## Hierarchy For All Packages

Package Hierarchies:
  org.biojava.bibliography, org.biojava.bio, org.biojava.bio.alignment, org.biojava.bio.annodb, org.biojava.bio.chromatogram, org.biojava.bio.chromatogram.graphic, org.biojava.bio.dist, org.biojava.bio.dp, org.biojava.bio.dp.onehead, org.biojava.bio.dp.twohead, org.biojava.bio.gui, org.biojava.bio.gui.glyph, org.biojava.bio.gui.sequence, org.biojava.bio.gui.sequence.tracklayout, org.biojava.bio.molbio, org.biojava.bio.program, org.biojava.bio.program.abi, org.biojava.bio.program.blast2html, org.biojava.bio.program.das, org.biojava.bio.program.das.dasalignment, org.biojava.bio.program.das.dasstructure, org.biojava.bio.program.formats, org.biojava.bio.program.gff, org.biojava.bio.program.gff3, org.biojava.bio.program.hmmer, org.biojava.bio.program.homologene, org.biojava.bio.program.indexdb, org.biojava.bio.program.phred, org.biojava.bio.program.sax, org.biojava.bio.program.sax.blastxml, org.biojava.bio.program.scf, org.biojava.bio.program.ssaha, org.biojava.bio.program.ssbind, org.biojava.bio.program.tagvalue, org.biojava.bio.program.unigene, org.biojava.bio.program.xff, org.biojava.bio.program.xml, org.biojava.bio.proteomics, org.biojava.bio.proteomics.aaindex, org.biojava.bio.search, org.biojava.bio.seq, org.biojava.bio.seq.db, org.biojava.bio.seq.db.biofetch, org.biojava.bio.seq.db.biosql, org.biojava.bio.seq.db.emblcd, org.biojava.bio.seq.db.flat, org.biojava.bio.seq.distributed, org.biojava.bio.seq.filter, org.biojava.bio.seq.homol, org.biojava.bio.seq.impl, org.biojava.bio.seq.io, org.biojava.bio.seq.io.agave, org.biojava.bio.seq.io.filterxml, org.biojava.bio.seq.io.game, org.biojava.bio.seq.io.game12, org.biojava.bio.seq.projection, org.biojava.bio.structure, org.biojava.bio.structure.align, org.biojava.bio.structure.align.helper, org.biojava.bio.structure.align.pairwise, org.biojava.bio.structure.gui, org.biojava.bio.structure.gui.events, org.biojava.bio.structure.gui.util, 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.jama, org.biojava.bio.structure.server, org.biojava.bio.symbol, org.biojava.bio.taxa, org.biojava.directory, org.biojava.naming, org.biojava.ontology, org.biojava.ontology.io, org.biojava.ontology.obo, org.biojava.stats.svm, org.biojava.stats.svm.tools, org.biojava.utils, org.biojava.utils.automata, org.biojava.utils.cache, org.biojava.utils.candy, org.biojava.utils.io, org.biojava.utils.lsid, org.biojava.utils.math, org.biojava.utils.net, org.biojava.utils.process, org.biojava.utils.regex, org.biojava.utils.stax, org.biojava.utils.walker, org.biojava.utils.xml, org.biojavax, org.biojavax.bio, org.biojavax.bio.db, org.biojavax.bio.db.biosql, org.biojavax.bio.db.ncbi, org.biojavax.bio.phylo, org.biojavax.bio.phylo.io.nexus, org.biojavax.bio.phylo.io.phylip, org.biojavax.bio.seq, org.biojavax.bio.seq.io, org.biojavax.bio.taxa, org.biojavax.bio.taxa.io, org.biojavax.ga, org.biojavax.ga.exception, org.biojavax.ga.functions, org.biojavax.ga.impl, org.biojavax.ga.util, org.biojavax.ontology, org.biojavax.utils

## Class Hierarchy

- java.lang.Object
  - org.biojava.bio.proteomics.aaindex.AAindexStreamReader (implements org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator)
  - org.biojava.bio.program.abi.ABIFParser
    - org.biojava.bio.program.abi.ABIFChromatogram.Parser
  - org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
  - org.biojava.bio.program.abi.ABITools
  - org.biojava.bio.program.abi.ABITrace
  - org.biojava.bio.program.blast2html.AbstractAlignmentStyler
    - org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  - 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
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.gui.sequence.AbiTraceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - org.biojava.bio.symbol.AbstractAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
      - org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
      - org.biojava.bio.symbol.SimpleAlphabet (implements java.io.Serializable)
      - org.biojava.bio.symbol.SingletonAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
    - org.biojava.bio.AbstractAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
      - org.biojava.bio.AnnotationChanger
      - org.biojava.bio.AnnotationRenamer
      - org.biojava.bio.BeanAsAnnotation
      - org.biojava.bio.seq.io.ReferenceAnnotation
      - org.biojava.bio.SimpleAnnotation
      - org.biojava.bio.SmallAnnotation
    - org.biojava.bio.gui.sequence.AbstractBeadRenderer (implements org.biojava.bio.gui.sequence.BeadFeatureRenderer, java.io.Serializable)
      - org.biojava.bio.gui.sequence.EllipticalBeadRenderer
      - org.biojava.bio.gui.sequence.RectangularBeadRenderer
      - org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
    - org.biojavax.bio.db.AbstractBioEntryDB (implements org.biojavax.bio.db.BioEntryDB)
      - org.biojavax.bio.db.AbstractRichSequenceDB (implements org.biojavax.bio.db.RichSequenceDB)
        - org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
        - org.biojavax.bio.db.ncbi.GenbankRichSequenceDB (implements org.biojavax.bio.db.RichSequenceDBLite)
        - org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB (implements org.biojavax.bio.db.RichSequenceDBLite)
        - org.biojavax.bio.db.HashRichSequenceDB (implements org.biojavax.bio.db.RichSequenceDB)
      - org.biojavax.bio.db.biosql.BioSQLBioEntryDB
      - org.biojavax.bio.db.HashBioEntryDB (implements org.biojavax.bio.db.BioEntryDB)
    - org.biojavax.ga.functions.AbstractCrossOverFunction (implements org.biojavax.ga.functions.CrossOverFunction)
      - org.biojavax.ga.functions.OrderCrossover
      - org.biojavax.ga.functions.SimpleCrossOverFunction
    - org.biojava.bio.dist.AbstractDistribution (implements org.biojava.bio.dist.Distribution)
      - org.biojava.bio.dist.AbstractOrderNDistribution (implements org.biojava.bio.dist.OrderNDistribution, java.io.Serializable)
      - org.biojava.bio.dist.SimpleDistribution (implements java.io.Serializable)
        - org.biojava.bio.dist.UntrainableDistribution
      - org.biojava.bio.dist.UniformDistribution (implements java.io.Serializable)
    - org.biojava.bio.seq.AbstractFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
      - org.biojava.bio.seq.MergeFeatureHolder (implements java.io.Serializable)
      - org.biojava.bio.seq.projection.ProjectedFeatureHolder (implements org.biojava.bio.seq.FeatureHolder, java.io.Serializable)
      - org.biojava.bio.seq.SimpleFeatureHolder (implements java.io.Serializable)
    - org.biojavax.ga.impl.AbstractGeneticAlgorithm (implements org.biojavax.ga.GeneticAlgorithm)
      - org.biojavax.ga.impl.SimpleGeneticAlgorithm
    - org.biojavax.ga.functions.AbstractMutationFunction (implements org.biojavax.ga.functions.MutationFunction)
      - org.biojavax.ga.functions.SimpleMutationFunction
      - org.biojavax.ga.functions.SwapMutationFunction
    - org.biojavax.ga.impl.AbstractOrganism (implements org.biojavax.ga.Organism)
      - org.biojavax.ga.impl.SimpleOrganism
    - org.biojava.bio.program.homologene.AbstractOrthologueSet (implements org.biojava.bio.program.homologene.OrthologueSet)
      - org.biojava.bio.program.homologene.SimpleOrthologueSet
    - org.biojava.bio.program.homologene.AbstractOrthoPairSet (implements org.biojava.bio.program.homologene.OrthoPairSet)
      - org.biojava.bio.program.homologene.SimpleOrthoPairSet
    - org.biojavax.ga.impl.AbstractPopulation (implements org.biojavax.ga.Population)
      - org.biojavax.ga.impl.SimplePopulation
    - org.biojava.bio.seq.db.AbstractSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
      - org.biojava.bio.seq.db.AnnotatedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
      - org.biojava.bio.seq.distributed.DistributedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
      - org.biojava.bio.seq.db.DummySequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
      - org.biojava.bio.seq.db.HashSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
      - org.biojava.bio.seq.db.IndexedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
      - org.biojava.bio.seq.db.SequenceDBWrapper (implements java.io.Serializable)
        - org.biojava.bio.seq.db.CachingSequenceDB
        - org.biojava.bio.seq.db.SubSequenceDB
        - org.biojava.bio.seq.db.ViewingSequenceDB
    - org.biojava.bio.symbol.AbstractSymbol (implements org.biojava.bio.symbol.Symbol)
      - org.biojava.bio.symbol.FundamentalAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
        - org.biojava.bio.dp.SimpleDotState (implements org.biojava.bio.dp.DotState, java.io.Serializable)
        - org.biojava.bio.dp.SimpleModelInState (implements org.biojava.bio.dp.ModelInState)
      - org.biojava.bio.symbol.SimpleAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - org.biojava.bio.symbol.AbstractSymbolList (implements org.biojava.bio.symbol.SymbolList)
      - org.biojava.bio.alignment.AbstractULAlignment (implements org.biojava.bio.alignment.UnequalLengthAlignment)
        - org.biojava.bio.alignment.FlexibleAlignment (implements org.biojava.bio.alignment.ARAlignment, org.biojava.bio.alignment.EditableAlignment)
      - org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment (implements org.biojava.bio.alignment.UnequalLengthAlignment)
      - org.biojava.bio.seq.impl.AssembledSymbolList
      - org.biojava.bio.symbol.ChunkedSymbolList (implements java.io.Serializable)
      - org.biojava.bio.symbol.DummySymbolList (implements java.io.Serializable)
      - org.biojava.bio.seq.impl.NewAssembledSymbolList
      - org.biojava.bio.symbol.PackedSymbolList (implements java.io.Serializable)
      - org.biojava.bio.symbol.SimpleAlignment (implements org.biojava.bio.symbol.Alignment, java.io.Serializable)
      - org.biojava.bio.symbol.SimpleGappedSymbolList (implements org.biojava.bio.symbol.GappedSymbolList, java.io.Serializable)
        - org.biojava.bio.seq.impl.SimpleGappedSequence (implements org.biojava.bio.seq.GappedSequence)
      - org.biojava.bio.symbol.SimpleSymbolList (implements org.biojava.utils.ChangeListener, java.io.Serializable)
    - org.biojava.bio.taxa.AbstractTaxon (implements org.biojava.bio.taxa.Taxon)
      - org.biojava.bio.taxa.SimpleTaxon
      - org.biojava.bio.taxa.WeakTaxon
    - org.biojava.ontology.AbstractTerm (implements org.biojava.ontology.Term)
      - org.biojava.ontology.RemoteTerm.Impl (implements org.biojava.ontology.RemoteTerm, java.io.Serializable)
      - org.biojava.ontology.Term.Impl (implements java.io.Serializable, org.biojava.ontology.Term)
        - org.biojava.ontology.Variable.Impl (implements org.biojava.ontology.Variable)
    - org.biojava.bio.gui.sequence.BasicFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - org.biojava.bio.seq.db.biosql.BioSQLSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
    - org.biojava.bio.gui.sequence.CrosshairRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)
    - org.biojava.bio.program.das.DAS
    - org.biojava.bio.program.das.DASSequence
    - org.biojava.bio.seq.impl.DummySequence (implements org.biojava.bio.seq.Sequence)
    - org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - org.biojava.bio.gui.sequence.FeatureLabelRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - org.biojava.bio.seq.FeatureTypes.RepositoryImpl (implements org.biojava.bio.seq.FeatureTypes.Repository)
    - org.biojava.bio.program.gff3.GFF3Record.Impl (implements org.biojava.bio.program.gff3.GFF3Record)
    - org.biojava.bio.dist.IndexedCount (implements org.biojava.bio.dist.Count, java.io.Serializable)
    - org.biojava.bio.gui.sequence.LabelledSequenceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - org.biojava.bio.seq.LazyFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
    - org.biojava.bio.MergeAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
    - org.biojava.bio.gui.sequence.MultiLineRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer, java.io.Serializable)
      - org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
        - org.biojava.bio.gui.sequence.PeptideDigestRenderer
    - org.biojava.bio.seq.NewSimpleAssembly (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.gui.sequence.OffsetRulerRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - org.biojava.ontology.Ontology.Impl (implements org.biojava.ontology.Ontology, java.io.Serializable)
    - org.biojava.ontology.OntologyTerm.Impl (implements org.biojava.ontology.OntologyTerm, java.io.Serializable)
    - org.biojava.bio.OverlayAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
    - org.biojava.bio.gui.sequence.OverlayRendererWrapper (implements org.biojava.bio.gui.sequence.OverlayMarker, org.biojava.bio.gui.sequence.SequenceRenderer, java.io.Serializable)
    - org.biojava.bio.dist.PairDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
    - org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, java.io.Serializable)
    - org.biojava.bio.gui.sequence.PairwiseFilteringRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, java.io.Serializable)
    - org.biojava.bio.gui.sequence.PairwiseOverlayRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, java.io.Serializable)
    - org.biojava.bio.search.SequenceDBSearchHit (implements org.biojava.bio.Annotatable, org.biojava.bio.search.SeqSimilaritySearchHit)
    - org.biojava.bio.search.SequenceDBSearchResult (implements org.biojava.bio.Annotatable, org.biojava.bio.search.SeqSimilaritySearchResult)
    - org.biojava.bio.search.SequenceDBSearchSubHit (implements org.biojava.bio.search.SeqSimilaritySearchSubHit)
    - org.biojava.bio.gui.sequence.SequenceRendererWrapper (implements org.biojava.bio.gui.sequence.SequenceRenderer, java.io.Serializable)
      - org.biojava.bio.gui.sequence.AlignmentRenderer
      - org.biojava.bio.gui.sequence.BumpedRenderer
      - org.biojava.bio.gui.sequence.FilteringRenderer
        - org.biojava.bio.gui.sequence.GlyphFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
          - org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer
      - org.biojava.bio.gui.sequence.GappedRenderer
      - org.biojava.bio.gui.sequence.PaddingRenderer
    - org.biojava.bio.seq.SimpleAssembly (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence)
    - org.biojavax.bio.SimpleBioEntry (implements org.biojavax.bio.BioEntry)
      - org.biojavax.bio.seq.ThinRichSequence (implements org.biojavax.bio.seq.RichSequence)
        - org.biojavax.bio.seq.SimpleRichSequence
    - org.biojavax.bio.SimpleBioEntryRelationship (implements org.biojavax.bio.BioEntryRelationship)
    - org.biojava.bio.symbol.SimpleCodonPref (implements org.biojava.bio.symbol.CodonPref)
    - org.biojavax.SimpleComment (implements org.biojavax.Comment)
    - org.biojavax.ontology.SimpleComparableOntology (implements org.biojavax.ontology.ComparableOntology)
    - org.biojavax.ontology.SimpleComparableTerm (implements org.biojavax.ontology.ComparableTerm)
    - org.biojavax.ontology.SimpleComparableTriple (implements org.biojavax.ontology.ComparableTriple)
    - org.biojavax.SimpleDocRef (implements org.biojavax.DocRef)
    - org.biojava.bio.dp.SimpleEmissionState (implements org.biojava.bio.dp.EmissionState, java.io.Serializable)
      - org.biojava.bio.dp.MagicalState
      - org.biojava.bio.program.hmmer.ProfileEmissionState
    - org.biojava.bio.seq.impl.SimpleFeature (implements org.biojava.bio.seq.Feature, org.biojava.bio.seq.RealizingFeatureHolder, java.io.Serializable)
      - org.biojava.bio.seq.impl.SimpleStrandedFeature (implements org.biojava.bio.seq.StrandedFeature)
        - org.biojava.bio.seq.impl.SimpleFramedFeature (implements org.biojava.bio.seq.Frame, org.biojava.bio.seq.FramedFeature)
        - org.biojava.bio.seq.impl.SimpleHomologyFeature (implements org.biojava.bio.seq.homol.HomologyFeature)
        - org.biojava.bio.seq.impl.SimpleRemoteFeature (implements org.biojava.bio.seq.RemoteFeature, java.io.Serializable)
        - org.biojava.bio.seq.impl.SimpleRestrictionSite (implements org.biojava.bio.molbio.RestrictionSite)
        - org.biojava.bio.seq.impl.SimpleSimilarityPairFeature (implements org.biojava.bio.seq.homol.SimilarityPairFeature)
    - org.biojava.bio.seq.homol.SimpleHomology (implements org.biojava.bio.seq.homol.Homology)
    - org.biojava.bio.gui.sequence.SimpleLabelRenderer (implements org.biojava.bio.gui.sequence.LabelRenderer)
    - org.biojava.bio.dp.SimpleMarkovModel (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
      - org.biojava.bio.program.hmmer.FullHmmerProfileHMM
      - org.biojava.bio.dp.ProfileHMM
        - org.biojava.bio.program.hmmer.HmmerProfileHMM
    - org.biojavax.SimpleNamespace (implements org.biojavax.Namespace)
    - org.biojavax.bio.taxa.SimpleNCBITaxon (implements org.biojavax.bio.taxa.NCBITaxon)
    - org.biojavax.SimpleNote (implements org.biojavax.Note)
    - org.biojavax.SimpleRankedCrossRef (implements org.biojavax.RankedCrossRef)
    - org.biojavax.SimpleRankedDocRef (implements org.biojavax.RankedDocRef)
    - org.biojavax.SimpleRichAnnotation (implements org.biojavax.RichAnnotation)
    - org.biojavax.bio.seq.SimpleRichFeature (implements org.biojavax.bio.seq.RichFeature)
    - org.biojavax.bio.seq.SimpleRichFeatureRelationship (implements org.biojavax.bio.seq.RichFeatureRelationship)
    - org.biojavax.bio.seq.SimpleRichLocation (implements org.biojavax.bio.seq.RichLocation)
      - org.biojavax.bio.seq.CompoundRichLocation (implements org.biojavax.bio.seq.RichLocation)
        - org.biojavax.bio.seq.MultiSourceCompoundRichLocation (implements org.biojavax.bio.seq.RichLocation)
    - org.biojava.bio.search.SimpleSeqSimilaritySearchHit (implements org.biojava.bio.search.SeqSimilaritySearchHit)
    - org.biojava.bio.search.SimpleSeqSimilaritySearchResult (implements org.biojava.bio.search.SeqSimilaritySearchResult)
    - org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit (implements org.biojava.bio.search.SeqSimilaritySearchSubHit)
    - org.biojava.bio.seq.impl.SimpleSequence (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence, java.io.Serializable)
      - org.biojava.bio.program.phred.PhredSequence (implements org.biojava.bio.program.phred.Qualitative)
      - org.biojava.bio.seq.impl.RevCompSequence
    - org.biojava.bio.gui.sequence.SixFrameRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - org.biojava.bio.gui.sequence.SixFrameZiggyRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer, java.io.Serializable)
    - org.biojava.bio.gui.sequence.StackedFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - org.biojava.bio.gui.sequence.TickFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - org.biojava.bio.dist.TranslatedDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
    - org.biojava.bio.seq.db.WebSequenceDB (implements org.biojava.bio.seq.db.SequenceDBLite)
      - org.biojava.bio.seq.db.NCBISequenceDB
    - org.biojava.bio.dp.WMAsMM (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
    - org.biojava.bio.gui.sequence.ZiggyFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer, java.io.Serializable)
  - org.biojava.bio.chromatogram.AbstractChromatogram (implements org.biojava.bio.chromatogram.Chromatogram)
    - org.biojava.bio.program.abi.ABIFChromatogram (implements java.io.Serializable)
    - org.biojava.bio.program.scf.SCF
    - org.biojava.bio.chromatogram.SimpleChromatogram
  - java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    - java.util.AbstractList<E> (implements java.util.List<E>)
      - org.biojava.utils.FileAsList (implements org.biojava.utils.Commitable)
      - org.biojava.utils.ListTools.Doublet (implements java.io.Serializable)
      - org.biojava.utils.ListTools.SeriesList
      - org.biojava.utils.ListTools.Triplet (implements java.io.Serializable)
      - org.biojava.utils.SingletonList (implements java.io.Serializable)
    - java.util.AbstractSet<E> (implements java.util.Set<E>)
      - org.biojava.utils.MergingSet
      - org.biojava.utils.SmallSet
      - org.biojavax.ga.util.WeightedSet (implements java.io.Serializable)
  - org.biojava.bio.symbol.AbstractLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
    - org.biojava.bio.symbol.AbstractRangeLocation
      - org.biojava.bio.symbol.FuzzyLocation (implements java.io.Serializable)
      - org.biojava.bio.symbol.PointLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
      - org.biojava.bio.symbol.RangeLocation (implements java.io.Serializable)
        - org.biojava.bio.symbol.MergeLocation
    - org.biojava.bio.symbol.FuzzyPointLocation
  - org.biojava.bio.symbol.AbstractLocationDecorator (implements org.biojava.bio.symbol.Location)
    - org.biojava.bio.symbol.BetweenLocation
    - org.biojava.bio.symbol.CircularLocation
  - org.biojava.bio.symbol.AbstractManyToOneTranslationTable (implements org.biojava.bio.symbol.ManyToOneTranslationTable)
    - org.biojava.bio.symbol.SimpleManyToOneTranslationTable (implements java.io.Serializable)
      - org.biojava.bio.symbol.SimpleGeneticCodeTable
  - java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    - org.biojava.utils.BeanAsMap
    - org.biojava.utils.OverlayMap
    - org.biojava.utils.SmallMap (implements java.io.Serializable)
    - org.biojava.utils.cache.WeakValueHashMap
  - org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor (implements org.biojava.bio.dp.twohead.PairDPCursor)
    - org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
    - org.biojava.bio.dp.twohead.MatrixPairDPCursor
  - org.biojava.bio.program.homologene.AbstractOrthoPairCollection (implements org.biojava.bio.program.homologene.OrthoPairCollection)
    - org.biojava.bio.program.homologene.SimpleOrthoPairCollection
      - org.biojava.bio.program.homologene.SimpleHomologeneDB (implements org.biojava.bio.program.homologene.HomologeneDB)
  - org.biojava.bio.symbol.AbstractReversibleTranslationTable (implements org.biojava.bio.symbol.ReversibleTranslationTable)
    - org.biojava.bio.symbol.SimpleReversibleTranslationTable (implements java.io.Serializable)
  - org.biojava.stats.svm.AbstractSVMClassifierModel (implements org.biojava.stats.svm.SVMClassifierModel)
    - org.biojava.stats.svm.SimpleSVMClassifierModel
  - org.biojava.stats.svm.AbstractSVMTarget (implements org.biojava.stats.svm.SVMTarget)
  - org.biojava.bio.dp.AbstractTrainer (implements org.biojava.bio.dp.TrainingAlgorithm)
    - org.biojava.bio.dp.BaumWelchSampler (implements java.io.Serializable)
    - org.biojava.bio.dp.BaumWelchTrainer (implements java.io.Serializable)
  - org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.program.tagvalue.AbstractWrapper (implements org.biojava.bio.program.tagvalue.TagValueWrapper)
  - org.biojava.bio.seq.io.agave.AGAVEDbId
  - org.biojava.bio.seq.io.agave.AGAVEIdAlias
  - org.biojava.bio.seq.io.agave.AGAVEMapLocation
  - org.biojava.bio.seq.io.agave.AGAVEMapPosition
  - org.biojava.bio.seq.io.agave.AGAVEMatchRegion
  - org.biojava.bio.seq.io.agave.AGAVEProperty
  - org.biojava.bio.seq.io.agave.AGAVEQueryRegion
  - org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
  - org.biojava.bio.seq.io.agave.AgaveWriter
  - org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  - org.biojava.bio.seq.io.agave.AGAVEXref
  - org.biojava.bio.seq.io.agave.AGAVEXrefs
  - org.biojava.bio.structure.gui.util.AlignedPosition
  - org.biojava.bio.seq.io.AlignIOConstants
  - org.biojava.bio.program.das.dasalignment.Alignment
  - org.biojava.bio.symbol.Alignment.SymbolListIterator (implements java.util.Iterator<E>)
  - org.biojava.bio.structure.gui.util.AlignmentCalc (implements java.lang.Runnable)
  - org.biojava.bio.program.blast2html.AlignmentMarker
  - org.biojava.bio.structure.align.pairwise.AligNPE
  - org.biojava.bio.structure.align.helper.AlignTools
  - org.biojava.bio.symbol.AlphabetManager
  - org.biojava.bio.program.ssbind.AlphabetResolver
  - org.biojava.bio.structure.AlphaCTools
  - org.biojava.bio.structure.align.pairwise.AltAligComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  - org.biojava.bio.program.tagvalue.AnnotationBuilder (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - org.biojava.bio.program.ssbind.AnnotationFactory
  - org.biojava.bio.AnnotationTools
  - org.biojava.bio.AnnotationType.Abstract (implements org.biojava.bio.AnnotationType)
    - org.biojava.bio.AnnotationType.Impl
  - org.biojava.utils.xml.AppBeanRunner
  - org.biojava.utils.automata.ArrayStateMachineToolkit
  - org.biojava.bio.gui.sequence.ArrowedFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
  - org.biojava.bio.gui.glyph.ArrowGlyph (implements org.biojava.bio.gui.glyph.Glyph)
  - org.biojava.bio.structure.AtomImpl (implements org.biojava.bio.structure.Atom)
  - org.biojava.bio.structure.AtomIterator (implements java.util.Iterator<E>)
  - org.biojava.bio.structure.Author
  - org.biojava.bio.dp.BackPointer
  - org.biojava.bio.gui.BarLogoPainter (implements org.biojava.bio.gui.LogoPainter)
  - org.biojava.bio.program.xml.BaseXMLWriter
  - org.biojava.bio.gui.sequence.BasicImapRenderer (implements org.biojava.bio.gui.sequence.ImageMapRenderer, java.io.Serializable)
  - org.biojava.bio.program.xff.BasicXFFHelper (implements org.biojava.bio.program.xff.XFFHelper)
    - org.biojava.bio.program.xff.PropertyWriter
  - org.biojava.bibliography.BiblioCriterion
  - org.biojava.bibliography.BiblioDescription
  - org.biojava.bibliography.BiblioEntryStatus
  - org.biojava.bibliography.BiblioJournal
  - org.biojava.bibliography.BiblioProvider
    - org.biojava.bibliography.BiblioOrganisation
    - org.biojava.bibliography.BiblioPerson
    - org.biojava.bibliography.BiblioService
  - org.biojava.bibliography.BiblioScope
  - org.biojava.bibliography.BiblioSubject
  - org.biojava.bibliography.BibRef
    - org.biojava.bibliography.BiblioArticle
      - org.biojava.bibliography.BiblioBookArticle
      - org.biojava.bibliography.BiblioJournalArticle
    - org.biojava.bibliography.BiblioBook
    - org.biojava.bibliography.BiblioPatent
    - org.biojava.bibliography.BiblioProceeding
    - org.biojava.bibliography.BiblioTechReport
    - org.biojava.bibliography.BiblioThesis
    - org.biojava.bibliography.BiblioWebResource
  - org.biojava.utils.math.BinarySearch
  - org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - org.biojava.bio.seq.db.BioIndex (implements org.biojava.bio.seq.db.IndexStore)
  - org.biojava.bio.structure.gui.BiojavaJmol
  - org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter (implements org.biojavax.bio.db.biosql.BioSQLFeatureFilter)
  - org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter (implements org.biojavax.bio.db.biosql.BioSQLFeatureFilter)
  - org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver (implements org.biojavax.CrossReferenceResolver)
  - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter (implements org.biojavax.bio.db.biosql.BioSQLFeatureFilter)
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
  - org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
  - org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder (implements org.biojavax.RichObjectBuilder)
  - org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - org.biojava.bio.program.indexdb.BioStore (implements org.biojava.bio.program.indexdb.IndexStore)
  - org.biojava.bio.program.indexdb.BioStoreFactory
  - org.biojava.bio.program.sax.BlastLikeSAXParser
  - org.biojava.bio.program.ssbind.BlastLikeSearchBuilder (implements org.biojava.bio.search.SearchBuilder)
  - org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter (implements org.biojava.bio.search.BlastLikeSearchFilter)
    - org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
    - org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
    - org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
    - org.biojava.bio.search.BlastLikeSearchFilter.Not
  - org.biojava.bio.search.BlastLikeSearchFilter.And
  - org.biojava.bio.search.BlastLikeSearchFilter.Or
  - org.biojava.bio.program.BlastLikeToXMLConverter
  - org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade (implements org.xml.sax.XMLReader)
  - org.biojava.bio.seq.ByLocationMinMaxComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.ByLocationMinMaxFeatureComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.structure.io.CAConverter
  - org.biojava.bio.structure.Calc
  - org.biojava.utils.candy.CandyEntry
  - org.biojava.bio.CardinalityConstraint
  - org.biojava.bio.dp.twohead.Cell
  - org.biojava.bio.structure.ChainImpl (implements org.biojava.bio.structure.Chain)
  - org.biojava.utils.cache.ChangeableCache
  - org.biojava.utils.ChangeAdapter (implements org.biojava.utils.ChangeListener)
    - org.biojava.utils.ChangeListener.ChangeEventRecorder
  - org.biojava.utils.ChangeForwarder (implements org.biojava.utils.ChangeListener)
    - org.biojava.bio.symbol.AbstractSymbolList.EditScreener
      - org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
    - org.biojava.bio.Annotatable.AnnotationForwarder
    - org.biojava.utils.ChangeForwarder.Retyper
    - org.biojava.bio.dist.Distribution.NullModelForwarder
    - org.biojava.bio.MergeAnnotation.PropertyForwarder
    - org.biojava.bio.OverlayAnnotation.PropertyForwarder
    - org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
    - org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
    - org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
  - org.biojava.utils.ChangeListener.AlwaysVetoListener (implements org.biojava.utils.ChangeListener)
  - org.biojava.utils.ChangeListener.LoggingListener (implements org.biojava.utils.ChangeListener)
  - org.biojava.utils.ChangeSupport
  - org.biojava.bio.program.tagvalue.ChangeTable
  - org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger (implements org.biojava.bio.program.tagvalue.ChangeTable.Changer)
  - org.biojava.utils.ChangeType (implements java.io.Serializable)
  - org.biojava.bio.structure.io.mmcif.model.ChemComp
  - org.biojava.bio.structure.io.mmcif.ChemCompConsumer (implements org.biojava.bio.structure.io.mmcif.MMcifConsumer)
  - org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
  - org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
  - org.biojava.bio.structure.jama.CholeskyDecomposition (implements java.io.Serializable)
  - org.biojava.bio.chromatogram.ChromatogramFactory
  - org.biojava.bio.chromatogram.graphic.ChromatogramGraphic (implements java.lang.Cloneable)
  - org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  - org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity (implements org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler)
  - org.biojava.bio.chromatogram.ChromatogramTools
  - org.biojava.bio.seq.io.ChunkedSymbolListFactory
  - org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer (implements org.biojava.bio.gui.sequence.CircularRenderer)
  - org.biojava.bio.gui.sequence.CircularFeaturesRenderer (implements org.biojava.bio.gui.sequence.CircularRenderer)
  - org.biojava.bio.gui.sequence.CircularMLR (implements org.biojava.bio.gui.sequence.CircularRenderer)
  - org.biojava.bio.gui.sequence.CircularPaddedRenderer (implements org.biojava.bio.gui.sequence.CircularRenderer)
  - org.biojava.stats.svm.tools.ClassifierExample
  - org.biojava.stats.svm.tools.Classify
  - org.biojava.utils.ClassTools
  - org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
  - org.biojava.bio.structure.align.ClusterAltAligs
  - org.biojava.bio.symbol.CodonPrefFilter.AcceptAll (implements org.biojava.bio.symbol.CodonPrefFilter)
  - org.biojava.bio.symbol.CodonPrefFilter.ByName (implements org.biojava.bio.symbol.CodonPrefFilter)
  - org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML (implements org.biojava.bio.symbol.CodonPrefFilter)
  - org.biojava.bio.symbol.CodonPrefTools
  - org.biojava.bio.CollectionConstraint.AllValuesIn (implements org.biojava.bio.CollectionConstraint)
  - org.biojava.bio.CollectionConstraint.And (implements org.biojava.bio.CollectionConstraint)
  - org.biojava.bio.CollectionConstraint.Contains (implements org.biojava.bio.CollectionConstraint)
  - org.biojava.bio.CollectionConstraint.Or (implements org.biojava.bio.CollectionConstraint)
  - org.biojava.bio.program.ssaha.CompactedDataStore (implements org.biojava.bio.program.ssaha.DataStore)
  - org.biojava.bio.program.ssaha.CompactedDataStoreFactory (implements org.biojava.bio.program.ssaha.DataStoreFactory)
  - 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.biojava.bio.gui.sequence.CircularRendererPanel
        - org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
        - org.biojava.bio.gui.DistributionLogo
        - javax.swing.JPanel (implements javax.accessibility.Accessible)
          - org.biojava.bio.structure.gui.JMatrixPanel
          - 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 javax.swing.event.ChangeListener)
          - org.biojava.bio.structure.gui.SequenceDisplay (implements javax.swing.event.ChangeListener)
          - org.biojava.bio.gui.sequence.SequencePanelWrapper
          - org.biojava.bio.structure.gui.util.SequenceScalePanel
        - javax.swing.JTree (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          - org.biojava.bio.gui.FeatureTree
        - org.biojava.bio.gui.sequence.PairwiseSequencePanel (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.PairwiseRenderContext, java.io.Serializable)
        - org.biojava.bio.gui.sequence.SequencePanel (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.SequenceRenderContext, javax.swing.SwingConstants)
        - org.biojava.bio.gui.sequence.SequencePoster (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.SequenceRenderContext, javax.swing.SwingConstants)
        - org.biojava.bio.gui.sequence.TranslatedSequencePanel (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.SequenceRenderContext)
      - java.awt.Window (implements javax.accessibility.Accessible)
        - java.awt.Frame (implements java.awt.MenuContainer)
          - javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - org.biojava.bio.structure.gui.AlignmentGui
            - org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
  - org.biojava.bio.molbio.Composition
    - org.biojava.bio.molbio.DNAComposition
  - org.biojava.bio.structure.Compound (implements java.lang.Cloneable)
  - org.biojava.utils.Constants
  - org.biojava.bio.structure.gui.util.CoordManager
  - org.biojavax.utils.CRC64Checksum (implements java.util.zip.Checksum)
  - org.biojavax.ga.functions.CrossOverFunction.NoCross (implements org.biojavax.ga.functions.CrossOverFunction)
  - org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  - org.biojava.bio.program.das.dasalignment.DASAlignmentClient
  - org.biojava.bio.program.das.DASLink
  - org.biojava.bio.program.das.DASSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - org.biojava.bio.program.das.dasstructure.DASStructureCall
  - org.biojava.bio.structure.io.DASStructureClient (implements org.biojava.bio.structure.io.StructureIO)
  - org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
  - org.biojava.bio.program.das.DataSource
    - org.biojava.bio.program.das.ReferenceServer (implements org.biojava.utils.Changeable)
  - org.biojava.bio.seq.db.biosql.DBHelper
    - org.biojava.bio.seq.db.biosql.HypersonicDBHelper
    - org.biojava.bio.seq.db.biosql.MySQLDBHelper
    - org.biojava.bio.seq.db.biosql.OracleDBHelper
    - org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
    - org.biojava.bio.seq.db.biosql.UnknownDBHelper
  - org.biojava.bio.seq.db.biosql.DBHelper.BioSequenceStyle
  - org.biojava.bio.seq.db.biosql.DBHelper.DeleteStyle
  - org.biojava.bio.seq.db.biosql.DBHelper.JoinStyle
  - org.biojava.bio.structure.DBRef (implements org.biojava.bio.structure.PDBRecord)
  - 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.program.blast2html.Blast2HTMLHandler
    - org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
    - org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
    - org.biojava.utils.stax.SAX2StAXAdaptor
    - org.biojava.bio.program.xml.SimpleXMLEmitter
    - org.biojava.bio.dist.XMLDistributionReader
  - org.biojava.ontology.DefaultOps (implements org.biojava.ontology.OntologyOps, java.io.Serializable)
  - org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory (implements org.biojava.bio.program.blast2html.URLGeneratorFactory)
  - org.biojava.bio.structure.server.DemoStructureServer (implements java.lang.Runnable, org.biojava.bio.structure.server.StructureListener)
  - org.biojava.utils.automata.DfaBuilder
  - java.util.Dictionary<K,V>
    - java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      - java.util.Properties
        - org.biojava.utils.TypedProperties
  - org.biojava.bio.proteomics.Digest
  - org.biojavax.bio.phylo.DistanceBasedTreeMethod
  - org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory (implements org.biojava.bio.dist.DistributionFactory, java.io.Serializable)
  - org.biojava.bio.dist.DistributionTools
  - org.biojava.bio.symbol.DNAAmbPack (implements org.biojava.bio.symbol.Packing, java.io.Serializable)
  - org.biojava.bio.symbol.DNANoAmbPack (implements org.biojava.bio.symbol.Packing, java.io.Serializable)
  - org.biojava.bio.gui.DNAStyle (implements org.biojava.bio.gui.SymbolStyle)
  - org.biojava.bio.seq.DNATools
  - org.biojavax.DocRefAuthor.Tools
  - org.biojava.bio.dp.DP
    - org.biojava.bio.dp.twohead.PairwiseDP (implements java.io.Serializable)
    - org.biojava.bio.dp.onehead.SingleDP (implements java.io.Serializable)
  - org.biojava.bio.dp.DP.ReverseIterator (implements java.util.Iterator<E>, java.io.Serializable)
  - org.biojava.bio.dp.twohead.DPCompiler (implements org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker)
  - org.biojava.bio.dp.DPFactory.DefaultFactory (implements org.biojava.bio.dp.DPFactory)
  - org.biojava.bio.dp.twohead.DPInterpreter (implements org.biojava.bio.dp.twohead.CellCalculatorFactory, java.io.Serializable)
  - org.biojava.bio.dp.twohead.DPInterpreter.Maker (implements org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker)
  - org.biojavax.DummyCrossReferenceResolver (implements org.biojavax.CrossReferenceResolver)
  - org.biojavax.bio.seq.DummyRichSequenceHandler (implements org.biojavax.bio.seq.RichSequenceHandler)
    - org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  - org.biojava.bio.seq.db.DummySequenceDBInstallation (implements org.biojava.bio.seq.db.SequenceDBInstallation)
  - org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator (implements org.biojava.bio.program.blast2html.DatabaseURLGenerator)
  - org.biojava.bio.taxa.EbiFormat (implements org.biojava.bio.taxa.TaxonParser)
  - org.biojava.bio.program.tagvalue.Echo (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - org.biojava.bio.EcNumber.Impl (implements org.biojava.bio.EcNumber)
  - org.biojava.bio.symbol.Edit (implements java.io.Serializable)
  - org.biojava.bio.structure.jama.EigenvalueDecomposition (implements java.io.Serializable)
  - org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer (implements org.biojava.bio.program.xff.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - org.biojava.bio.program.xff.ElementRecognizer.ByLocalName (implements org.biojava.bio.program.xff.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - org.biojava.bio.program.xff.ElementRecognizer.ByNSName (implements org.biojava.bio.program.xff.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - org.biojava.bio.program.xff.ElementRecognizer.HasAttribute (implements org.biojava.bio.program.xff.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - org.biojava.bio.program.formats.Embl (implements org.biojava.bio.program.formats.Format)
  - org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
    - org.biojava.bio.seq.db.emblcd.AcnumHitReader
    - org.biojava.bio.seq.db.emblcd.AcnumTrgReader
    - org.biojava.bio.seq.db.emblcd.DivisionLkpReader
    - org.biojava.bio.seq.db.emblcd.EntryNamIdxReader
  - org.biojava.bio.seq.db.EmblCDROMIndexStore (implements org.biojava.bio.seq.db.IndexStore)
  - org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
    - org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
  - org.biojava.bio.seq.io.EmblFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
  - org.biojava.bio.seq.io.EmblLikeFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - org.biojava.bio.seq.io.EmblLikeLocationParser
  - org.biojava.bio.seq.io.EmblProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.EmblReferenceComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.dp.twohead.EmissionCache (implements java.io.Serializable)
  - org.biojava.bio.structure.io.mmcif.model.Entity
  - org.biojava.bio.program.formats.Enzyme (implements org.biojava.bio.program.formats.Format)
  - java.util.EventObject (implements java.io.Serializable)
    - org.biojava.utils.ChangeEvent
    - org.biojava.utils.ParseErrorEvent
    - org.biojava.bio.gui.sequence.SequenceViewerEvent
    - org.biojava.stats.svm.TrainingEvent
  - org.biojava.utils.ExecRunner
  - org.biojava.utils.process.ExternalProcess
  - org.biojava.bio.seq.io.FastaAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.io.FastaFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - org.biojavax.bio.seq.io.FastaHeader
  - org.biojava.bio.program.sax.FastaSearchSAXParser (implements org.biojava.bio.search.SearchContentHandler)
  - org.biojava.bio.program.sax.FastaSequenceSAXParser
  - org.biojava.utils.xml.FastXMLWriter
  - org.biojava.bio.seq.Feature.ByLocationComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.Feature.Template (implements java.lang.Cloneable, java.io.Serializable)
    - org.biojavax.bio.seq.RichFeature.Template
    - org.biojava.bio.seq.StrandedFeature.Template
      - org.biojava.bio.seq.ComponentFeature.Template
      - org.biojava.bio.seq.FramedFeature.Template
      - org.biojava.bio.seq.homol.HomologyFeature.Template
      - org.biojava.bio.seq.RemoteFeature.Template
      - org.biojava.bio.molbio.RestrictionSite.Template
      - org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  - org.biojava.bio.seq.FeatureFilter.And (implements org.biojava.bio.seq.FeatureFilter)
  - org.biojava.bio.seq.FeatureFilter.ByAncestor (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByAnnotationType (implements org.biojava.bio.seq.OptimizableFilter)
    - org.biojava.bio.seq.FeatureFilter.AnnotationContains
    - org.biojava.bio.seq.FeatureFilter.ByAnnotation
    - org.biojava.bio.seq.FeatureFilter.HasAnnotation
  - org.biojava.bio.seq.FeatureFilter.ByChild (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByClass (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByComponentName (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByDescendant (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByFeature (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByPairwiseScore (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByParent (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.BySequenceName (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.BySource (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ByType (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ContainedByLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.FrameFilter (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.Not (implements org.biojava.bio.seq.FeatureFilter)
  - org.biojava.bio.seq.FeatureFilter.OnlyChildren (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.OnlyDescendants (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.Or (implements org.biojava.bio.seq.FeatureFilter)
  - org.biojava.bio.seq.FeatureFilter.OverlapsLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureFilter.StrandFilter (implements org.biojava.bio.seq.OptimizableFilter)
  - org.biojava.bio.seq.FeatureHolderUtils
  - org.biojava.bio.seq.impl.FeatureImpl
  - org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker (implements org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)
  - org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker (implements org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)
  - org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker (implements org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)
  - org.biojava.bio.seq.io.FeatureTableParser
  - org.biojava.bio.seq.FeatureTypes
  - org.biojava.bio.seq.db.FetchURL
  - org.biojava.bio.structure.io.FileConvert
  - org.biojava.bio.search.FilteringContentHandler.FilterVisitor (implements org.biojava.utils.walker.Visitor)
  - org.biojava.bio.search.FilterTest.Equals (implements org.biojava.bio.search.FilterTest)
  - org.biojava.bio.search.FilterTest.FindRegex
  - org.biojava.bio.search.FilterTest.GreaterThan (implements org.biojava.bio.search.FilterTest)
  - org.biojava.bio.search.FilterTest.LessThan (implements org.biojava.bio.search.FilterTest)
  - org.biojava.bio.search.FilterTest.MatchRegex
  - org.biojava.bio.seq.filter.FilterTransformer (implements org.biojava.utils.walker.Visitor)
  - org.biojava.bio.seq.FilterUtils
  - org.biojava.bio.seq.FilterUtils.DelegatingTransformer (implements org.biojava.bio.seq.FilterUtils.FilterTransformer)
  - org.biojava.utils.automata.FiniteAutomaton
    - org.biojava.utils.automata.Nfa (implements org.biojava.utils.automata.NfaBuilder)
  - org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler (implements org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler)
  - org.biojava.utils.cache.FixedSizeCache (implements org.biojava.utils.cache.Cache)
  - org.biojava.utils.cache.FixedSizeMap (implements org.biojava.utils.cache.CacheMap)
  - org.biojava.bio.structure.server.FlatFileInstallation (implements org.biojava.bio.structure.server.PDBInstallation)
  - org.biojava.bio.program.unigene.FlatFileUnigeneFactory (implements org.biojava.bio.program.unigene.UnigeneFactory)
  - org.biojava.bio.seq.db.flat.FlatSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - org.biojava.bio.program.tagvalue.Formats
  - org.biojava.bio.program.formats.FormatTools
  - org.biojava.bio.structure.align.pairwise.FragmentJoiner
  - org.biojava.bio.structure.align.pairwise.FragmentPair
  - org.biojava.bio.seq.FramedFeature.ReadingFrame (implements org.biojava.bio.seq.Frame, java.io.Serializable)
  - org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
  - org.biojava.bio.seq.io.GAMEFormat (implements org.biojava.bio.seq.io.SequenceFormat)
  - org.biojava.bio.structure.align.helper.GapArray
  - org.biojavax.ga.GAStoppingCriteria.MaximumGeneration (implements org.biojavax.ga.GAStoppingCriteria)
  - org.biojavax.ga.util.GATools
  - org.biojava.bio.seq.io.GenbankFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
    - org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  - org.biojava.bio.seq.io.GenbankFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
    - org.biojava.bio.seq.io.GenbankXmlFormat
    - org.biojava.bio.seq.io.GenpeptFormat
  - org.biojavax.bio.seq.io.GenbankLocationParser
  - org.biojava.bio.seq.io.GenbankProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.db.GenbankSequenceDB
  - org.biojava.bio.seq.io.GenEmblFeatureComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.io.GenEmblPropertyComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.seq.GeneticCodes
  - org.biojava.bio.seq.db.GenpeptSequenceDB
  - org.biojava.bio.program.gff3.GFF3Parser
  - org.biojava.bio.seq.distributed.GFFDataSource (implements org.biojava.bio.seq.distributed.DistDataSource)
  - org.biojava.bio.program.gff.GFFEntrySet
  - org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler (implements org.biojava.bio.program.gff.GFFErrorHandler)
  - org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler (implements org.biojava.bio.program.gff.GFFErrorHandler)
  - org.biojava.bio.program.gff.GFFFilterer (implements org.biojava.bio.program.gff.GFFDocumentHandler)
  - org.biojava.bio.program.gff.GFFParser
  - org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - org.biojava.bio.program.gff.GFFRecordFilter.NotFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - org.biojava.bio.program.gff.GFFTools
  - org.biojava.bio.program.gff.GFFWriter (implements org.biojava.bio.program.gff.GFFDocumentHandler)
  - org.biojava.bio.gui.glyph.GlyphUtils
  - org.biojava.ontology.io.GOParser
  - org.biojava.bio.structure.align.pairwise.Gotoh
  - org.biojava.bio.structure.GroupIterator (implements java.util.Iterator<E>)
  - org.biojava.bio.structure.GroupType
  - org.biojava.bio.gui.sequence.GUITools
  - org.biojavax.bio.seq.io.HashedFastaIterator (implements org.biojavax.bio.seq.RichSequenceIterator)
  - org.biojava.bio.gui.sequence.HeadlessRenderContext (implements org.biojava.bio.gui.sequence.SequenceRenderContext)
  - org.biojava.bio.gui.glyph.HelixGlyph (implements org.biojava.bio.gui.glyph.Glyph)
  - org.biojava.bio.structure.HetatomImpl (implements org.biojava.bio.structure.Group)
    - org.biojava.bio.structure.AminoAcidImpl (implements org.biojava.bio.structure.AminoAcid)
    - org.biojava.bio.structure.NucleotideImpl (implements org.biojava.bio.structure.Group)
  - org.biojava.bio.program.ssaha.HitMerger (implements org.biojava.bio.program.ssaha.SearchListener)
  - org.biojava.bio.program.hmmer.HmmerProfileParser
  - org.biojava.bio.program.homologene.HomologeneTools
  - org.biojava.bio.program.blast2html.HTMLRenderer
  - org.biojava.bio.seq.db.IDMaker.ByName (implements org.biojava.bio.seq.db.IDMaker, java.io.Serializable)
  - org.biojava.bio.seq.db.IDMaker.ByURN (implements org.biojava.bio.seq.db.IDMaker, java.io.Serializable)
  - org.biojava.bio.dist.IgnoreCountsTrainer (implements org.biojava.bio.dist.DistributionTrainer)
  - org.biojava.bio.gui.sequence.ImageMap.ClientSide (implements org.biojava.bio.gui.sequence.ImageMap, java.io.Serializable)
  - org.biojava.bio.gui.sequence.ImageMap.HotSpot (implements java.io.Serializable)
  - org.biojava.bio.gui.sequence.ImageMap.ServerSide (implements org.biojava.bio.gui.sequence.ImageMap, java.io.Serializable)
  - org.biojava.bio.program.tagvalue.Index2Model
  - org.biojava.bio.annodb.IndexedAnnotationDB (implements org.biojava.bio.annodb.AnnotationDB)
  - org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory (implements org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory)
  - org.biojava.utils.IndexedChangeHub (implements org.biojava.utils.ChangeHub)
  - org.biojava.utils.IndexedChangeHub.ListenerMemento
  - org.biojava.bio.program.tagvalue.Indexer (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - org.biojava.bio.program.tagvalue.Indexer2 (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - org.biojava.bio.structure.align.helper.IndexPair
    - org.biojava.bio.structure.align.helper.AligMatEl
  - org.biojava.bio.program.indexdb.IndexTools
  - org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList (implements org.biojava.bio.symbol.SymbolList)
  - java.io.InputStream (implements java.io.Closeable)
    - org.biojava.utils.io.CachingInputStream (implements org.biojava.utils.io.Seekable)
    - java.io.FilterInputStream
      - java.io.BufferedInputStream
        - org.biojavax.bio.seq.io.DebuggingRichSeqIOListener (implements org.biojavax.bio.seq.io.RichSeqIOListener)
      - org.biojava.utils.io.UncompressInputStream
  - org.biojava.utils.io.InputStreamProvider
  - org.biojava.bio.proteomics.IsoelectricPointCalc
  - org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator (implements org.biojava.utils.math.ComputeObject)
  - org.biojava.utils.JDBCConnectionPool
  - org.biojava.utils.JDBCPooledDataSource
  - org.biojava.bio.structure.gui.events.JmolAlignedPositionListener (implements org.biojava.bio.structure.gui.events.AlignmentPositionListener)
  - org.biojava.bio.structure.align.helper.JointFragments
  - org.biojava.bio.structure.JournalArticle
  - java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    - org.biojava.bio.structure.gui.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
  - org.biojava.bio.search.KnuthMorrisPrattSearch
  - org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing (implements org.biojava.bio.gui.sequence.LabelRenderer)
  - org.biojava.utils.io.LargeBuffer
  - org.biojava.bio.gui.sequence.LayeredRenderer
  - org.biojava.bio.annodb.LazyFilteredAnnotationDB (implements org.biojava.bio.annodb.AnnotationDB)
  - org.biojava.bio.seq.impl.LazyFilterFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
  - org.biojava.bio.annodb.LazySearchedAnnotationDB (implements org.biojava.bio.annodb.AnnotationDB)
  - org.biojava.utils.lsid.LifeScienceIdentifier (implements java.io.Serializable)
  - org.biojava.bio.program.formats.Ligand
  - org.biojava.bio.program.formats.Ligand.Compound (implements org.biojava.bio.program.formats.Format)
  - org.biojava.bio.program.formats.Ligand.Enzyme (implements org.biojava.bio.program.formats.Format)
  - org.biojava.bio.program.formats.Ligand.Reaction (implements org.biojava.bio.program.formats.Format)
  - org.biojava.bio.dp.twohead.LightPairDPCursor (implements org.biojava.bio.dp.twohead.PairDPCursor)
  - org.biojava.stats.svm.LinearKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
  - org.biojava.bio.gui.sequence.LineInfo
  - org.biojava.bio.program.tagvalue.LineSplitParser (implements java.lang.Cloneable, org.biojava.bio.program.tagvalue.TagValueParser)
  - org.biojava.utils.ListTools (implements java.io.Serializable)
  - org.biojava.bio.symbol.LocationTools
  - org.biojava.bio.structure.jama.LUDecomposition (implements java.io.Serializable)
  - org.biojava.bio.program.ssaha.MappedDataStoreFactory (implements org.biojava.bio.program.ssaha.DataStoreFactory)
  - org.biojava.bio.proteomics.MassCalc
  - org.biojava.utils.regex.Matcher
  - org.biojava.bio.structure.jama.Maths
  - org.biojava.bio.structure.jama.Matrix (implements java.lang.Cloneable, java.io.Serializable)
  - org.biojava.bio.search.MaxMismatchMatcher (implements org.biojava.bio.search.BioMatcher)
  - org.biojava.bio.search.MaxMismatchPattern (implements org.biojava.bio.search.BioPattern)
  - org.biojava.bio.program.Meme
  - org.biojava.bio.structure.gui.util.MenuCreator
  - org.biojava.bio.annodb.MergingAnnotationDB (implements org.biojava.bio.annodb.AnnotationDB)
  - org.biojava.utils.MergingIterator (implements java.util.Iterator<E>)
  - 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.biojava.bio.symbol.MotifTools
  - org.biojava.bio.seq.io.MSFAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - org.biojavax.bio.phylo.MultipleHitCorrection
  - org.biojavax.ga.functions.MutationFunction.NoMutation (implements org.biojavax.ga.functions.MutationFunction)
  - org.biojava.bio.structure.Mutator
  - org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator (implements org.biojava.bio.program.blast2html.DatabaseURLGenerator)
  - org.biojava.stats.svm.NestedKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
    - org.biojava.stats.svm.CachingKernel
    - org.biojava.stats.svm.DiagonalAddKernel
    - org.biojava.stats.svm.DiagonalCachingKernel
    - org.biojava.stats.svm.ListSumKernel
    - org.biojava.stats.svm.NormalizingKernel
    - org.biojava.stats.svm.PolynomialKernel
    - org.biojava.stats.svm.RadialBaseKernel
  - org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract (implements org.biojavax.bio.phylo.io.nexus.NexusBlock)
    - org.biojavax.bio.phylo.io.nexus.CharactersBlock
      - org.biojavax.bio.phylo.io.nexus.DataBlock
    - org.biojavax.bio.phylo.io.nexus.DistancesBlock
    - org.biojavax.bio.phylo.io.nexus.TaxaBlock
    - org.biojavax.bio.phylo.io.nexus.TreesBlock
  - org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract (implements org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder)
    - org.biojavax.bio.phylo.io.nexus.CharactersBlockBuilder (implements org.biojavax.bio.phylo.io.nexus.CharactersBlockListener)
      - org.biojavax.bio.phylo.io.nexus.DataBlockBuilder (implements org.biojavax.bio.phylo.io.nexus.DataBlockListener)
    - org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder (implements org.biojavax.bio.phylo.io.nexus.DistancesBlockListener)
    - org.biojavax.bio.phylo.io.nexus.TaxaBlockBuilder (implements org.biojavax.bio.phylo.io.nexus.TaxaBlockListener)
    - org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder (implements org.biojavax.bio.phylo.io.nexus.TreesBlockListener)
  - org.biojavax.bio.phylo.io.nexus.NexusBlockParser.Abstract (implements org.biojavax.bio.phylo.io.nexus.NexusBlockParser)
    - org.biojavax.bio.phylo.io.nexus.CharactersBlockParser
      - org.biojavax.bio.phylo.io.nexus.DataBlockParser
    - org.biojavax.bio.phylo.io.nexus.DistancesBlockParser
    - org.biojavax.bio.phylo.io.nexus.TaxaBlockParser
    - org.biojavax.bio.phylo.io.nexus.TreesBlockParser
  - org.biojavax.bio.phylo.io.nexus.NexusComment (implements org.biojavax.bio.phylo.io.nexus.NexusObject)
  - org.biojavax.bio.phylo.io.nexus.NexusFile
  - org.biojavax.bio.phylo.io.nexus.NexusFileFormat
  - org.biojavax.bio.phylo.io.nexus.NexusFileListener.Abstract (implements org.biojavax.bio.phylo.io.nexus.NexusFileListener)
    - org.biojavax.bio.phylo.io.nexus.NexusFileBuilder
  - org.biojava.utils.automata.NfaSubModel (implements org.biojava.utils.automata.NfaBuilder)
  - org.biojava.bio.program.ssaha.NIODataStoreFactory (implements org.biojava.bio.program.ssaha.DataStoreFactory)
  - org.biojava.bio.seq.NucleotideTools
  - org.biojava.naming.ObdaContext (implements javax.naming.directory.DirContext)
  - org.biojava.naming.ObdaInitialContextFactory (implements javax.naming.spi.InitialContextFactory)
  - org.biojava.directory.OBDARegistryParser
  - org.biojava.naming.ObdaUriParser (implements javax.naming.NameParser)
  - org.biojava.utils.ObjectUtil
  - org.biojava.ontology.obo.OboFileHandler (implements org.biojava.ontology.obo.OboFileEventListener)
  - org.biojava.ontology.obo.OboFileParser
  - org.biojava.ontology.obo.OboFileParser.SOPair
  - org.biojava.ontology.io.OboParser
  - org.biojava.ontology.OntoTools
  - org.biojava.bio.dist.OrderNDistributionFactory (implements org.biojava.bio.dist.DistributionFactory)
  - org.biojava.bio.seq.io.OrganismParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.And (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByAccession (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByTitle (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.Not (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.Or (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.Xor (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.And (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.ByRef (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.Not (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.Or (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.Xor (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.And (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.Not (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.Or (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.symbol.PackedSymbolListFactory (implements org.biojava.bio.symbol.SymbolListFactory)
  - org.biojava.bio.symbol.PackingFactory
  - org.biojava.bio.dp.twohead.PairDPMatrix (implements org.biojava.bio.dp.DPMatrix, java.io.Serializable)
  - org.biojava.bio.program.tagvalue.Parser
  - org.biojava.bio.program.tagvalue.ParserListener
  - org.biojavax.bio.phylo.ParsimonyTreeMethod
  - org.biojava.utils.regex.Pattern
  - org.biojava.utils.automata.PatternBlitz
  - org.biojava.utils.regex.PatternFactory
  - org.biojava.utils.automata.PatternMaker
  - 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)
  - org.biojava.bio.structure.io.PDBMSDReader (implements org.biojava.bio.structure.io.StructureIO)
  - org.biojava.bio.program.sax.PdbSAXParser
  - org.biojava.bio.structure.io.PDBSRSReader (implements org.biojava.bio.structure.io.StructureIO)
  - org.biojava.bio.program.PdbToXMLConverter
  - org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
  - org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
  - org.biojava.bio.program.phred.PhredFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - org.biojava.bio.program.phred.PhredTools
  - org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder (implements org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener)
  - org.biojavax.bio.phylo.io.phylip.PHYLIPFileFormat
  - org.biojava.bio.gui.PlainBlock (implements org.biojava.bio.gui.BlockPainter)
  - org.biojava.bio.gui.PlainStyle (implements org.biojava.bio.gui.SymbolStyle)
  - org.biojavax.bio.seq.PositionResolver.AverageResolver (implements org.biojavax.bio.seq.PositionResolver)
  - org.biojavax.bio.seq.PositionResolver.MaximalResolver (implements org.biojavax.bio.seq.PositionResolver)
  - org.biojavax.bio.seq.PositionResolver.MinimalResolver (implements org.biojavax.bio.seq.PositionResolver)
  - org.biojava.bio.structure.server.PrepareIndexFile
    - org.biojava.bio.structure.server.PrepareMMcifIndexFile
  - org.biojava.utils.xml.PrettyXMLWriter (implements org.biojava.utils.xml.XMLWriter)
  - org.biojava.utils.ProcessTools
  - org.biojava.bio.seq.projection.ProjectedFeature (implements org.biojava.bio.seq.Feature, org.biojava.bio.seq.projection.Projection)
  - org.biojava.bio.seq.projection.ProjectionEngine
  - org.biojava.bio.seq.projection.ProjectionUtils
  - org.biojava.bio.PropertyConstraint.And (implements org.biojava.bio.PropertyConstraint)
  - org.biojava.bio.PropertyConstraint.ByAnnotationType (implements org.biojava.bio.PropertyConstraint)
  - org.biojava.bio.PropertyConstraint.ByClass (implements org.biojava.bio.PropertyConstraint)
  - org.biojava.bio.PropertyConstraint.Enumeration (implements org.biojava.bio.PropertyConstraint)
  - org.biojava.bio.PropertyConstraint.ExactValue (implements org.biojava.bio.PropertyConstraint)
  - org.biojava.bio.PropertyConstraint.Or (implements org.biojava.bio.PropertyConstraint)
  - org.biojavax.ga.functions.ProportionalSelection (implements org.biojavax.ga.functions.SelectionFunction)
  - org.biojava.bio.proteomics.Protease (implements java.io.Serializable)
  - org.biojava.bio.proteomics.ProteaseManager
  - org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.ProteinTools
  - org.biojava.bio.structure.jama.QRDecomposition (implements java.io.Serializable)
  - java.io.RandomAccessFile (implements java.io.Closeable, java.io.DataInput, java.io.DataOutput)
    - org.biojava.utils.io.RAF
  - java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    - java.io.BufferedReader
      - org.biojava.utils.io.CountedBufferedReader
    - org.biojava.utils.io.RandomAccessReader
  - org.biojava.utils.process.ReaderWriterPipe (implements java.lang.Runnable)
    - org.biojava.utils.process.ReaderInputHandler (implements org.biojava.utils.process.InputHandler)
    - org.biojava.utils.process.WriterOutputHandler (implements org.biojava.utils.process.OutputHandler)
  - org.biojava.bio.program.indexdb.Record.Impl (implements org.biojava.bio.program.indexdb.Record)
  - org.biojava.bio.gui.glyph.RectangleGlyph (implements org.biojava.bio.gui.glyph.Glyph)
  - org.biojava.bio.gui.sequence.RectangularImapRenderer (implements org.biojava.bio.gui.sequence.BeadFeatureRenderer, org.biojava.bio.gui.sequence.ImageMapRenderer, java.io.Serializable)
  - java.lang.ref.Reference<T>
    - java.lang.ref.WeakReference<T>
      - org.biojava.utils.cache.KeyedWeakReference
  - org.biojava.bio.structure.io.mmcif.model.Refine
  - org.biojava.bio.program.tagvalue.RegexChanger (implements org.biojava.bio.program.tagvalue.ChangeTable.Changer)
  - org.biojava.bio.program.tagvalue.RegexParser (implements org.biojava.bio.program.tagvalue.TagValueParser)
  - org.biojava.bio.program.tagvalue.RegexSplitter (implements org.biojava.bio.program.tagvalue.ChangeTable.Splitter)
  - org.biojava.directory.Registry
  - org.biojava.directory.RegistryConfiguration.Composite (implements org.biojava.directory.RegistryConfiguration)
  - org.biojava.directory.RegistryConfiguration.Impl (implements org.biojava.directory.RegistryConfiguration)
  - org.biojava.bio.seq.RemoteFeature.Region
  - org.biojava.bio.seq.projection.ReparentContext (implements org.biojava.bio.seq.projection.ProjectionContext, java.io.Serializable)
    - org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
    - org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
    - org.biojava.bio.seq.projection.TranslateFlipContext
  - org.biojava.utils.RepeatedCharSequence (implements java.lang.CharSequence)
  - org.biojava.utils.xml.ResourceEntityResolver (implements org.xml.sax.EntityResolver)
  - org.biojava.bio.molbio.RestrictionEnzyme (implements java.io.Serializable)
  - org.biojava.bio.molbio.RestrictionEnzymeManager
  - org.biojava.bio.molbio.RestrictionMapper (implements org.biojava.bio.seq.SequenceAnnotator)
  - org.biojavax.bio.seq.RichFeature.Tools
  - org.biojavax.bio.seq.RichLocation.Strand (implements java.lang.Comparable<T>)
  - org.biojavax.bio.seq.RichLocation.Tools
  - org.biojavax.RichObjectFactory
  - org.biojavax.bio.seq.io.RichSeqIOAdapter (implements org.biojavax.bio.seq.io.RichSeqIOListener)
    - org.biojavax.bio.seq.io.SimpleRichSequenceBuilder (implements org.biojavax.bio.seq.io.RichSequenceBuilder)
  - org.biojavax.bio.seq.RichSequence.IOTools
  - org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator (implements org.biojavax.bio.seq.RichSequenceIterator)
  - org.biojavax.bio.seq.RichSequence.Terms
    - org.biojavax.bio.seq.io.EMBLFormat.Terms
    - org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
    - org.biojavax.bio.seq.io.GenbankFormat.Terms
    - org.biojavax.bio.seq.io.INSDseqFormat.Terms
    - org.biojavax.bio.seq.io.UniProtFormat.Terms
    - org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  - org.biojavax.bio.seq.RichSequence.Tools
  - org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat (implements org.biojavax.bio.seq.io.RichSequenceFormat)
    - org.biojavax.bio.seq.io.EMBLxmlFormat
    - org.biojavax.bio.seq.io.INSDseqFormat
    - org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
      - org.biojavax.bio.seq.io.EMBLFormat
      - org.biojavax.bio.seq.io.FastaFormat
      - org.biojavax.bio.seq.io.GenbankFormat
      - org.biojavax.bio.seq.io.UniProtFormat
    - org.biojavax.bio.seq.io.UniProtXMLFormat
  - org.biojavax.bio.seq.io.RichStreamReader (implements org.biojavax.bio.seq.RichSequenceIterator)
  - org.biojavax.bio.seq.io.RichStreamWriter
  - org.biojava.bio.seq.RNATools
  - org.biojava.bio.gui.sequence.RulerRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
  - org.biojava.bio.seq.io.agave.SAX2StAXAdaptor (implements org.xml.sax.ContentHandler)
  - org.biojava.bio.dp.ScoreType.NullModel (implements org.biojava.bio.dp.ScoreType, java.io.Serializable)
  - org.biojava.bio.dp.ScoreType.Odds (implements org.biojava.bio.dp.ScoreType, java.io.Serializable)
  - org.biojava.bio.dp.ScoreType.Probability (implements org.biojava.bio.dp.ScoreType, java.io.Serializable)
  - org.biojava.utils.regex.Search
  - org.biojava.bio.search.SearchContentAdapter (implements org.biojava.bio.search.SearchContentHandler)
    - org.biojava.bio.search.FilteringContentHandler (implements org.biojava.bio.search.BlastLikeSearchFilter.Node)
  - org.biojava.bio.search.SearchContentFilter (implements org.biojava.bio.search.SearchContentHandler)
  - org.biojava.bio.search.SearchContentHandlerDebugger (implements org.biojava.bio.search.SearchContentHandler)
  - org.biojava.bio.program.ssaha.SearchListener.Echo (implements org.biojava.bio.program.ssaha.SearchListener)
  - org.biojava.bio.program.ssaha.SearchListener.Tee (implements org.biojava.bio.program.ssaha.SearchListener)
  - org.biojava.bio.program.ssaha.SearchListener.Wrapper (implements org.biojava.bio.program.ssaha.SearchListener)
    - org.biojava.bio.program.ssaha.SearchListener.FilterByLength
  - org.biojavax.ga.functions.SelectionFunction.SelectAll (implements org.biojavax.ga.functions.SelectionFunction)
  - org.biojavax.ga.functions.SelectionFunction.Threshold (implements org.biojavax.ga.functions.SelectionFunction)
  - org.biojava.bio.search.SeqContentPattern (implements org.biojava.bio.search.BioPattern)
  - org.biojava.bio.seq.io.SeqIOAdapter (implements org.biojava.bio.seq.io.SeqIOListener)
  - org.biojava.bio.seq.io.SeqIOConstants
  - org.biojava.bio.seq.io.SeqIOEventEmitter
  - org.biojava.bio.seq.io.SeqIOFilter (implements org.biojava.bio.seq.io.SeqIOListener)
  - org.biojava.bio.seq.io.SeqIOTools
  - org.biojava.bio.structure.io.SeqRes2AtomAligner
  - org.biojava.bio.program.ssbind.SeqSimilarityAdapter (implements org.xml.sax.ContentHandler)
  - org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.alignment.SequenceAlignment
    - org.biojava.bio.alignment.NeedlemanWunsch
      - org.biojava.bio.alignment.SmithWaterman
  - org.biojava.bio.program.sax.SequenceAlignmentSAXParser
  - org.biojava.bio.seq.io.SequenceBuilderBase (implements org.biojava.bio.seq.io.SequenceBuilder)
    - org.biojava.bio.seq.io.SequenceDBSequenceBuilder
    - org.biojava.bio.seq.io.SimpleAssemblyBuilder
    - org.biojava.bio.seq.io.SimpleSequenceBuilder
    - org.biojava.bio.seq.io.SmartSequenceBuilder
  - org.biojava.bio.seq.io.SequenceBuilderFilter (implements org.biojava.bio.seq.io.SequenceBuilder)
    - org.biojava.bio.seq.io.EmblProcessor (implements org.biojava.utils.ParseErrorSource)
    - org.biojava.bio.seq.io.FastaDescriptionLineParser
    - org.biojava.bio.seq.io.GenbankProcessor (implements org.biojava.utils.ParseErrorSource)
      - org.biojava.bio.seq.io.ProteinRefSeqProcessor
    - org.biojava.bio.seq.io.OrganismParser
    - org.biojava.bio.seq.io.SwissprotProcessor (implements org.biojava.utils.ParseErrorSource)
  - org.biojava.bio.seq.distributed.SequenceDBDataSource (implements org.biojava.bio.seq.distributed.DistDataSource)
  - org.biojava.bio.structure.gui.util.SequenceMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  - org.biojava.bio.gui.sequence.SequencePanel.Border (implements java.io.Serializable, javax.swing.SwingConstants)
  - org.biojava.bio.gui.sequence.SequencePoster.Border (implements java.io.Serializable, javax.swing.SwingConstants)
  - org.biojava.bio.gui.sequence.SequenceRenderContext.Border (implements java.io.Serializable, javax.swing.SwingConstants)
  - org.biojava.bio.program.gff.SequencesAsGFF
  - org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer (implements org.biojava.bio.program.ssaha.SequenceStreamer)
  - org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer (implements org.biojava.bio.program.ssaha.SequenceStreamer)
  - org.biojava.bio.seq.SequenceTools
  - org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
  - org.biojava.bio.gui.sequence.SequenceViewerSupport
  - org.biojava.utils.Services
  - org.biojava.stats.svm.SigmoidKernel (implements org.biojava.stats.svm.SVMKernel)
  - org.biojava.bio.program.homologene.SimilarityType.PlaceHolder (implements org.biojava.bio.program.homologene.SimilarityType)
  - org.biojava.bio.alignment.SimpleAlignmentElement (implements org.biojava.bio.alignment.AlignmentElement)
  - org.biojava.bio.annodb.SimpleAnnotationDB (implements org.biojava.bio.annodb.AnnotationDB)
  - org.biojava.bio.seq.io.agave.SimpleAnnotFilter (implements org.biojava.bio.seq.io.agave.AGAVEAnnotFilter)
    - org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
    - org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
  - org.biojava.bio.dist.SimpleDistribution.Trainer (implements org.biojava.bio.dist.DistributionTrainer)
  - org.biojava.bio.dist.SimpleDistributionTrainer (implements org.biojava.bio.dist.DistributionTrainer, java.io.Serializable)
  - org.biojava.bio.dist.SimpleDistributionTrainerContext (implements org.biojava.bio.dist.DistributionTrainerContext, java.io.Serializable)
    - org.biojava.bio.dp.SimpleModelTrainer (implements org.biojava.bio.dp.ModelTrainer, java.io.Serializable)
  - org.biojava.bio.seq.SimpleFeatureRealizer (implements org.biojava.bio.seq.FeatureRealizer, java.io.Serializable)
  - org.biojavax.ga.functions.SimpleGACrossResult (implements org.biojavax.ga.functions.GACrossResult)
  - org.biojava.bio.symbol.SimpleGappedSymbolList.Block (implements java.io.Serializable)
  - org.biojava.bio.program.gff.SimpleGFFRecord (implements org.biojava.bio.program.gff.GFFRecord)
  - org.biojava.bio.dp.SimpleHMMTrainer (implements org.biojava.bio.dp.HMMTrainer)
  - org.biojava.bio.program.homologene.SimpleHomologeneBuilder (implements org.biojava.bio.program.homologene.HomologeneBuilder)
  - org.biojava.bio.seq.db.SimpleIndex (implements org.biojava.bio.seq.db.Index)
  - org.biojava.stats.svm.SimpleItemValue (implements org.biojava.stats.svm.ItemValue)
  - 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.biojavax.bio.taxa.SimpleNCBITaxonName (implements java.lang.Comparable<T>)
  - org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader (implements org.biojavax.bio.taxa.io.NCBITaxonomyLoader)
  - org.biojava.bio.program.homologene.SimpleOrthologue (implements org.biojava.bio.program.homologene.Orthologue)
  - org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator (implements org.biojava.bio.program.homologene.OrthologueSet.Iterator)
  - org.biojava.bio.program.homologene.SimpleOrthoPair (implements org.biojava.bio.program.homologene.OrthoPair)
  - org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator (implements org.biojava.bio.program.homologene.OrthoPairCollection.Iterator)
  - org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator (implements org.biojava.bio.program.homologene.OrthoPairSet.Iterator)
  - org.biojavax.bio.seq.SimplePosition (implements org.biojavax.bio.seq.Position)
  - org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver (implements org.biojava.bio.seq.RemoteFeature.Resolver)
  - org.biojavax.SimpleRichObjectBuilder (implements org.biojavax.RichObjectBuilder)
  - org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory (implements org.biojavax.bio.seq.io.RichSequenceBuilderFactory)
  - org.biojava.bio.seq.db.SimpleSequenceDBInstallation (implements org.biojava.bio.seq.db.SequenceDBInstallation)
  - org.biojava.bio.seq.impl.SimpleSequenceFactory (implements org.biojava.bio.seq.SequenceFactory, java.io.Serializable)
  - org.biojava.bio.structure.server.SimpleStructureServer (implements org.biojava.bio.structure.server.StructureListener, org.biojava.bio.structure.server.StructureServer)
  - org.biojava.stats.svm.SimpleSVMTarget (implements org.biojava.stats.svm.SVMTarget)
  - org.biojava.bio.symbol.SimpleSymbolListFactory (implements org.biojava.bio.symbol.SymbolListFactory)
  - org.biojava.bio.symbol.SimpleSymbolPropertyTable (implements org.biojava.bio.symbol.SymbolPropertyTable)
    - org.biojava.bio.proteomics.aaindex.AAindex
  - org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB (implements org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB)
  - org.biojava.bio.gui.SimpleSymbolStyle (implements org.biojava.bio.gui.SymbolStyle)
  - org.biojava.bio.program.tagvalue.SimpleTagValueWrapper (implements org.biojava.bio.program.tagvalue.TagValueWrapper)
    - org.biojava.bio.program.tagvalue.Aggregator
    - org.biojava.bio.program.tagvalue.MultiTagger
    - org.biojava.bio.program.tagvalue.RegexFieldFinder
    - org.biojava.bio.program.tagvalue.TagDelegator
    - org.biojava.bio.program.tagvalue.TagDropper
    - org.biojava.bio.program.tagvalue.TagRenamer
    - org.biojava.bio.program.tagvalue.ValueChanger
  - org.biojava.bio.taxa.SimpleTaxonFactory (implements org.biojava.bio.taxa.TaxonFactory)
  - org.biojava.utils.SimpleThreadPool (implements org.biojava.utils.ThreadPool)
  - org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout (implements org.biojava.bio.gui.sequence.tracklayout.TrackLayout)
  - org.biojava.bio.symbol.SimpleTranslationTable (implements java.io.Serializable)
  - org.biojava.bio.dp.SimpleWeightMatrix (implements java.io.Serializable, org.biojava.bio.dp.WeightMatrix)
  - org.biojava.bio.dp.onehead.SingleDPMatrix (implements org.biojava.bio.dp.DPMatrix, java.io.Serializable)
  - org.biojava.bio.structure.jama.SingularValueDecomposition (implements java.io.Serializable)
  - org.biojava.bio.dp.onehead.SmallCursor
  - org.biojava.stats.svm.SMORegressionTrainer
  - org.biojava.stats.svm.SMOTrainer
  - org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector (implements org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector)
  - org.biojava.utils.cache.SoftReferenceCache (implements org.biojava.utils.cache.Cache)
  - org.biojava.stats.svm.SparseVector (implements java.io.Serializable)
  - org.biojava.stats.svm.SparseVector.NormalizingKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
  - org.biojava.bio.program.unigene.SQLUnigeneFactory (implements org.biojava.bio.program.unigene.UnigeneFactory)
  - org.biojava.bio.structure.SSBond (implements org.biojava.bio.structure.PDBRecord)
  - org.biojava.bio.gui.StackedLogoPainter (implements org.biojava.bio.gui.LogoPainter)
  - org.biojava.bio.structure.StandardAminoAcid
  - org.biojava.bio.program.tagvalue.StateMachine (implements org.biojava.bio.program.tagvalue.TagValueWrapper)
  - org.biojava.bio.program.tagvalue.StateMachine.BasicState (implements org.biojava.bio.program.tagvalue.StateMachine.State)
  - org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - org.biojava.bio.program.tagvalue.StateMachine.Transition
  - org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
  - org.biojava.utils.StaticMemberPlaceHolder (implements java.io.Serializable)
  - org.biojava.utils.stax.StAXContentHandlerBase (implements org.biojava.utils.stax.StAXContentHandler)
    - org.biojava.bio.program.sax.blastxml.BlastXMLParser
    - org.biojava.utils.stax.BooleanElementHandlerBase
    - org.biojava.utils.stax.ByteElementHandlerBase
    - org.biojava.utils.stax.CharElementHandlerBase
    - org.biojava.utils.stax.DoubleElementHandlerBase
    - org.biojava.bio.program.xff.FeatureHandler
      - org.biojava.bio.program.xff.StrandedFeatureHandler
    - org.biojava.utils.stax.FloatElementHandlerBase
    - org.biojava.utils.stax.IntElementHandlerBase
    - org.biojava.bio.program.xff.LocationHandlerBase
    - org.biojava.utils.stax.LongElementHandlerBase
    - org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
    - org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
      - org.biojava.bio.program.ssbind.AlignmentStAXHandler
      - org.biojava.bio.program.ssbind.HeaderStAXHandler
      - org.biojava.bio.program.ssbind.HitStAXHandler
      - org.biojava.bio.program.ssbind.HSPStAXHandler
      - org.biojava.bio.program.ssbind.HSPSummaryStAXHandler
    - org.biojava.bio.seq.io.game.SequenceContentHandlerBase
      - org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
    - org.biojava.bio.seq.io.game.StAXFeatureHandler
      - org.biojava.bio.seq.io.game.GAMEAnnotationHandler (implements org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf)
      - org.biojava.bio.seq.io.game.GAMEFeatureSetHandler (implements org.biojava.bio.seq.io.game.GAMENameCallbackItf, org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf)
      - org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
      - org.biojava.bio.seq.io.game.GAMEHandler
    - org.biojava.bio.seq.io.game12.StAXFeatureHandler
      - org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
      - org.biojava.bio.seq.io.game12.GAMEAspectHandler
      - org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
      - org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
      - org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
      - org.biojava.bio.seq.io.game12.GAMEGeneHandler
      - org.biojava.bio.seq.io.game12.GAMEHandler
      - org.biojava.bio.seq.io.game12.GAMEPropertyHandler
      - org.biojava.bio.seq.io.game12.GAMESeqHandler
      - org.biojava.bio.seq.io.game12.GAMESeqRelHandler
        - org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.SeqRelHandler
      - org.biojava.bio.seq.io.game12.GAMESpanHandler
    - org.biojava.bio.seq.io.game.StAXPropertyHandler
      - org.biojava.bio.seq.io.game.GAMEAspectPropHandler
      - org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
      - org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler
      - org.biojava.bio.seq.io.game.GAMEGenePropHandler (implements org.biojava.bio.seq.io.game.GAMENameCallbackItf)
      - org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
      - org.biojava.bio.seq.io.game.GAMESeqPropHandler (implements org.biojava.bio.seq.io.game.GAMENameCallbackItf)
      - org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
      - org.biojava.bio.seq.io.game.GAMESpanPropHandler
    - org.biojava.utils.stax.StringElementHandlerBase
      - org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
      - org.biojava.bio.seq.io.game.GAMENamePropHandler
      - org.biojava.bio.seq.io.game.GAMETypePropHandler
      - org.biojava.bio.program.xff.PropDetailHandler
    - org.biojava.bio.program.xff.XFFFeatureSetHandler
    - org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
  - org.biojava.bio.seq.io.agave.StAXContentHandlerBase (implements org.biojava.bio.seq.io.agave.StAXContentHandler)
    - org.biojava.bio.seq.io.agave.StAXFeatureHandler
      - org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler (implements org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler (implements org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
      - org.biojava.bio.seq.io.agave.AGAVECdsHandler
      - org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler (implements org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEClassificationHandler (implements org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVECompResultHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEComputationHandler
      - org.biojava.bio.seq.io.agave.AGAVEContigHandler (implements org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
      - org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEGeneHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEHandler (implements org.biojava.bio.seq.io.agave.AGAVECallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
      - org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
      - org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
      - org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
      - org.biojava.bio.seq.io.agave.AGAVETranscriptHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
    - org.biojava.bio.seq.io.agave.StAXPropertyHandler
      - org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
      - org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVENotePropHandler
      - org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
      - org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
      - org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
      - org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
      - org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf)
  - org.biojava.bio.program.ssbind.StAXHandlerBinding
  - org.biojava.bio.gui.sequence.StopRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
  - org.biojava.bio.seq.StrandedFeature.Strand (implements java.io.Serializable)
  - org.biojava.bio.seq.StrandParser
  - org.biojava.bio.structure.align.pairwise.StrCompAlignment (implements org.biojava.bio.structure.align.pairwise.Alignable)
  - org.biojava.utils.process.StreamPipe (implements java.lang.Runnable)
    - org.biojava.utils.process.SimpleInputHandler (implements org.biojava.utils.process.InputHandler)
    - org.biojava.utils.process.SimpleOutputHandler (implements org.biojava.utils.process.OutputHandler)
  - org.biojava.bio.seq.io.StreamReader (implements org.biojava.utils.ParseErrorListener, org.biojava.bio.seq.SequenceIterator)
  - org.biojava.bio.seq.io.StreamWriter
  - org.biojavax.utils.StringTools
  - 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.server.StructureEventImpl (implements org.biojava.bio.structure.server.StructureEvent)
  - org.biojava.bio.structure.server.StructureFetcherRunnable (implements java.lang.Runnable)
  - org.biojava.bio.structure.StructureImpl (implements org.biojava.bio.structure.Structure)
  - org.biojava.bio.structure.align.StructurePairAligner
  - org.biojava.bio.proteomics.StructureTools
  - org.biojava.bio.structure.StructureTools
  - org.biojava.bio.gui.sequence.SubCircularRendererContext (implements org.biojava.bio.gui.sequence.CircularRendererContext)
  - org.biojava.bio.gui.sequence.SubPairwiseRenderContext (implements org.biojava.bio.gui.sequence.PairwiseRenderContext)
  - org.biojava.bio.seq.impl.SubSequence (implements org.biojava.bio.seq.Sequence, java.io.Serializable)
  - org.biojava.bio.gui.sequence.SubSequenceRenderContext (implements org.biojava.bio.gui.sequence.SequenceRenderContext)
  - org.biojava.bio.alignment.SubstitutionMatrix
  - org.biojava.bio.symbol.SuffixTree (implements java.io.Serializable)
  - org.biojava.bio.symbol.SuffixTree.SuffixNode (implements java.io.Serializable)
  - org.biojava.stats.svm.tools.SuffixTreeKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
  - org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - org.biojava.bio.structure.SVDSuperimposer
  - org.biojava.stats.svm.tools.SVM_Light
  - org.biojava.stats.svm.tools.SVM_Light.LabelledVector
  - org.biojava.stats.svm.SVMRegressionModel
  - org.biojava.bio.program.formats.Swissprot (implements org.biojava.bio.program.formats.Format)
  - org.biojava.bio.seq.io.SwissprotFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
  - org.biojava.bio.seq.io.SwissprotProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - org.biojava.bio.seq.db.SwissprotSequenceDB
  - org.biojava.bio.seq.io.SymbolListCharSequence (implements java.lang.CharSequence)
  - org.biojava.bio.symbol.SymbolListViews
  - org.biojava.bio.gui.sequence.SymbolSequenceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
  - org.biojava.bio.seq.io.SymbolTokenization.TokenType
  - org.biojava.ontology.Synonym (implements java.lang.Comparable<T>)
  - org.biojava.directory.SystemRegistry
  - org.biojava.ontology.io.TabDelimParser
  - org.biojava.bio.seq.db.TabIndexStore (implements org.biojava.bio.seq.db.IndexStore, java.io.Serializable)
  - org.biojava.bio.program.tagvalue.TagMapper (implements org.biojava.bio.program.tagvalue.PropertyChanger)
  - org.biojava.bio.program.tagvalue.TagValue
  - org.biojava.bio.program.homologene.Taxon.TaxonStub (implements org.biojava.bio.program.homologene.Taxon)
  - org.biojava.bio.seq.db.biosql.TaxonSQL
  - org.biojava.bio.seq.impl.TemplateUtils
  - org.biojava.bio.gui.TextBlock (implements org.biojava.bio.gui.BlockPainter)
  - org.biojava.bio.gui.TextLogoPainter (implements org.biojava.bio.gui.LogoPainter)
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Error
      - java.lang.AssertionError
        - org.biojava.utils.AssertionFailure
      - org.biojava.bio.BioError
    - java.lang.Exception
      - org.biojava.utils.xml.AppException
      - org.biojava.bibliography.BibRefException
      - org.biojava.bio.BioException
        - org.biojava.utils.automata.AutomatonException
        - org.biojava.bio.taxa.CircularReferenceException
        - org.biojava.bio.program.das.dasalignment.DASException
        - org.biojava.bio.program.homologene.DuplicateTaxonException
        - org.biojava.bio.symbol.IllegalAlphabetException
        - org.biojava.bio.seq.db.IllegalIDException
        - org.biojava.bio.symbol.IllegalSymbolException
        - org.biojava.bio.dp.IllegalTransitionException
        - org.biojava.bio.seq.io.ParseException
        - org.biojava.bio.structure.io.PDBParseException
        - org.biojava.utils.regex.RegexException
        - org.biojava.bio.structure.StructureException
        - org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
      - org.biojava.utils.candy.CandyException
      - org.biojava.utils.CommitFailure
      - org.biojavax.CrossReferenceResolutionException
      - org.biojava.bio.program.gff.IgnoreRecordException
      - org.biojavax.ga.exception.IllegalOrganismException
      - org.biojava.utils.lsid.LifeScienceIdentifierParseException
      - org.biojava.ontology.OntologyException
        - org.biojava.ontology.AlreadyExistsException
        - org.biojava.ontology.InvalidTermException
      - org.biojava.utils.ParserException
      - org.biojava.utils.ProcessTimeoutException
      - org.biojava.directory.RegistryException
        - org.biojava.directory.ProviderNotFoundException
      - java.lang.RuntimeException
        - org.biojava.bio.BioRuntimeException
          - org.biojava.bio.alignment.IllegalAlignmentEditException
        - org.biojava.utils.ChangeVetoException
      - org.biojava.bio.program.ssaha.SearchException
  - org.biojavax.ga.functions.TournamentSelection (implements org.biojavax.ga.functions.SelectionFunction)
  - org.biojava.stats.svm.tools.Train
  - org.biojava.bio.dp.TrainerTransition (implements java.io.Serializable)
  - org.biojava.stats.svm.tools.TrainRegression
  - org.biojava.bio.dp.Transition (implements java.io.Serializable)
  - org.biojavax.bio.phylo.io.nexus.TreesBlock.NewickTreeString
  - org.biojava.utils.TriState
  - org.biojava.bio.gui.glyph.TurnGlyph (implements org.biojava.bio.gui.glyph.Glyph)
  - org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph (implements org.biojava.bio.gui.glyph.Glyph)
  - org.biojava.bio.symbol.UkkonenSuffixTree
  - org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
  - org.biojava.utils.Unchangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.seq.io.AlternateTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
    - org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB (implements org.biojava.bio.seq.db.SequenceDBLite)
    - org.biojava.bio.seq.io.CharacterTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
    - org.biojava.bio.program.das.DASSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
    - org.biojava.bio.symbol.DoubleAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - org.biojava.bio.symbol.DoubleAlphabet.DoubleRange (implements org.biojava.bio.symbol.BasisSymbol, java.io.Serializable)
    - org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - org.biojavax.EmptyRichAnnotation (implements org.biojavax.RichAnnotation, java.io.Serializable)
    - org.biojavax.bio.seq.EmptyRichLocation (implements org.biojavax.bio.seq.RichLocation)
    - org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
    - org.biojava.bio.seq.db.flat.FlatSequenceDB (implements org.biojava.bio.seq.db.SequenceDBLite)
    - org.biojava.bio.dist.GapDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
    - org.biojava.bio.symbol.IntegerAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - org.biojava.ontology.IntegerOntology (implements org.biojava.ontology.Ontology)
    - org.biojava.ontology.IntegerOntology.IntTerm (implements org.biojava.ontology.Term)
    - org.biojava.bio.symbol.RelabeledAlignment (implements org.biojava.bio.symbol.Alignment)
    - org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment (implements org.biojava.bio.symbol.Alignment)
    - org.biojavax.SimpleCrossRef (implements org.biojavax.CrossRef)
    - org.biojavax.SimpleDocRefAuthor (implements org.biojavax.DocRefAuthor)
    - org.biojava.bio.dp.SimpleStatePath (implements java.io.Serializable, org.biojava.bio.dp.StatePath)
    - org.biojava.bio.symbol.SoftMaskedAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet)
    - org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization (implements org.biojava.bio.seq.io.SymbolTokenization)
    - org.biojava.ontology.Triple.Impl (implements java.io.Serializable, org.biojava.ontology.Triple)
    - org.biojava.bio.seq.impl.ViewSequence (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence, java.io.Serializable)
      - org.biojava.bio.seq.CircularView
    - org.biojava.bio.seq.io.WordTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
      - org.biojava.bio.seq.io.CrossProductTokenization
      - org.biojava.bio.seq.io.DoubleTokenization
      - org.biojava.bio.seq.io.IntegerTokenization
      - org.biojava.bio.seq.io.NameTokenization
      - org.biojava.bio.seq.io.SubIntegerTokenization
  - org.biojava.bio.program.unigene.UnigeneTools
  - org.biojavax.bio.seq.io.UniProtCommentParser
  - org.biojavax.bio.seq.io.UniProtCommentParser.Event
  - org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  - org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  - org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
  - org.biojavax.bio.seq.io.UniProtLocationParser
  - org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout (implements org.biojava.bio.gui.sequence.tracklayout.TrackLayout)
  - org.biojava.bio.seq.io.agave.UtilHelper
  - org.biojava.bio.program.ssbind.ViewSequenceFactory
    - org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder (implements org.biojava.bio.search.SearchContentHandler)
    - org.biojava.bio.program.ssbind.SimilarityPairBuilder (implements org.biojava.bio.search.SearchContentHandler)
  - org.biojava.utils.walker.WalkerFactory
  - org.biojava.utils.cache.WeakCacheMap (implements org.biojava.utils.cache.CacheMap)
  - org.biojava.bio.taxa.WeakTaxonFactory (implements org.biojava.bio.taxa.TaxonFactory)
  - org.biojava.bio.dp.WeightMatrixAnnotator (implements org.biojava.bio.seq.SequenceAnnotator, java.io.Serializable)
  - org.biojava.bio.program.xff.XFFTools
  - org.biojava.bio.program.xff.XFFWriter
  - org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  - org.biojava.utils.xml.XMLBeans
  - org.biojava.bio.dist.XMLDistributionWriter
  - org.biojava.bio.seq.io.filterxml.XMLFilterHandler
  - org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  - org.biojava.bio.dp.XmlMarkovModel
  - org.biojavax.utils.XMLTools
  - org.biojava.bio.gui.sequence.ZiggyImapRenderer (implements org.biojava.bio.gui.sequence.ImageMapRenderer, java.io.Serializable)

## Interface Hierarchy

- org.biojava.utils.ActivityListener
- org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
- org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
- org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
- org.biojava.bio.seq.io.agave.AGAVECallbackItf
- org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
- org.biojava.bio.structure.align.pairwise.Alignable
- org.biojava.bio.alignment.AlignmentElement
- org.biojava.bio.seq.io.AlignmentFormat
- org.biojava.bio.structure.gui.events.AlignmentPositionListener
- org.biojava.bio.annodb.AnnotationDB
- org.biojava.bio.AnnotationType
- org.biojava.utils.xml.AppEntry
- org.biojava.bio.structure.Atom
- org.biojava.bibliography.BibRefQuery
- org.biojava.bibliography.BibRefSupport
- org.biojavax.bio.db.BioEntryDBLite
  - org.biojavax.bio.db.BioEntryDB
    - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.RichSequenceDBLite, org.biojava.bio.seq.db.SequenceDB)
  - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojavax.bio.db.RichSequenceDBLite, org.biojava.bio.seq.db.SequenceDB)
  - org.biojavax.bio.db.RichSequenceDBLite (also extends org.biojava.bio.seq.db.SequenceDBLite)
    - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojava.bio.seq.db.SequenceDB)
- org.biojavax.bio.BioEntryIterator
  - org.biojavax.bio.seq.RichSequenceIterator (also extends org.biojava.bio.seq.SequenceIterator)
- org.biojava.bio.search.BioMatcher
- org.biojava.bio.search.BioPattern
- org.biojava.bio.search.BlastLikeSearchFilter.Node
- org.biojava.bio.gui.BlockPainter
- org.biojava.bio.program.tagvalue.BoundaryFinder
- org.biojava.utils.cache.Cache
- org.biojava.utils.cache.CacheMap
- org.biojava.utils.cache.CacheReference
- org.biojava.bio.dp.twohead.CellCalculator
- org.biojava.bio.dp.twohead.CellCalculatorFactory
- org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker
- org.biojava.bio.structure.Chain
- org.biojava.utils.Changeable
  - org.biojava.bio.symbol.Alignment
    - org.biojava.bio.alignment.ARAlignment
    - org.biojava.bio.dp.StatePath
    - org.biojava.bio.alignment.UnequalLengthAlignment
  - org.biojava.bio.symbol.Alphabet
    - org.biojava.bio.symbol.FiniteAlphabet
  - org.biojava.bio.symbol.AlphabetIndex
  - org.biojava.bio.Annotatable
    - org.biojava.bio.symbol.Alphabet
      - org.biojava.bio.symbol.FiniteAlphabet
    - org.biojava.bio.symbol.AtomicSymbol
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.State
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.symbol.BasisSymbol
      - org.biojava.bio.symbol.AtomicSymbol
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
        - org.biojava.bio.dp.State
          - org.biojava.bio.dp.DotState
          - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.State
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
    - org.biojavax.bio.BioEntry (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable)
      - org.biojavax.bio.seq.RichSequence (also extends org.biojava.bio.seq.Sequence)
    - org.biojavax.ontology.ComparableTerm (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojava.ontology.Term)
    - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojava.ontology.Triple)
    - org.biojava.bio.seq.ComponentFeature
    - org.biojavax.CrossRef (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RichAnnotatable)
    - org.biojava.bio.dp.DotState
    - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - org.biojava.bio.seq.Feature (also extends org.biojava.bio.seq.FeatureHolder)
      - org.biojava.bio.seq.ComponentFeature
      - org.biojava.bio.seq.FramedFeature
      - org.biojava.bio.seq.homol.HomologyFeature
      - org.biojava.bio.seq.RemoteFeature
      - org.biojava.bio.molbio.RestrictionSite
      - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
      - org.biojava.bio.seq.homol.SimilarityPairFeature
      - org.biojava.bio.seq.StrandedFeature
        - org.biojava.bio.seq.ComponentFeature
        - org.biojava.bio.seq.FramedFeature
        - org.biojava.bio.seq.homol.HomologyFeature
        - org.biojava.bio.seq.RemoteFeature
        - org.biojava.bio.molbio.RestrictionSite
        - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder)
        - org.biojava.bio.seq.homol.SimilarityPairFeature
    - org.biojava.bio.seq.FeatureTypes.Repository
    - org.biojava.bio.seq.FeatureTypes.Type
    - org.biojava.bio.symbol.FiniteAlphabet
    - org.biojava.bio.seq.FramedFeature
    - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.program.gff3.GFF3Record
    - org.biojava.bio.seq.homol.HomologyFeature
    - org.biojava.bio.dp.ModelInState
    - org.biojava.ontology.OntologyTerm
    - org.biojava.bio.seq.RemoteFeature
    - org.biojava.ontology.RemoteTerm
    - org.biojava.bio.molbio.RestrictionSite
    - org.biojavax.RichAnnotatable
      - org.biojavax.bio.BioEntry (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RankedCrossRefable)
        - org.biojavax.bio.seq.RichSequence (also extends org.biojava.bio.seq.Sequence)
      - org.biojavax.CrossRef (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>)
      - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
      - org.biojavax.bio.seq.RichLocation (also extends java.lang.Comparable<T>, org.biojava.bio.symbol.Location)
      - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
    - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
    - org.biojavax.bio.seq.RichLocation (also extends java.lang.Comparable<T>, org.biojava.bio.symbol.Location, org.biojavax.RichAnnotatable)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.search.SeqSimilaritySearchHit
    - org.biojava.bio.search.SeqSimilaritySearchResult
    - org.biojava.bio.search.SeqSimilaritySearchSubHit
    - org.biojava.bio.seq.Sequence (also extends org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.SymbolList)
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
      - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry)
    - org.biojava.bio.seq.homol.SimilarityPairFeature
    - org.biojava.bio.dp.State
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.seq.StrandedFeature
      - org.biojava.bio.seq.ComponentFeature
      - org.biojava.bio.seq.FramedFeature
      - org.biojava.bio.seq.homol.HomologyFeature
      - org.biojava.bio.seq.RemoteFeature
      - org.biojava.bio.molbio.RestrictionSite
      - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder)
      - org.biojava.bio.seq.homol.SimilarityPairFeature
    - org.biojava.bio.symbol.Symbol
      - org.biojava.bio.symbol.AtomicSymbol
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
        - org.biojava.bio.dp.State
          - org.biojava.bio.dp.DotState
          - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.symbol.BasisSymbol
        - org.biojava.bio.symbol.AtomicSymbol
          - org.biojava.bio.dp.DotState
          - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
          - org.biojava.bio.dp.ModelInState
          - org.biojava.bio.dp.State
            - org.biojava.bio.dp.DotState
            - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
            - org.biojava.bio.dp.ModelInState
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
        - org.biojava.bio.dp.State
          - org.biojava.bio.dp.DotState
          - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.State
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.seq.io.SymbolTokenization
    - org.biojava.bio.taxa.Taxon
    - org.biojava.ontology.Term
      - org.biojavax.ontology.ComparableTerm (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RankedCrossRefable)
      - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojava.ontology.Triple)
      - org.biojava.ontology.OntologyTerm
      - org.biojava.ontology.RemoteTerm
      - org.biojava.ontology.Triple
        - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>)
      - org.biojava.ontology.Variable
    - org.biojava.ontology.Triple
      - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>)
    - org.biojava.bio.program.unigene.UnigeneCluster
    - org.biojava.ontology.Variable
  - org.biojava.bio.Annotation
    - org.biojavax.RichAnnotation
  - org.biojava.bio.alignment.ARAlignment
  - org.biojava.bio.symbol.AtomicSymbol
    - org.biojava.bio.dp.DotState
    - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.dp.State
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
  - org.biojava.bio.symbol.BasisSymbol
    - org.biojava.bio.symbol.AtomicSymbol
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.State
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.dp.DotState
    - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.dp.State
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
  - org.biojavax.bio.BioEntry (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojava.bio.seq.Sequence)
  - org.biojavax.bio.BioEntryRelationship (also extends java.lang.Comparable<T>)
  - org.biojavax.Comment (also extends java.lang.Comparable<T>)
  - org.biojavax.ontology.ComparableOntology (also extends java.lang.Comparable<T>, org.biojava.ontology.Ontology)
  - org.biojavax.ontology.ComparableTerm (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojava.ontology.Term)
  - org.biojavax.ontology.ComparableTriple (also extends java.lang.Comparable<T>, org.biojava.ontology.Triple)
  - org.biojava.bio.seq.ComponentFeature
  - org.biojava.bio.dist.Count
  - org.biojavax.ga.functions.CrossOverFunction
  - org.biojavax.CrossRef (also extends java.lang.Comparable<T>, org.biojavax.RichAnnotatable)
  - org.biojava.bio.dist.Distribution
    - org.biojava.bio.dist.OrderNDistribution
  - org.biojavax.DocRef (also extends java.lang.Comparable<T>)
  - org.biojavax.DocRefAuthor (also extends java.lang.Comparable<T>)
  - org.biojava.bio.dp.DotState
  - org.biojava.bio.dp.EmissionState (also extends org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
  - org.biojava.bio.seq.Feature (also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder)
    - org.biojava.bio.seq.ComponentFeature
    - org.biojava.bio.seq.FramedFeature
    - org.biojava.bio.seq.homol.HomologyFeature
    - org.biojava.bio.seq.RemoteFeature
    - org.biojava.bio.molbio.RestrictionSite
    - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
    - org.biojava.bio.seq.homol.SimilarityPairFeature
    - org.biojava.bio.seq.StrandedFeature
      - org.biojava.bio.seq.ComponentFeature
      - org.biojava.bio.seq.FramedFeature
      - org.biojava.bio.seq.homol.HomologyFeature
      - org.biojava.bio.seq.RemoteFeature
      - org.biojava.bio.molbio.RestrictionSite
      - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder)
      - org.biojava.bio.seq.homol.SimilarityPairFeature
  - org.biojava.bio.seq.FeatureHolder
    - org.biojava.bio.seq.ComponentFeature
    - org.biojava.bio.seq.Feature (also extends org.biojava.bio.Annotatable)
      - org.biojava.bio.seq.ComponentFeature
      - org.biojava.bio.seq.FramedFeature
      - org.biojava.bio.seq.homol.HomologyFeature
      - org.biojava.bio.seq.RemoteFeature
      - org.biojava.bio.molbio.RestrictionSite
      - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
      - org.biojava.bio.seq.homol.SimilarityPairFeature
      - org.biojava.bio.seq.StrandedFeature
        - org.biojava.bio.seq.ComponentFeature
        - org.biojava.bio.seq.FramedFeature
        - org.biojava.bio.seq.homol.HomologyFeature
        - org.biojava.bio.seq.RemoteFeature
        - org.biojava.bio.molbio.RestrictionSite
        - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder)
        - org.biojava.bio.seq.homol.SimilarityPairFeature
    - org.biojava.bio.seq.FramedFeature
    - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.seq.homol.HomologyFeature
    - org.biojava.bio.seq.RealizingFeatureHolder
    - org.biojava.bio.seq.RemoteFeature
    - org.biojava.bio.molbio.RestrictionSite
    - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.symbol.SymbolList)
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
      - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry)
    - org.biojava.bio.seq.homol.SimilarityPairFeature
    - org.biojava.bio.seq.StrandedFeature
      - org.biojava.bio.seq.ComponentFeature
      - org.biojava.bio.seq.FramedFeature
      - org.biojava.bio.seq.homol.HomologyFeature
      - org.biojava.bio.seq.RemoteFeature
      - org.biojava.bio.molbio.RestrictionSite
      - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder)
      - org.biojava.bio.seq.homol.SimilarityPairFeature
  - org.biojava.bio.seq.FeatureTypes.Repository
  - org.biojava.bio.seq.FeatureTypes.Type
  - org.biojava.bio.symbol.FiniteAlphabet
  - org.biojava.bio.seq.FramedFeature
  - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
  - org.biojava.bio.symbol.GappedSymbolList
    - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.seq.Sequence)
  - org.biojavax.ga.GeneticAlgorithm
  - org.biojava.bio.program.gff3.GFF3Record
  - org.biojava.bio.seq.homol.HomologyFeature
  - org.biojava.bio.dp.MarkovModel
  - org.biojava.bio.dp.ModelInState
  - org.biojavax.ga.functions.MutationFunction
  - org.biojavax.Namespace (also extends java.lang.Comparable<T>)
  - org.biojavax.bio.taxa.NCBITaxon (also extends java.lang.Comparable<T>)
  - org.biojavax.Note (also extends java.lang.Comparable<T>)
  - org.biojava.ontology.Ontology
    - org.biojavax.ontology.ComparableOntology (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>)
  - org.biojava.ontology.OntologyTerm
  - org.biojava.bio.dist.OrderNDistribution
  - org.biojavax.ga.Organism
  - org.biojavax.ga.Population
  - org.biojavax.RankedCrossRef (also extends java.lang.Comparable<T>)
  - org.biojavax.RankedCrossRefable
    - org.biojavax.bio.BioEntry (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RichAnnotatable)
      - org.biojavax.bio.seq.RichSequence (also extends org.biojava.bio.seq.Sequence)
    - org.biojavax.ontology.ComparableTerm (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojava.ontology.Term)
    - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
  - org.biojavax.RankedDocRef (also extends java.lang.Comparable<T>)
  - org.biojava.bio.seq.RealizingFeatureHolder
  - org.biojava.bio.seq.RemoteFeature
  - org.biojava.ontology.RemoteTerm
  - org.biojava.bio.molbio.RestrictionSite
  - org.biojavax.RichAnnotatable
    - org.biojavax.bio.BioEntry (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RankedCrossRefable)
      - org.biojavax.bio.seq.RichSequence (also extends org.biojava.bio.seq.Sequence)
    - org.biojavax.CrossRef (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>)
    - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
    - org.biojavax.bio.seq.RichLocation (also extends java.lang.Comparable<T>, org.biojava.bio.symbol.Location)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
  - org.biojavax.RichAnnotation
  - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
  - org.biojavax.bio.seq.RichFeatureRelationship (also extends java.lang.Comparable<T>)
  - org.biojavax.bio.seq.RichLocation (also extends java.lang.Comparable<T>, org.biojava.bio.symbol.Location, org.biojavax.RichAnnotatable)
  - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
  - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojavax.bio.db.RichSequenceDBLite, org.biojava.bio.seq.db.SequenceDB)
  - org.biojavax.bio.db.RichSequenceDBLite (also extends org.biojavax.bio.db.BioEntryDBLite, org.biojava.bio.seq.db.SequenceDBLite)
    - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojava.bio.seq.db.SequenceDB)
  - org.biojava.bio.search.SeqSimilaritySearchHit
  - org.biojava.bio.search.SeqSimilaritySearchResult
  - org.biojava.bio.search.SeqSimilaritySearchSubHit
  - org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.SymbolList)
    - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry)
  - org.biojava.bio.seq.db.SequenceDB
    - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojavax.bio.db.RichSequenceDBLite)
  - org.biojava.bio.seq.db.SequenceDBLite
    - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojavax.bio.db.RichSequenceDBLite, org.biojava.bio.seq.db.SequenceDB)
    - org.biojavax.bio.db.RichSequenceDBLite (also extends org.biojavax.bio.db.BioEntryDBLite)
      - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojava.bio.seq.db.SequenceDB)
    - org.biojava.bio.seq.db.SequenceDB
      - org.biojavax.bio.db.RichSequenceDB (also extends org.biojavax.bio.db.BioEntryDB, org.biojavax.bio.db.RichSequenceDBLite)
  - org.biojava.bio.seq.homol.SimilarityPairFeature
  - org.biojava.bio.dp.State
    - org.biojava.bio.dp.DotState
    - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
    - org.biojava.bio.dp.ModelInState
  - org.biojava.bio.dp.StatePath
  - org.biojava.bio.seq.StrandedFeature
    - org.biojava.bio.seq.ComponentFeature
    - org.biojava.bio.seq.FramedFeature
    - org.biojava.bio.seq.homol.HomologyFeature
    - org.biojava.bio.seq.RemoteFeature
    - org.biojava.bio.molbio.RestrictionSite
    - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder)
    - org.biojava.bio.seq.homol.SimilarityPairFeature
  - org.biojava.bio.symbol.Symbol
    - org.biojava.bio.symbol.AtomicSymbol
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.State
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.symbol.BasisSymbol
      - org.biojava.bio.symbol.AtomicSymbol
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
        - org.biojava.bio.dp.State
          - org.biojava.bio.dp.DotState
          - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
      - org.biojava.bio.dp.State
        - org.biojava.bio.dp.DotState
        - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.dp.DotState
    - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - org.biojava.bio.dp.ModelInState
    - org.biojava.bio.dp.State
      - org.biojava.bio.dp.DotState
      - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - org.biojava.bio.dp.ModelInState
  - org.biojava.bio.symbol.SymbolList
    - org.biojava.bio.symbol.Alignment
      - org.biojava.bio.alignment.ARAlignment
      - org.biojava.bio.dp.StatePath
      - org.biojava.bio.alignment.UnequalLengthAlignment
    - org.biojava.bio.alignment.ARAlignment
    - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.symbol.GappedSymbolList
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.seq.Sequence)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
    - org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder)
      - org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
      - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry)
    - org.biojava.bio.dp.StatePath
    - org.biojava.bio.alignment.UnequalLengthAlignment
  - org.biojava.bio.seq.io.SymbolTokenization
  - org.biojava.bio.taxa.Taxon
  - org.biojava.ontology.Term
    - org.biojavax.ontology.ComparableTerm (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojavax.RankedCrossRefable)
    - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>, org.biojava.ontology.Triple)
    - org.biojava.ontology.OntologyTerm
    - org.biojava.ontology.RemoteTerm
    - org.biojava.ontology.Triple
      - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>)
    - org.biojava.ontology.Variable
  - org.biojava.ontology.Triple
    - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, java.lang.Comparable<T>)
  - org.biojava.bio.alignment.UnequalLengthAlignment
  - org.biojava.bio.program.unigene.UnigeneCluster
  - org.biojava.bio.program.unigene.UnigeneDB
  - org.biojava.ontology.Variable
- org.biojava.utils.ChangeHub
- org.biojava.bio.program.tagvalue.ChangeTable.Changer
- org.biojava.bio.program.tagvalue.ChangeTable.Splitter
- org.biojava.bio.chromatogram.Chromatogram
- org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler
- org.biojava.bio.gui.sequence.CircularFeatureRenderer
- org.biojava.bio.gui.sequence.CircularRenderer
- org.biojava.bio.gui.sequence.CircularRendererContext
- java.lang.Cloneable
  - org.biojava.bio.structure.Structure
- org.biojava.bio.symbol.CodonPref
- org.biojava.bio.symbol.CodonPrefFilter
- org.biojava.bio.CollectionConstraint
- org.biojava.bio.program.blast2html.ColourCommand
- org.biojava.utils.Commitable
- java.lang.Comparable<T>
  - org.biojavax.bio.BioEntry (also extends org.biojava.utils.Changeable, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable)
    - org.biojavax.bio.seq.RichSequence (also extends org.biojava.bio.seq.Sequence)
  - org.biojavax.bio.BioEntryRelationship (also extends org.biojava.utils.Changeable)
  - org.biojavax.Comment (also extends org.biojava.utils.Changeable)
  - org.biojavax.ontology.ComparableOntology (also extends org.biojava.utils.Changeable, org.biojava.ontology.Ontology)
  - org.biojavax.ontology.ComparableTerm (also extends org.biojava.utils.Changeable, org.biojavax.RankedCrossRefable, org.biojava.ontology.Term)
  - org.biojavax.ontology.ComparableTriple (also extends org.biojava.utils.Changeable, org.biojava.ontology.Triple)
  - org.biojavax.CrossRef (also extends org.biojava.utils.Changeable, org.biojavax.RichAnnotatable)
  - org.biojavax.DocRef (also extends org.biojava.utils.Changeable)
  - org.biojavax.DocRefAuthor (also extends org.biojava.utils.Changeable)
  - org.biojavax.Namespace (also extends org.biojava.utils.Changeable)
  - org.biojavax.bio.taxa.NCBITaxon (also extends org.biojava.utils.Changeable)
  - org.biojavax.Note (also extends org.biojava.utils.Changeable)
  - org.biojavax.RankedCrossRef (also extends org.biojava.utils.Changeable)
  - org.biojavax.RankedDocRef (also extends org.biojava.utils.Changeable)
  - org.biojavax.bio.seq.RichFeature (also extends org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojavax.bio.seq.RichFeatureRelationshipHolder, org.biojava.bio.seq.StrandedFeature)
  - org.biojavax.bio.seq.RichFeatureRelationship (also extends org.biojava.utils.Changeable)
  - org.biojavax.bio.seq.RichLocation (also extends org.biojava.bio.symbol.Location, org.biojavax.RichAnnotatable)
  - org.biojavax.bio.seq.RichSequence (also extends org.biojavax.bio.BioEntry, org.biojava.bio.seq.Sequence)
- org.biojava.utils.math.ComputeObject
- org.biojavax.CrossReferenceResolver
- org.biojava.bio.program.blast2html.DatabaseURLGenerator
- java.io.DataInput
  - org.biojava.bio.program.abi.ABIFParser.DataAccess (also extends org.biojava.utils.io.Seekable)
- org.biojava.bio.program.ssaha.DataStore
- org.biojava.bio.program.ssaha.DataStoreFactory
- org.biojava.bio.seq.io.agave.DelegationManager
- org.biojava.utils.stax.DelegationManager
- org.biojava.bio.seq.distributed.DistDataSource
- org.biojava.bio.dist.DistributionFactory
- org.biojava.bio.dist.DistributionTrainer
- org.biojava.bio.dist.DistributionTrainerContext
  - org.biojava.bio.dp.ModelTrainer
- org.biojava.bio.dp.onehead.DPCursor
- org.biojava.bio.dp.DPFactory
- org.biojava.bio.dp.DPMatrix
- org.biojava.bio.EcNumber
- org.biojava.bio.alignment.EditableAlignment
- org.biojava.bio.program.xff.ElementRecognizer
- org.biojava.bio.seq.io.agave.ElementRecognizer
- org.biojava.bio.seq.io.game.ElementRecognizer
- java.util.EventListener
  - org.biojava.utils.candy.CandyFinder
  - org.biojava.utils.candy.CandyVocabulary
  - org.biojava.utils.ChangeListener
  - org.biojava.utils.ParseErrorListener
  - java.beans.PropertyChangeListener
    - org.biojava.utils.candy.CandyFinder
    - org.biojava.utils.candy.CandyVocabulary
  - org.biojava.bio.gui.sequence.SequenceViewerListener
  - org.biojava.bio.gui.sequence.SequenceViewerMotionListener
  - org.biojava.stats.svm.TrainingListener
- org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker
- org.biojava.bio.seq.FeatureRealizer
- org.biojava.bio.gui.sequence.FeatureRenderer
  - org.biojava.bio.gui.sequence.BeadFeatureRenderer
  - org.biojava.bio.gui.sequence.ImageMapRenderer
- org.biojava.bio.gui.sequence.FeatureSource
- org.biojava.bio.search.FilterTest
- org.biojava.bio.seq.FilterUtils.FilterTransformer
- org.biojavax.ga.functions.FitnessFunction
- org.biojava.bio.program.formats.Format
- org.biojava.bio.seq.Frame
- org.biojava.bio.symbol.FuzzyPointLocation.PointResolver
- org.biojavax.ga.functions.GACross
- org.biojavax.ga.functions.GACrossResult
- org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
- org.biojava.bio.seq.io.game.GAMENameCallbackItf
- org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf
- org.biojavax.ga.GAStoppingCriteria
- org.biojava.bio.program.gff3.GFF3DocumentHandler
- org.biojava.bio.program.gff.GFFDocumentHandler
- org.biojava.bio.program.gff.GFFErrorHandler
- org.biojava.bio.program.gff.GFFRecord
- org.biojava.bio.program.gff.GFFRecordFilter
- org.biojava.bio.gui.glyph.Glyph
- org.biojava.bio.structure.Group
  - org.biojava.bio.structure.AminoAcid
- org.biojava.bio.dp.HMMTrainer
- org.biojava.bio.program.homologene.HomologeneBuilder
- org.biojava.bio.program.homologene.HomologeneDB
- org.biojava.bio.seq.homol.Homology
- org.biojava.bio.seq.homol.HomologyDB
- org.biojava.utils.lsid.Identifiable
- org.biojava.bio.seq.db.IDMaker
- org.biojava.bio.gui.sequence.ImageMap
- org.biojava.bio.seq.db.Index
- org.biojava.bio.program.indexdb.IndexStore
- org.biojava.bio.seq.db.IndexStore
- org.biojava.utils.xml.Initializable
- org.biojava.stats.svm.ItemValue
- org.biojava.bio.gui.sequence.LabelRenderer
- org.biojava.utils.ListTools.Mapper
- org.biojava.bio.symbol.Location
  - org.biojavax.bio.seq.RichLocation (also extends java.lang.Comparable<T>, org.biojavax.RichAnnotatable)
- org.biojava.bio.gui.LogoContext
- org.biojava.bio.gui.LogoPainter
- org.biojava.bio.structure.io.mmcif.MMcifConsumer
- org.biojava.bio.structure.io.mmcif.MMcifParser
- org.biojavax.bio.taxa.io.NCBITaxonomyLoader
- org.biojavax.bio.phylo.io.nexus.NexusBlockListener
  - org.biojavax.bio.phylo.io.nexus.CharactersBlockListener
    - org.biojavax.bio.phylo.io.nexus.DataBlockListener
  - org.biojavax.bio.phylo.io.nexus.DataBlockListener
  - org.biojavax.bio.phylo.io.nexus.DistancesBlockListener
  - org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder
  - org.biojavax.bio.phylo.io.nexus.TaxaBlockListener
  - org.biojavax.bio.phylo.io.nexus.TreesBlockListener
- org.biojavax.bio.phylo.io.nexus.NexusBlockParser
- org.biojavax.bio.phylo.io.nexus.NexusFileListener
- org.biojavax.bio.phylo.io.nexus.NexusObject
  - org.biojavax.bio.phylo.io.nexus.NexusBlock
- org.biojava.utils.automata.NfaBuilder
- org.biojava.ontology.obo.OboFileEventListener
- org.biojava.ontology.OntologyFactory
- org.biojava.ontology.OntologyOps
- org.biojava.bio.program.homologene.Orthologue
- org.biojava.bio.program.homologene.OrthologueFilter
- org.biojava.bio.program.homologene.OrthologueSet
- org.biojava.bio.program.homologene.OrthologueSet.Iterator
- org.biojava.bio.program.homologene.OrthoPair
- org.biojava.bio.program.homologene.OrthoPairCollection
- org.biojava.bio.program.homologene.OrthoPairCollection.Iterator
- org.biojava.bio.program.homologene.OrthoPairFilter
- org.biojava.bio.program.homologene.OrthoPairSet
- org.biojava.bio.program.homologene.OrthoPairSet.Iterator
- org.biojava.bio.program.homologene.OrthoPairSetFilter
- org.biojava.bio.gui.sequence.OverlayMarker
- org.biojava.bio.symbol.Packing
- org.biojava.bio.dp.twohead.PairDPCursor
- org.biojava.bio.gui.sequence.PairwiseSequenceRenderer
- org.biojava.utils.ParseErrorSource
- org.biojava.utils.automata.PatternListener
- org.biojava.bio.structure.server.PDBFilter
- org.biojava.bio.structure.server.PDBInstallation
- org.biojava.bio.structure.PDBRecord
- org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
- org.biojavax.bio.seq.Position
- org.biojavax.bio.seq.PositionResolver
- org.biojava.bio.seq.projection.Projection
- org.biojava.bio.seq.projection.ProjectionContext
- org.biojava.bio.seq.projection.ProjectionEngine.Instantiator
- org.biojava.bio.seq.projection.ProjectionEngine.TemplateProjector
- org.biojava.bio.program.tagvalue.PropertyChanger
- org.biojava.bio.PropertyConstraint
- org.biojava.bio.program.phred.Qualitative
- org.biojava.bio.alignment.QualitativeAlignment
- org.biojava.bio.program.indexdb.Record
- org.biojava.directory.RegistryConfiguration
- org.biojava.bio.seq.RemoteFeature.Resolver
- org.biojavax.bio.seq.RichFeatureRelationshipHolder
  - org.biojavax.bio.seq.RichFeature (also extends java.lang.Comparable<T>, org.biojavax.RankedCrossRefable, org.biojavax.RichAnnotatable, org.biojava.bio.seq.StrandedFeature)
- org.biojavax.RichObjectBuilder
- org.biojavax.bio.seq.RichSequenceHandler
- java.lang.Runnable
  - org.biojava.utils.process.InputHandler
  - org.biojava.utils.process.OutputHandler
- org.biojava.bio.dp.ScoreType
- org.biojava.utils.regex.Search.Listener
- org.biojava.bio.search.SearchContentHandler
  - org.biojava.bio.search.SearchBuilder
- org.biojava.bio.program.ssaha.SearchListener
- org.biojava.utils.io.Seekable
  - org.biojava.bio.program.abi.ABIFParser.DataAccess (also extends java.io.DataInput)
- org.biojavax.ga.functions.SelectionFunction
- org.biojava.bio.seq.io.SeqIOListener
  - org.biojavax.bio.seq.io.RichSeqIOListener
    - org.biojavax.bio.seq.io.RichSequenceBuilder (also extends org.biojava.bio.seq.io.SequenceBuilder)
  - org.biojavax.bio.seq.io.RichSequenceBuilder (also extends org.biojavax.bio.seq.io.RichSeqIOListener, org.biojava.bio.seq.io.SequenceBuilder)
  - org.biojava.bio.seq.io.SeqFileFormer
  - org.biojava.bio.seq.io.SequenceBuilder
    - org.biojavax.bio.seq.io.RichSequenceBuilder (also extends org.biojavax.bio.seq.io.RichSeqIOListener)
- org.biojava.bio.search.SeqSimilaritySearcher
- org.biojava.bio.seq.SequenceAnnotator
- org.biojava.bio.seq.io.SequenceBuilderFactory
  - org.biojavax.bio.seq.io.RichSequenceBuilderFactory
- org.biojava.bio.seq.db.SequenceDBInstallation
- org.biojava.directory.SequenceDBProvider
- org.biojava.bio.seq.SequenceFactory
- org.biojava.bio.seq.io.SequenceFormat
  - org.biojavax.bio.seq.io.RichSequenceFormat
- org.biojava.bio.seq.io.agave.SequenceHandler
- org.biojava.bio.seq.SequenceIterator
  - org.biojavax.bio.seq.RichSequenceIterator (also extends org.biojavax.bio.BioEntryIterator)
- org.biojava.bio.gui.sequence.SequenceRenderer
- org.biojava.bio.program.ssaha.SequenceStreamer
- java.io.Serializable
  - org.biojavax.bio.db.biosql.BioSQLFeatureFilter
  - org.biojava.bio.search.BlastLikeSearchFilter
  - org.biojava.bio.seq.FeatureFilter
    - org.biojavax.bio.db.biosql.BioSQLFeatureFilter
    - org.biojava.bio.seq.OptimizableFilter
  - org.biojava.bio.symbol.FuzzyLocation.RangeResolver
  - org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory
  - org.biojava.bio.seq.OptimizableFilter
- org.biojava.bio.program.homologene.SimilarityType
- org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
- org.biojava.bio.program.tagvalue.StateMachine.ExitNotification
- org.biojava.bio.program.tagvalue.StateMachine.State
- org.biojava.utils.automata.StateMachineFactory
- org.biojava.utils.automata.StateMachineInstance
- org.biojava.bio.seq.io.agave.StAXContentHandler
- org.biojava.utils.stax.StAXContentHandler
  - org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler
  - org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
  - org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler
- org.biojava.bio.program.ssbind.StAXHandlerFactory
- org.biojava.bio.seq.io.agave.StAXHandlerFactory
- org.biojava.bio.seq.io.game.StAXHandlerFactory
- org.biojava.bio.seq.io.game12.StAXHandlerFactory
- org.biojava.bio.dp.StoppingCriteria
- org.biojava.bio.seq.io.StreamParser
- 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.server.StructureServer
- org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler
- org.biojava.stats.svm.SVMClassifierModel
- org.biojava.stats.svm.SVMKernel
- org.biojava.stats.svm.SVMTarget
- javax.swing.SwingConstants
  - org.biojava.bio.gui.sequence.PairwiseRenderContext
  - org.biojava.bio.gui.sequence.SequenceRenderContext
    - org.biojava.bio.gui.sequence.PairwiseRenderContext
- org.biojava.bio.symbol.SymbolListFactory
- org.biojava.bio.symbol.SymbolPropertyTable
- org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
- org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator
- org.biojava.bio.seq.io.SymbolReader
- org.biojava.bio.gui.SymbolStyle
- org.biojava.bio.program.tagvalue.TagValueContext
- org.biojava.bio.program.tagvalue.TagValueListener
  - org.biojava.bio.program.tagvalue.TagValueWrapper
- org.biojava.bio.program.tagvalue.TagValueParser
- org.biojava.bio.program.homologene.Taxon
- org.biojava.bio.taxa.TaxonFactory
- org.biojava.bio.taxa.TaxonParser
- org.biojava.utils.ThreadPool
- org.biojava.bio.gui.sequence.tracklayout.TrackLayout
- org.biojava.bio.dp.Trainable
  - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State)
- org.biojava.bio.dp.TrainingAlgorithm
- org.biojava.stats.svm.TrainingContext
- org.biojava.bio.dp.TransitionTrainer
- org.biojava.bio.symbol.TranslationTable
  - org.biojava.bio.symbol.ManyToOneTranslationTable
  - org.biojava.bio.symbol.ReversibleTranslationTable
- org.biojava.bio.program.unigene.UnigeneFactory
- org.biojava.utils.net.URLFactory
- org.biojava.bio.program.blast2html.URLGeneratorFactory
- org.biojava.utils.walker.Visitor
- org.biojava.utils.walker.Walker
- org.biojava.bio.dp.WeightMatrix
- org.biojava.bio.symbol.WobbleDistribution
- org.biojava.bio.program.xff.XFFHelper
- org.biojava.bio.program.xff.XFFPartHandlerFactory
- org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory
- org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory
- org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter
- org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter
- org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory
- org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter
- org.biojava.utils.xml.XMLWritable
- org.biojava.utils.xml.XMLWriter

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - org.biojava.bio.structure.io.mmcif.chem.ResidueType (implements java.io.Serializable)
    - org.biojava.bio.structure.io.mmcif.chem.PolymerType (implements java.io.Serializable)