)
  • org.forester.surfacing.PrintableDomainSimilarity (implements org.forester.surfacing.DomainSimilarity)
  • org.forester.application.printAllSpecies
  • org.forester.application.printSameOrder
  • org.biojava3.aaproperties.profeat.ProfeatProperties
  • org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl (implements org.biojava3.aaproperties.profeat.IProfeatProperties)
  • org.biojava3.phylo.ProgessListenerStub (implements org.biojava3.phylo.NJTreeProgressListener)
  • 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.phylogenydata.PropertyParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • 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.phylogenydata.ProteinDomainParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.forester.surfacing.ProteinId (implements java.lang.Comparable<T>)
  • org.biojava3.protmod.structure.ProteinModificationIdentifier
  • org.biojava3.protmod.ProteinModificationImpl (implements java.lang.Comparable<T>, org.biojava3.protmod.ProteinModification)
  • org.biojava3.protmod.ProteinModificationImpl.Builder
  • org.biojava3.protmod.ProteinModificationRegistry
  • org.biojava3.protmod.io.ProteinModificationXmlReader
  • org.biojava3.core.sequence.io.ProteinSequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
    • org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
  • org.biojava.bio.structure.jama.QRDecomposition (implements java.io.Serializable)
  • org.forester.datastructures.Queue
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • org.biojava3.core.sequence.io.BufferedReaderBytesRead
  • org.biojava.bio.structure.io.mmcif.ReducedChemCompProvider (implements org.biojava.bio.structure.io.mmcif.ChemCompProvider)
  • org.forester.phylogeny.data.Reference (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.ReferenceParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava.bio.structure.io.mmcif.model.Refine
  • org.biojava3.ws.hmmer.RemoteHmmerScan (implements org.biojava3.ws.hmmer.HmmerScan)
  • org.biojava.bio.structure.scop.RemoteScopInstallation (implements org.biojava.bio.structure.scop.ScopDatabase)
  • org.biojava.bio.structure.align.xml.RepresentativeXMLConverter
  • org.biojava.bio.structure.ResidueNumber (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava3.phylo.ResidueProperties
  • org.biojava.bio.structure.align.util.ResourceManager
  • org.forester.application.rio
  • org.forester.sdi.RIO
  • org.forester.sdi.RIOn
  • org.biojava3.core.sequence.io.RNASequenceCreator (implements org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava3.ronn.RonnConstraint
  • javax.swing.RowSorter<M>
    • javax.swing.DefaultRowSorter<M,I>
      • javax.swing.table.TableRowSorter<M>
        • org.biojava.bio.structure.align.gui.MyTableRowSorter
  • org.biojava.bio.structure.io.SandboxStyleStructureProvider (implements org.biojava.bio.structure.io.StructureProvider)
  • org.biojava3.sequencing.io.fastq.SangerFastqReader
  • org.biojava3.sequencing.io.fastq.SangerFastqWriter
  • org.forester.phylogenyinference.SankoffParsimony<STATE_TYPE>
  • org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix (implements org.biojava3.alignment.template.SubstitutionMatrix<C>)
  • javax.xml.bind.SchemaOutputResolver
    • org.biojava3.aaproperties.xml.SchemaGenerator
  • org.biojava.bio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider (implements org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider)
  • org.biojava.bio.structure.scop.ScopDescription (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.bio.structure.scop.server.ScopDescriptions (implements java.io.Serializable)
  • org.biojava.bio.structure.scop.ScopDomain (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.bio.structure.scop.server.ScopDomains (implements java.io.Serializable)
  • org.biojava.bio.structure.scop.ScopFactory
  • org.biojava.bio.structure.scop.ScopInstallation (implements org.biojava.bio.structure.scop.ScopDatabase)
    • org.biojava.bio.structure.scop.BerkeleyScopInstallation (implements org.biojava.bio.structure.scop.ScopDatabase)
  • org.biojava.bio.structure.gui.util.ScopInstallationInstance
  • org.biojava.bio.structure.scop.ScopNode (implements java.io.Serializable)
  • org.biojava.bio.structure.scop.server.ScopNodes (implements java.io.Serializable)
  • org.biojava3.phylo.ScoreMatrix
  • org.forester.application.sdi
  • org.forester.sdi.SDI
    • org.forester.sdi.GSDI
    • org.forester.sdi.SDIse
    • org.forester.sdi.TaxonomyAssigner
  • org.forester.application.sdi_r
  • org.forester.sdi.SDIdirectory
  • org.forester.sdi.SDIR
  • org.biojava.bio.structure.secstruc.SecStruc
  • org.biojava.bio.structure.domain.pdp.Segment (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.bio.structure.domain.pdp.SegmentComparator (implements java.util.Comparator<T>)
  • org.biojava3.structure.gui.SelectionImpl (implements org.biojava3.structure.gui.Selection)
  • org.biojava.bio.structure.io.SeqRes2AtomAligner
  • org.forester.phylogeny.data.Sequence (implements org.forester.phylogeny.data.PhylogenyData)
  • org.biojava3.core.sequence.storage.SequenceAsStringHelper<C>
  • org.biojava3.core.sequence.SequenceComparator (implements java.util.Comparator<T>)
  • org.biojava3.core.sequence.loader.SequenceFileProxyLoader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava3.core.sequence.template.SequenceMixin
  • org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator<C> (implements java.util.Iterator<E>)
  • org.biojava.bio.structure.gui.util.SequenceMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava3.core.sequence.SequenceOptimizationHints
  • org.forester.io.parsers.phyloxml.phylogenydata.SequenceParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava3.core.sequence.template.SequenceProxyView<C> (implements org.biojava3.core.sequence.template.SequenceView<C>)
    • org.biojava3.core.sequence.views.ComplementSequenceView<C>
    • org.biojava3.core.sequence.views.ReversedSequenceView<C>
    • org.biojava3.core.sequence.views.RnaSequenceView (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.forester.phylogeny.data.SequenceRelation (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.SequenceRelationParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.biojava3.core.util.SequenceTools
  • org.biojava3.data.sequence.SequenceUtil
  • org.biojava.bio.structure.domain.SerializableCache<K,V>
    • org.biojava.bio.structure.scop.CachedRemoteScopInstallation (implements org.biojava.bio.structure.scop.ScopDatabase)
    • org.biojava.bio.structure.domain.RemoteDomainProvider (implements org.biojava.bio.structure.domain.DomainProvider)
    • org.biojava.bio.structure.domain.RemotePDPProvider (implements org.biojava.bio.structure.domain.PDPProvider)
  • org.forester.application.shin
  • org.forester.sdi.Shin
  • org.biojava.bio.structure.domain.pdp.ShortSegmentRemover
  • org.biojava.bio.structure.align.gui.ShowPDBIDListener (implements java.awt.event.ActionListener)
  • org.biojava.bio.structure.io.sifts.SiftsEntity (implements java.io.Serializable)
  • org.biojava.bio.structure.io.sifts.SiftsMappingProvider
  • org.biojava.bio.structure.io.sifts.SiftsResidue (implements java.io.Serializable)
  • org.biojava.bio.structure.io.sifts.SiftsSegment (implements java.io.Serializable)
  • org.biojava.bio.structure.io.sifts.SiftsXMLParser
  • org.biojava.bio.structure.align.fatcat.calc.SigEva
  • org.biojava3.alignment.SimpleAlignedSequence<S,C> (implements org.biojava3.alignment.template.AlignedSequence<S,C>)
  • org.forester.surfacing.SimpleDomain (implements org.forester.surfacing.Domain)
  • org.biojava3.alignment.SimpleGapPenalty (implements org.biojava3.alignment.template.GapPenalty)
  • org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer (implements org.biojava.bio.structure.io.mmcif.MMcifConsumer)
  • org.biojava.bio.structure.io.mmcif.SimpleMMcifParser (implements org.biojava.bio.structure.io.mmcif.MMcifParser)
  • org.forester.development.SimpleMutableMsa (implements org.forester.development.Msa)
  • org.biojava3.core.sequence.location.SimplePoint (implements org.biojava3.core.sequence.location.template.Point)
    • org.biojava3.core.sequence.location.FuzzyPoint
  • org.biojava3.alignment.SimpleProfile<S,C> (implements org.biojava3.alignment.template.Profile<S,C>)
    • org.biojava3.alignment.SimpleProfilePair<S,C> (implements org.biojava3.alignment.template.ProfilePair<S,C>)
    • org.biojava3.alignment.SimpleSequencePair<S,C> (implements org.biojava3.alignment.template.SequencePair<S,C>)
  • org.biojava.bio.structure.server.SimpleStructureServer (implements org.biojava.bio.structure.server.StructureListener, org.biojava.bio.structure.server.StructureServer)
  • org.biojava3.alignment.SimpleSubstitutionMatrix<C> (implements org.biojava3.alignment.template.SubstitutionMatrix<C>)
  • org.biojava3.core.sequence.storage.SingleCompoundSequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.bio.structure.jama.SingularValueDecomposition (implements java.io.Serializable)
  • org.biojava.bio.structure.Site (implements java.lang.Comparable<T>, org.biojava.bio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.bio.structure.align.seq.SmithWaterman3DParameters (implements org.biojava.bio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava3.sequencing.io.fastq.SolexaFastqReader
  • org.biojava3.sequencing.io.fastq.SolexaFastqWriter
  • org.biojava3.genome.util.SplitFasta
  • org.biojava.bio.structure.SSBond (implements org.biojava.bio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.bio.structure.StandardAminoAcid
  • org.biojava.bio.structure.align.ce.StartupParameters
  • org.biojava.bio.structure.align.pairwise.StrCompAlignment (implements org.biojava.bio.structure.align.pairwise.Alignable)
  • org.biojava3.core.util.StringManipulationHelper
  • org.biojava3.core.sequence.loader.StringProxySequenceReader<C> (implements org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.forester.application.strip
  • org.biojava.bio.structure.align.StrucAligParameters
  • org.biojava.bio.structure.io.mmcif.model.Struct
  • org.biojava.bio.structure.io.mmcif.model.StructKeywords
  • org.biojava.bio.structure.align.gui.StructureAlignmentDisplay
  • org.biojava.bio.structure.align.StructureAlignmentFactory
  • org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol (implements java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener)
  • org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer
  • org.biojava3.protmod.structure.StructureAtom
  • org.biojava3.protmod.structure.StructureAtomLinkage
  • org.biojava3.protmod.io.StructureAtomXMLConverter
  • org.biojava.bio.structure.server.StructureEventImpl (implements org.biojava.bio.structure.server.StructureEvent)
  • org.biojava.bio.structure.server.StructureFetcherRunnable (implements java.lang.Runnable)
  • org.biojava3.protmod.structure.StructureGroup (implements java.lang.Comparable<T>)
  • org.biojava3.protmod.io.StructureGroupXMLConverter
  • org.biojava.bio.structure.StructureImpl (implements java.io.Serializable, org.biojava.bio.structure.Structure)
  • org.biojava.bio.structure.align.client.StructureName (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.bio.structure.align.StructurePairAligner
  • org.biojava.bio.structure.io.StructureSequenceMatcher
  • org.biojava.bio.structure.StructureTools
  • org.biojava3.protmod.structure.StructureUtil
  • org.biojava3.alignment.SubstitutionMatrixHelper
  • org.forester.application.support_statistics
  • org.forester.application.support_transfer
  • org.forester.development.SupportCount
  • org.forester.application.surf_paup
  • org.forester.application.surfacing
  • org.forester.application.surfacing_old
  • org.forester.surfacing.SurfacingConstants
  • org.forester.surfacing.SurfacingUtil
  • org.biojava.bio.structure.SVDSuperimposer
  • org.forester.phylogenyinference.SymmetricalDistanceMatrixParser (implements org.forester.phylogenyinference.DistanceMatrixParser)
  • org.biojava.bio.structure.align.util.SynchronizedOutFile
  • org.biojava.bio.structure.align.gui.SystemInfo
  • org.forester.application.ta
  • org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
  • org.biojava3.core.sequence.transcription.Table.Codon (implements org.biojava3.core.sequence.template.Compound)
  • org.forester.phylogeny.data.Taxonomy (implements org.forester.phylogeny.data.PhylogenyData)
  • org.biojava3.core.sequence.TaxonomyID
  • org.forester.io.parsers.phyloxml.phylogenydata.TaxonomyParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.forester.development.Test
  • org.forester.test.Test
  • org.forester.go.TestGo
  • org.forester.sdi.TestGSDI
  • org.forester.pccx.TestPccx
  • org.forester.phylogenyinference.TestPhylogenyReconstruction
  • org.forester.surfacing.TestSurfacing
  • java.lang.Thread (implements java.lang.Runnable)
    • org.biojava3.phylo.TreeConstructor<C,D>
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • org.biojava3.core.exceptions.CompoundNotFoundError
      • org.biojava3.core.exceptions.FileAccessError
      • org.biojava3.core.exceptions.HeaderParseException
      • org.biojava3.core.exceptions.SequenceLengthError
    • java.lang.Exception
      • org.biojava.bio.structure.align.util.ConfigurationException
      • java.io.IOException
        • org.forester.io.parsers.nexus.NexusFormatException
        • org.forester.io.parsers.nhx.NHXFormatException
        • org.forester.io.parsers.PhylogenyParserException
      • org.biojava.bio.structure.align.client.JobKillException
      • org.biojava.bio.structure.io.PDBParseException
      • java.lang.RuntimeException
        • org.biojava3.core.exceptions.ParserException
        • org.forester.io.parsers.phyloxml.PhyloXmlException
          • org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException
        • org.biojava3.core.exceptions.TranslationException
      • org.biojava.bio.structure.StructureException
      • org.biojava.bio.structure.UnknownPdbAminoAcidException
  • org.biojava3.ronn.Timer
  • org.forester.io.parsers.tol.TolParser (implements org.forester.io.parsers.PhylogenyParser)
  • org.forester.io.parsers.tol.TolXmlMapping
  • org.biojava3.core.sequence.transcription.TranscriptionEngine
  • org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
  • org.forester.archaeopteryx.TreeFontSet
  • org.biojava.bio.structure.scop.server.TreeSetStringWrapper (implements java.io.Serializable)
  • org.forester.tools.TreeSplitMatrix
  • org.biojava3.core.sequence.loader.UniprotProxySequenceReader<C> (implements org.biojava3.core.sequence.features.DatabaseReferenceInterface, org.biojava3.core.sequence.features.FeaturesKeyWordInterface, org.biojava3.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava3.genome.uniprot.UniprotToFasta
  • org.forester.phylogeny.data.Uri (implements org.forester.phylogeny.data.PhylogenyData)
  • org.forester.io.parsers.phyloxml.phylogenydata.UriParser (implements org.forester.io.parsers.phyloxml.phylogenydata.PhylogenyDataPhyloXmlParser)
  • org.forester.archaeopteryx.UrlTreeReader (implements java.lang.Runnable)
  • org.biojava.bio.structure.align.util.UserConfiguration
  • org.biojava3.aaproperties.Utils
  • org.forester.archaeopteryx.webservices.WebservicesManager
  • org.forester.archaeopteryx.webservices.WebserviceUtil
  • org.biojava.bio.structure.align.webstart.WebStartDBSearch
  • org.biojava.bio.structure.align.webstart.WebStartDBSearchResults
  • org.biojava.bio.structure.align.webstart.WebStartMain
  • org.biojava3.core.sequence.views.WindowedSequence<C> (implements java.lang.Iterable<T>)
  • org.forester.util.WindowsUtils
  • org.forester.io.parsers.phyloxml.XmlElement
  • org.biojava3.core.util.XMLHelper
  • org.biojava.bio.structure.scop.server.XMLUtil

Interface Hierarchy

• org.biojava3.alignment.aaindex.AAIndexProvider
• org.biojava3.core.sequence.template.Accessioned
  • org.biojava3.core.sequence.location.template.AccesionedLocation (also extends org.biojava3.core.sequence.location.template.Location)
  • org.biojava3.alignment.template.AlignedSequence<S,C>
    • org.biojava3.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava3.core.sequence.location.template.Location (also extends java.lang.Iterable<T>)
    • org.biojava3.core.sequence.location.template.AccesionedLocation (also extends org.biojava3.core.sequence.template.Accessioned)
  • org.biojava3.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava3.core.sequence.template.ProxySequenceReader<C>
  • org.biojava3.core.sequence.template.Sequence<C> (also extends java.lang.Iterable<T>)
    • org.biojava3.alignment.template.AlignedSequence<S,C>
      • org.biojava3.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava3.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava3.core.sequence.template.ProxySequenceReader<C>
    • org.biojava3.core.sequence.template.SequenceReader<C>
      • org.biojava3.core.sequence.template.ProxySequenceReader<C>
    • org.biojava3.core.sequence.template.SequenceView<C>
  • org.biojava3.core.sequence.template.SequenceReader<C>
    • org.biojava3.core.sequence.template.ProxySequenceReader<C>
  • org.biojava3.core.sequence.template.SequenceView<C>
• org.biojava.bio.structure.align.pairwise.Alignable
• org.biojava.bio.structure.gui.events.AlignmentPositionListener
• org.biojava.bio.structure.align.events.AlignmentProgressListener
• org.biojava.bio.structure.align.gui.autosuggest.AutoSuggestProvider
• org.biojava.bio.structure.Chain
• org.forester.phylogenyinference.CharacterStateMatrix<S>
• org.biojava.bio.structure.io.mmcif.ChemCompProvider
• java.lang.Cloneable
  • org.biojava.bio.structure.Atom (also extends org.biojava.bio.structure.PDBRecord)
  • org.biojava.bio.structure.Structure
• org.biojava.bio.structure.gui.util.color.ColorInterpolator
• org.forester.surfacing.CombinableDomains
• java.lang.Comparable<T>
  • org.forester.surfacing.BinaryDomainCombination
  • org.forester.surfacing.Domain
  • org.forester.surfacing.DomainSimilarity
  • 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.biojava3.core.sequence.location.template.Point
  • org.forester.surfacing.Species
• org.biojava3.core.sequence.template.Compound
  • org.biojava3.core.sequence.template.ComplementCompound
• org.biojava3.core.sequence.template.CompoundSet<C>
• org.biojava3.core.sequence.template.CompoundTranslator<F,T>
• org.biojava.bio.structure.align.ce.ConfigStrucAligParams
• org.biojava.bio.structure.gui.util.color.ContinuousColorMapper
• org.forester.pccx.Coverage
• org.forester.pccx.CoverageCalculationMethod
• org.forester.pccx.CoverageCalculationOptions
• org.forester.pccx.CoverageExtender
• org.biojava3.core.sequence.features.DatabaseReferenceInterface
• org.forester.util.DescriptiveStatistics
• org.forester.phylogenyinference.DistanceMatrix
• org.forester.phylogenyinference.DistanceMatrixParser
• org.forester.phylogenyinference.DistanceMethod
• org.biojava.bio.structure.domain.DomainProvider
• org.forester.surfacing.DomainSimilarityCalculator
• org.forester.phylogeny.Edge
• org.biojava3.core.sequence.edits.Edit<C>
• org.forester.development.Factory
• org.biojava3.core.sequence.io.template.FastaHeaderFormatInterface<S,C>
• org.biojava3.core.sequence.io.template.FastaHeaderParserInterface<S,C>
• org.biojava3.sequencing.io.fastq.FastqReader
• org.biojava3.sequencing.io.fastq.FastqWriter
• org.biojava3.genome.parsers.gff.FeatureI
• org.biojava3.core.sequence.features.FeatureInterface<S,C>
• org.biojava3.core.sequence.features.FeaturesKeyWordInterface
• org.biojava3.alignment.template.GapPenalty
• org.forester.surfacing.GenomeWideCombinableDomains
• org.biojava.bio.structure.Group
  • org.biojava.bio.structure.AminoAcid
• org.biojava3.alignment.template.HierarchicalClusterer<S,C>
• org.biojava3.ws.hmmer.HmmerScan
• org.biojava3.core.sequence.io.util.IOUtils.ReaderProcessor
• org.biojava3.aaproperties.IPeptideProperties
• org.biojava3.aaproperties.profeat.IProfeatProperties
• java.lang.Iterable<T>
  • org.biojava3.core.sequence.location.template.Location (also extends org.biojava3.core.sequence.template.Accessioned)
    • org.biojava3.core.sequence.location.template.AccesionedLocation (also extends org.biojava3.core.sequence.template.Accessioned)
  • org.biojava3.alignment.template.Profile<S,C>
    • org.biojava3.alignment.template.MutableProfile<S,C>
      • org.biojava3.alignment.template.MutableProfilePair<S,C> (also extends org.biojava3.alignment.template.ProfilePair<S,C>)
      • org.biojava3.alignment.template.MutableSequencePair<S,C> (also extends org.biojava3.alignment.template.SequencePair<S,C>)
    • org.biojava3.alignment.template.MutableProfilePair<S,C> (also extends org.biojava3.alignment.template.MutableProfile<S,C>, org.biojava3.alignment.template.ProfilePair<S,C>)
    • org.biojava3.alignment.template.MutableSequencePair<S,C> (also extends org.biojava3.alignment.template.MutableProfile<S,C>, org.biojava3.alignment.template.SequencePair<S,C>)
    • org.biojava3.alignment.template.ProfilePair<S,C>
      • org.biojava3.alignment.template.MutableProfilePair<S,C> (also extends org.biojava3.alignment.template.MutableProfile<S,C>)
    • org.biojava3.alignment.template.ProfileView<S,C>
    • org.biojava3.alignment.template.SequencePair<S,C>
      • org.biojava3.alignment.template.MutableSequencePair<S,C> (also extends org.biojava3.alignment.template.MutableProfile<S,C>)
  • org.biojava3.core.sequence.template.Sequence<C> (also extends org.biojava3.core.sequence.template.Accessioned)
    • org.biojava3.alignment.template.AlignedSequence<S,C>
      • org.biojava3.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava3.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava3.core.sequence.template.ProxySequenceReader<C>
    • org.biojava3.core.sequence.template.SequenceReader<C>
      • org.biojava3.core.sequence.template.ProxySequenceReader<C>
    • org.biojava3.core.sequence.template.SequenceView<C>
• java.util.Iterator<E>
  • org.forester.phylogeny.iterators.PhylogenyNodeIterator
• org.biojava3.core.sequence.template.LightweightProfile<S,C>
• org.biojava.bio.structure.align.ce.MatrixListener
• org.biojava.bio.structure.io.mmcif.MMcifConsumer
• org.biojava.bio.structure.io.mmcif.MMcifParser
• org.biojava3.protmod.ModificationCondition
• org.biojava3.protmod.structure.ModifiedCompound
• org.forester.development.Msa
• org.forester.development.MsaFactory
  • org.forester.development.StreamBasedMsaFactory
• org.biojava3.phylo.NJTreeProgressListener
• org.forester.surfacing.PairwiseDomainSimilarity
• org.forester.surfacing.PairwiseDomainSimilarityCalculator
• org.biojava3.sequencing.io.fastq.ParseListener
• org.biojava.bio.structure.server.PDBFilter
• org.biojava.bio.structure.server.PDBInstallation
• org.biojava.bio.structure.PDBRecord
  • org.biojava.bio.structure.Atom (also extends java.lang.Cloneable)
• org.biojava.bio.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.phylogenydata.PhylogenyDataPhyloXmlParser
• org.forester.phylogeny.factories.PhylogenyFactory
• org.forester.phylogeny.PhylogenyNodeI
• org.forester.io.parsers.PhylogenyParser
• org.biojava3.core.sequence.location.template.Point.Resolver<T>
• org.forester.surfacing.Protein
• org.biojava3.protmod.ProteinModification
• org.biojava3.ws.alignment.RemotePairwiseAlignmentService
• java.lang.Runnable
  • org.biojava.bio.structure.align.gui.AlignmentCalculationRunnable
• org.biojava.bio.structure.scop.ScopDatabase
• org.biojava3.alignment.template.Scorer
  • org.biojava3.alignment.template.Aligner<S,C>
    • org.biojava3.alignment.template.MatrixAligner<S,C>
    • org.biojava3.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava3.alignment.template.PairwiseSequenceScorer<S,C>)
    • org.biojava3.alignment.template.PartitionRefiner<S,C> (also extends org.biojava3.alignment.template.ProfileProfileScorer<S,C>)
    • org.biojava3.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava3.alignment.template.ProfileProfileScorer<S,C>)
    • org.biojava3.alignment.template.RescoreRefiner<S,C>
  • org.biojava3.alignment.template.MatrixAligner<S,C>
  • org.biojava3.alignment.template.PairInProfileScorer<S,C>
  • org.biojava3.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava3.alignment.template.Aligner<S,C>, org.biojava3.alignment.template.PairwiseSequenceScorer<S,C>)
  • org.biojava3.alignment.template.PairwiseSequenceScorer<S,C>
    • org.biojava3.alignment.template.PairInProfileScorer<S,C>
    • org.biojava3.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava3.alignment.template.Aligner<S,C>)
  • org.biojava3.alignment.template.PartitionRefiner<S,C> (also extends org.biojava3.alignment.template.Aligner<S,C>, org.biojava3.alignment.template.ProfileProfileScorer<S,C>)
  • org.biojava3.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava3.alignment.template.Aligner<S,C>, org.biojava3.alignment.template.ProfileProfileScorer<S,C>)
  • org.biojava3.alignment.template.ProfileProfileScorer<S,C>
    • org.biojava3.alignment.template.PartitionRefiner<S,C> (also extends org.biojava3.alignment.template.Aligner<S,C>)
    • org.biojava3.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava3.alignment.template.Aligner<S,C>)
  • org.biojava3.alignment.template.RescoreRefiner<S,C>
• org.forester.pccx.ScoringMethodForExternalNode
• org.biojava3.structure.gui.Selection
• org.forester.development.Sequence
• org.biojava3.core.sequence.io.template.SequenceCreatorInterface<C>
• org.biojava3.core.sequence.io.template.SequenceParserInterface
• java.io.Serializable
  • org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties
  • org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties
• org.biojava3.sequencing.io.fastq.StreamListener
• org.biojava.bio.structure.align.StructureAlignment
• org.biojava.bio.structure.server.StructureEvent
• org.biojava.bio.structure.io.StructureIO
  • org.biojava.bio.structure.io.StructureIOFile
• org.biojava.bio.structure.server.StructureListener
• org.biojava.bio.structure.gui.util.StructurePairSelector
• org.biojava.bio.structure.io.StructureProvider
• org.biojava.bio.structure.server.StructureServer
• org.biojava3.structure.gui.StructureViewer
• org.biojava3.alignment.template.SubstitutionMatrix<C>
• org.biojava3.core.sequence.transcription.Table
• javax.swing.tree.TreeNode
  • org.biojava3.alignment.template.GuideTreeNode<S,C>
• org.biojava.bio.structure.align.ce.UserArgumentProcessor
• org.biojava3.core.util.XMLWriter

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biojava.bio.structure.Element (implements java.io.Serializable)
    • org.biojava.bio.structure.BondType
    • org.biojava.bio.structure.PDBStatus.Status
    • org.biojava.bio.structure.ElementType (implements java.io.Serializable)
    • org.biojava.bio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
    • org.biojava.bio.structure.io.mmcif.chem.PolymerType (implements java.io.Serializable)
    • org.biojava.bio.structure.io.mmcif.chem.ResidueType (implements java.io.Serializable)
    • org.biojava.bio.structure.scop.ScopCategory (implements java.io.Serializable)
    • org.biojava3.aaproperties.PeptideProperties.SingleLetterAACode
    • org.biojava3.aaproperties.CommandPrompt.PropertyName
    • org.biojava3.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
    • org.biojava3.aaproperties.profeat.IProfeatProperties.GROUPING
    • org.biojava3.aaproperties.profeat.IProfeatProperties.TRANSITION
    • org.biojava3.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
    • org.biojava3.alignment.Alignments.PairInProfileScorerType
    • org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType
    • org.biojava3.alignment.Alignments.PairwiseSequenceScorerType
    • org.biojava3.alignment.Alignments.ProfileProfileAlignerType
    • org.biojava3.alignment.Alignments.RefinerType
    • org.biojava3.alignment.routines.AlignerHelper.Last
    • org.biojava3.alignment.template.GapPenalty.Type
    • org.biojava3.alignment.template.AlignedSequence.Step
    • org.biojava3.alignment.template.Profile.StringFormat
    • org.biojava3.core.sequence.Strand
    • org.biojava3.core.sequence.DataSource
    • org.biojava3.core.sequence.DNASequence.DNAType
    • org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage
    • org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection
    • org.biojava3.core.sequence.template.LightweightProfile.StringFormat
    • org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
    • org.biojava3.core.sequence.transcription.Frame
    • org.biojava3.phylo.TreeType
    • org.biojava3.phylo.TreeConstructionAlgorithm
    • org.biojava3.protmod.ModificationOccurrenceType
    • org.biojava3.protmod.ModificationCategory
    • org.biojava3.ronn.RonnConstraint.Threshold
    • org.biojava3.sequencing.io.fastq.FastqVariant
    • org.biojava3.structure.gui.RenderStyle
    • org.biojava3.ws.alignment.qblast.BlastMatrixEnum
    • org.biojava3.ws.alignment.qblast.BlastOutputParameterEnum
    • org.biojava3.ws.alignment.qblast.BlastProgramEnum
    • org.biojava3.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
    • org.biojava3.ws.alignment.qblast.BlastAlignmentParameterEnum
    • org.biojava3.ws.alignment.qblast.BlastOutputFormatEnum
    • org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat
    • org.forester.go.GoXRef.Type
    • org.forester.go.GoSubset.Type
    • org.forester.go.GoNameSpace.GoNamespaceType
    • org.forester.go.GoRelationship.Type
    • org.forester.go.OBOparser.ReturnType
    • org.forester.go.etc.OntologizerResult.TYPE
    • org.forester.io.parsers.HmmscanPerDomainTableParser.FilterType
    • org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
    • org.forester.io.parsers.HmmscanPerDomainTableParser.ReturnType
    • org.forester.io.parsers.HmmPfamOutputParser.FilterType
    • org.forester.io.parsers.HmmPfamOutputParser.ReturnType
    • org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION
    • org.forester.io.writers.PhylogenyWriter.FORMAT
    • org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE
    • org.forester.phylogeny.data.Property.AppliesTo
    • org.forester.phylogeny.data.Event.EventType
    • org.forester.phylogenyinference.DistanceMatrix.Format
    • org.forester.phylogenyinference.CharacterStateMatrix.BinaryStates
    • org.forester.phylogenyinference.CharacterStateMatrix.Format
    • org.forester.phylogenyinference.CharacterStateMatrix.GainLossStates
    • org.forester.phylogenyinference.CharacterStateMatrix.NucleotideStates
    • org.forester.phylogenyinference.SymmetricalDistanceMatrixParser.InputMatrixType
    • org.forester.surfacing.DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
    • org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION
    • org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
    • org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField
    • org.forester.surfacing.DomainSimilarityCalculator.Detailedness
    • org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput
    • org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
    • org.forester.surfacing.BinaryDomainCombination.DomainCombinationType
    • org.forester.surfacing.BinaryDomainCombination.OutputFormat
    • org.forester.tools.PhylogenyDecorator.FIELD
    • org.forester.util.ForesterUtil.PhylogenyNodeField