## Hierarchy For All Packages

Package Hierarchies:
  org.biojava.bibliography, org.biojava.bio, org.biojava.bio.alignment, 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.sequence, 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.gff, org.biojava.bio.program.hmmer, 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.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.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.seq.ragbag, org.biojava.bio.symbol, org.biojava.bio.taxa, org.biojava.directory, org.biojava.stats.svm, org.biojava.stats.svm.tools, org.biojava.utils, 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.stax, org.biojava.utils.xml

## Class Hierarchy

- class java.lang.Object
  - class org.biojava.bio.program.abi.ABIFParser
    - class org.biojava.bio.program.abi.ABIFChromatogram.Parser
  - class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
  - class org.biojava.bio.program.abi.ABITools
  - class org.biojava.bio.program.abi.ABITrace
  - class org.biojava.bio.program.blast2html.AbstractAlignmentStyler (implements org.biojava.bio.program.blast2html.AlignmentStyler)
    - class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  - class org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - class org.biojava.bio.gui.sequence.AbiTraceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - class org.biojava.bio.symbol.AbstractAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
      - class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
      - class org.biojava.bio.symbol.SimpleAlphabet (implements java.io.Serializable)
      - class org.biojava.bio.symbol.SingletonAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
    - class org.biojava.bio.AbstractAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
      - class org.biojava.bio.AnnotationChanger
      - class org.biojava.bio.AnnotationRenamer
      - class org.biojava.bio.BeanAsAnnotation
      - class org.biojava.bio.SimpleAnnotation
      - class org.biojava.bio.SmallAnnotation
    - class org.biojava.bio.gui.sequence.AbstractBeadRenderer (implements org.biojava.bio.gui.sequence.BeadFeatureRenderer, java.io.Serializable)
      - class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
      - class org.biojava.bio.gui.sequence.RectangularBeadRenderer
      - class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
    - class org.biojava.bio.dist.AbstractDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
      - class org.biojava.bio.dist.AbstractOrderNDistribution (implements org.biojava.bio.dist.OrderNDistribution)
      - class org.biojava.bio.dist.SimpleDistribution (implements java.io.Serializable)
        - class org.biojava.bio.dist.UntrainableDistribution
      - class org.biojava.bio.dist.UniformDistribution (implements java.io.Serializable)
    - class org.biojava.bio.seq.AbstractFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
      - class org.biojava.bio.seq.MergeFeatureHolder
      - class org.biojava.bio.seq.ProjectedFeatureHolder (implements org.biojava.bio.seq.FeatureHolder, org.biojava.bio.seq.projection.ProjectionContext)
      - class org.biojava.bio.seq.SimpleFeatureHolder
    - class org.biojava.bio.seq.db.AbstractSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
      - class org.biojava.bio.seq.db.AnnotatedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
      - class org.biojava.bio.seq.distributed.DistributedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
      - class org.biojava.bio.seq.db.DummySequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
      - class org.biojava.bio.seq.db.HashSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
      - class org.biojava.bio.seq.db.IndexedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
      - class org.biojava.bio.seq.db.SequenceDBWrapper (implements java.io.Serializable)
        - class org.biojava.bio.seq.db.CachingSequenceDB
        - class org.biojava.bio.seq.db.SubSequenceDB
        - class org.biojava.bio.seq.db.ViewingSequenceDB
    - class org.biojava.bio.symbol.AbstractSymbol (implements org.biojava.bio.symbol.Symbol)
      - class org.biojava.bio.symbol.FundamentalAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
        - class org.biojava.bio.dp.SimpleDotState (implements org.biojava.bio.dp.DotState, java.io.Serializable)
        - class org.biojava.bio.dp.SimpleModelInState (implements org.biojava.bio.dp.ModelInState)
      - class org.biojava.bio.symbol.SimpleSymbol (implements java.io.Serializable, org.biojava.bio.symbol.Symbol)
        - class org.biojava.bio.symbol.SimpleBasisSymbol (implements org.biojava.bio.symbol.BasisSymbol)
          - class org.biojava.bio.symbol.SimpleAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol)
    - class org.biojava.bio.symbol.AbstractSymbolList (implements org.biojava.bio.symbol.SymbolList)
      - class org.biojava.bio.alignment.AbstractULAlignment (implements org.biojava.bio.alignment.UnequalLengthAlignment)
        - class org.biojava.bio.alignment.FlexibleAlignment (implements org.biojava.bio.alignment.ARAlignment, org.biojava.bio.alignment.EditableAlignment)
      - class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment (implements org.biojava.bio.alignment.UnequalLengthAlignment)
      - class org.biojava.bio.seq.impl.AssembledSymbolList
      - class org.biojava.bio.symbol.DummySymbolList (implements java.io.Serializable)
      - class org.biojava.bio.symbol.PackedDnaSymbolList (implements java.io.Serializable)
      - class org.biojava.bio.symbol.PackedSymbolList (implements java.io.Serializable)
      - class org.biojava.bio.symbol.SimpleAlignment (implements org.biojava.bio.symbol.Alignment, java.io.Serializable)
      - class org.biojava.bio.symbol.SimpleGappedSymbolList (implements org.biojava.bio.symbol.GappedSymbolList, java.io.Serializable)
        - class org.biojava.bio.seq.SimpleGappedSequence (implements org.biojava.bio.seq.GappedSequence)
      - class org.biojava.bio.symbol.SimpleSymbolList (implements org.biojava.utils.ChangeListener, java.io.Serializable)
    - class org.biojava.bio.taxa.AbstractTaxon (implements org.biojava.bio.taxa.Taxon)
      - class org.biojava.bio.taxa.SimpleTaxon
      - class org.biojava.bio.taxa.WeakTaxon
    - class org.biojava.bio.gui.sequence.BasicFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - class org.biojava.bio.gui.sequence.CrosshairRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer)
    - class org.biojava.bio.program.das.DAS
    - class org.biojava.bio.program.das.DASSequence (implements org.biojava.bio.program.das.DASSequenceI)
    - class org.biojava.bio.seq.DummySequence (implements org.biojava.bio.seq.Sequence)
    - class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - class org.biojava.bio.gui.sequence.FeatureLabelRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - class org.biojava.bio.seq.FeatureTypes.RepositoryImpl (implements org.biojava.bio.seq.FeatureTypes.Repository)
    - class org.biojava.bio.dist.IndexedCount (implements org.biojava.bio.dist.Count, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.LabelledSequenceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - class org.biojava.bio.seq.LazyFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
    - class org.biojava.bio.MergeAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.MultiLineRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer, java.io.Serializable)
    - class org.biojava.bio.OverlayAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.OverlayRendererWrapper (implements org.biojava.bio.gui.sequence.OverlayMarker, org.biojava.bio.gui.sequence.SequenceRenderer, java.io.Serializable)
    - class org.biojava.bio.dist.PairDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer (implements org.biojava.bio.gui.sequence.PairwiseSequenceRenderer, java.io.Serializable)
    - class org.biojava.bio.search.SequenceDBSearchHit (implements org.biojava.bio.Annotatable, org.biojava.bio.search.SeqSimilaritySearchHit)
    - class org.biojava.bio.search.SequenceDBSearchResult (implements org.biojava.bio.Annotatable, org.biojava.bio.search.SeqSimilaritySearchResult)
    - class org.biojava.bio.search.SequenceDBSearchSubHit (implements org.biojava.bio.search.SeqSimilaritySearchSubHit)
    - class org.biojava.bio.gui.sequence.SequenceRendererWrapper (implements org.biojava.bio.gui.sequence.SequenceRenderer, java.io.Serializable)
      - class org.biojava.bio.gui.sequence.AlignmentRenderer
      - class org.biojava.bio.gui.sequence.BumpedRenderer
      - class org.biojava.bio.gui.sequence.FilteringRenderer
      - class org.biojava.bio.gui.sequence.PaddingRenderer
    - class org.biojava.bio.seq.SimpleAssembly (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence)
    - class org.biojava.bio.dp.SimpleEmissionState (implements org.biojava.bio.dp.EmissionState, java.io.Serializable)
      - class org.biojava.bio.dp.MagicalState
      - class org.biojava.bio.program.hmmer.ProfileEmissionState
    - class org.biojava.bio.seq.impl.SimpleFeature (implements org.biojava.bio.seq.Feature, org.biojava.bio.seq.RealizingFeatureHolder, java.io.Serializable)
      - class org.biojava.bio.seq.impl.SimpleStrandedFeature (implements org.biojava.bio.seq.StrandedFeature)
        - class org.biojava.bio.seq.impl.SimpleFramedFeature (implements org.biojava.bio.seq.Frame, org.biojava.bio.seq.FramedFeature)
        - class org.biojava.bio.seq.impl.SimpleHomologyFeature (implements org.biojava.bio.seq.homol.HomologyFeature)
        - class org.biojava.bio.seq.impl.SimpleRemoteFeature (implements org.biojava.bio.seq.RemoteFeature, java.io.Serializable)
        - class org.biojava.bio.seq.impl.SimpleRestrictionSite (implements org.biojava.bio.molbio.RestrictionSite)
        - class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature (implements org.biojava.bio.seq.homol.SimilarityPairFeature)
    - class org.biojava.bio.seq.homol.SimpleHomology (implements org.biojava.bio.seq.homol.Homology)
    - class org.biojava.bio.gui.sequence.SimpleLabelRenderer (implements org.biojava.bio.gui.sequence.LabelRenderer)
    - class org.biojava.bio.dp.SimpleMarkovModel (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
      - class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
      - class org.biojava.bio.dp.ProfileHMM
        - class org.biojava.bio.program.hmmer.HmmerProfileHMM
    - class org.biojava.bio.search.SimpleSeqSimilaritySearchHit (implements org.biojava.bio.search.SeqSimilaritySearchHit)
    - class org.biojava.bio.search.SimpleSeqSimilaritySearchResult (implements org.biojava.bio.search.SeqSimilaritySearchResult)
    - class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit (implements org.biojava.bio.search.SeqSimilaritySearchSubHit)
    - class org.biojava.bio.seq.impl.SimpleSequence (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence, java.io.Serializable)
      - class org.biojava.bio.program.phred.PhredSequence (implements org.biojava.bio.program.phred.Qualitative)
      - class org.biojava.bio.seq.impl.RevCompSequence
    - class org.biojava.bio.gui.sequence.SixFrameRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
    - class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.StackedFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - class org.biojava.bio.gui.sequence.TickFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
    - class org.biojava.bio.dist.TranslatedDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
    - class org.biojava.bio.seq.db.WebSequenceDB (implements org.biojava.bio.seq.db.SequenceDBLite)
      - class org.biojava.bio.seq.db.NCBISequenceDB
    - class org.biojava.bio.dp.WMAsMM (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
    - class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer, java.io.Serializable)
  - class org.biojava.bio.chromatogram.AbstractChromatogram (implements org.biojava.bio.chromatogram.Chromatogram)
    - class org.biojava.bio.program.abi.ABIFChromatogram
    - class org.biojava.bio.program.scf.SCF
    - class org.biojava.bio.chromatogram.SimpleChromatogram
  - class java.util.AbstractCollection (implements java.util.Collection)
    - class java.util.AbstractList (implements java.util.List)
      - class org.biojava.utils.FileAsList (implements org.biojava.utils.Commitable)
      - class org.biojava.utils.ListTools.Doublet (implements java.io.Serializable)
      - class org.biojava.utils.ListTools.Triplet (implements java.io.Serializable)
      - class org.biojava.utils.SingletonList (implements java.io.Serializable)
    - class java.util.AbstractSet (implements java.util.Set)
      - class org.biojava.utils.SmallSet
  - class org.biojava.bio.seq.io.AbstractGenEmblFileFormer
    - class org.biojava.bio.seq.io.EmblFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
    - class org.biojava.bio.seq.io.GenbankFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
      - class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
    - class org.biojava.bio.seq.io.SwissprotFileFormer (implements org.biojava.bio.seq.io.SeqFileFormer)
  - class org.biojava.bio.symbol.AbstractLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
    - class org.biojava.bio.symbol.AbstractRangeLocation
      - class org.biojava.bio.symbol.FuzzyLocation (implements java.io.Serializable)
      - class org.biojava.bio.symbol.PointLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
      - class org.biojava.bio.symbol.RangeLocation (implements java.io.Serializable)
        - class org.biojava.bio.symbol.MergeLocation
    - class org.biojava.bio.symbol.FuzzyPointLocation
  - class org.biojava.bio.symbol.AbstractLocationDecorator (implements org.biojava.bio.symbol.Location)
    - class org.biojava.bio.symbol.BetweenLocation
    - class org.biojava.bio.symbol.CircularLocation
  - class java.util.AbstractMap (implements java.util.Map)
    - class org.biojava.utils.BeanAsMap
    - class org.biojava.utils.OverlayMap
    - class org.biojava.utils.SmallMap (implements java.io.Serializable)
    - class org.biojava.utils.cache.WeakValueHashMap
  - class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor (implements org.biojava.bio.dp.twohead.PairDPCursor)
    - class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
    - class org.biojava.bio.dp.twohead.MatrixPairDPCursor
  - class org.biojava.bio.program.sax.AbstractNativeAppSAXParser (implements org.biojava.bio.program.sax.NamespaceConfigurationIF, org.xml.sax.XMLReader)
    - class org.biojava.bio.program.sax.BlastLikeSAXParser
    - class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
    - class org.biojava.bio.program.sax.FastaSearchSAXParser (implements org.biojava.bio.search.SearchContentHandler)
    - class org.biojava.bio.program.sax.FastaSequenceSAXParser
    - class org.biojava.bio.program.sax.PdbSAXParser
    - class org.biojava.bio.program.sax.SequenceAlignmentSAXParser
  - class org.biojava.stats.svm.AbstractSVMClassifierModel (implements org.biojava.stats.svm.SVMClassifierModel)
    - class org.biojava.stats.svm.SimpleSVMClassifierModel
  - class org.biojava.stats.svm.AbstractSVMTarget (implements org.biojava.stats.svm.SVMTarget)
  - class org.biojava.bio.dp.AbstractTrainer (implements org.biojava.bio.dp.TrainingAlgorithm)
    - class org.biojava.bio.dp.BaumWelchSampler (implements java.io.Serializable)
    - class org.biojava.bio.dp.BaumWelchTrainer (implements java.io.Serializable)
  - class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator (implements java.util.Comparator)
  - class org.biojava.bio.seq.io.agave.AGAVEDbId
  - class org.biojava.bio.seq.io.agave.AGAVEIdAlias
  - class org.biojava.bio.seq.io.agave.AGAVEMapLocation
  - class org.biojava.bio.seq.io.agave.AGAVEMapPosition
  - class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
  - class org.biojava.bio.seq.io.agave.AGAVEProperty
  - class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
  - class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
  - class org.biojava.bio.seq.io.agave.AgaveWriter
  - class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  - class org.biojava.bio.seq.io.agave.AGAVEXref
  - class org.biojava.bio.seq.io.agave.AGAVEXrefs
  - class org.biojava.bio.seq.io.AlignIOConstants
  - class org.biojava.bio.symbol.Alignment.SymbolListIterator (implements java.util.Iterator)
  - class org.biojava.bio.program.blast2html.AlignmentMarker
  - class org.biojava.bio.symbol.AlphabetManager
  - class org.biojava.bio.program.ssbind.AlphabetResolver
  - class org.biojava.bio.program.tagvalue.AnnotationBuilder (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - class org.biojava.bio.program.ssbind.AnnotationFactory
  - class org.biojava.bio.AnnotationTools
  - class org.biojava.bio.AnnotationType.Abstract (implements org.biojava.bio.AnnotationType)
    - class org.biojava.bio.AnnotationType.Impl
  - class org.biojava.utils.xml.AppBeanRunner
  - class org.biojava.bio.dp.BackPointer
  - class org.biojava.bio.gui.BarLogoPainter (implements org.biojava.bio.gui.LogoPainter)
  - class org.biojava.bio.program.xml.BaseXMLWriter
  - class org.biojava.bio.program.xff.BasicXFFHelper (implements org.biojava.bio.program.xff.XFFHelper)
    - class org.biojava.bio.program.xff.PropertyWriter
  - class org.biojava.bibliography.BiblioCriterion
  - class org.biojava.bibliography.BiblioDescription
  - class org.biojava.bibliography.BiblioEntryStatus
  - class org.biojava.bibliography.BiblioJournal
  - class org.biojava.bibliography.BiblioProvider
    - class org.biojava.bibliography.BiblioOrganisation
    - class org.biojava.bibliography.BiblioPerson
    - class org.biojava.bibliography.BiblioService
  - class org.biojava.bibliography.BiblioScope
  - class org.biojava.bibliography.BiblioSubject
  - class org.biojava.bibliography.BibRef
    - class org.biojava.bibliography.BiblioArticle
      - class org.biojava.bibliography.BiblioBookArticle
      - class org.biojava.bibliography.BiblioJournalArticle
    - class org.biojava.bibliography.BiblioBook
    - class org.biojava.bibliography.BiblioPatent
    - class org.biojava.bibliography.BiblioProceeding
    - class org.biojava.bibliography.BiblioTechReport
    - class org.biojava.bibliography.BiblioThesis
    - class org.biojava.bibliography.BiblioWebResource
  - class org.biojava.utils.math.BinarySearch
  - class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - class org.biojava.bio.seq.db.BioIndex (implements org.biojava.bio.seq.db.IndexStore)
  - class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
  - class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - class org.biojava.bio.program.indexdb.BioStore (implements org.biojava.bio.program.indexdb.IndexStore)
  - class org.biojava.bio.program.indexdb.BioStoreFactory
  - class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder (implements org.biojava.bio.search.SearchBuilder)
  - class org.biojava.bio.program.BlastLikeToXMLConverter
  - class org.biojava.utils.candy.CandyEntry
  - class org.biojava.bio.CardinalityConstraint
  - class org.biojava.bio.dp.twohead.Cell
  - class org.biojava.utils.cache.ChangeableCache
  - class org.biojava.utils.ChangeAdapter (implements org.biojava.utils.ChangeListener)
  - class org.biojava.utils.ChangeForwarder (implements org.biojava.utils.ChangeListener)
    - class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
      - class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
    - class org.biojava.bio.Annotatable.AnnotationForwarder
    - class org.biojava.bio.dist.Distribution.NullModelForwarder
    - class org.biojava.bio.dp.MarkovModel.DistributionForwarder
    - class org.biojava.bio.MergeAnnotation.PropertyForwarder
    - class org.biojava.bio.OverlayAnnotation.PropertyForwarder
    - class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
    - class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
    - class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
  - class org.biojava.utils.ChangeListener.AlwaysVetoListener (implements org.biojava.utils.ChangeListener)
  - class org.biojava.utils.ChangeListener.LoggingListener (implements org.biojava.utils.ChangeListener)
  - class org.biojava.utils.ChangeSupport
  - class org.biojava.bio.program.tagvalue.ChangeTable
  - class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger (implements org.biojava.bio.program.tagvalue.ChangeTable.Changer)
  - class org.biojava.utils.ChangeType (implements java.io.Serializable)
  - class org.biojava.bio.chromatogram.ChromatogramFactory
  - class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic (implements java.lang.Cloneable)
  - class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  - class org.biojava.bio.chromatogram.ChromatogramTools
  - class org.biojava.bio.seq.io.ChunkedSymbolListBuilder
  - class org.biojava.bio.seq.io.ChunkedSymbolListFactory
  - class org.biojava.stats.svm.tools.ClassifierExample
  - class org.biojava.stats.svm.tools.Classify
  - class org.biojava.bio.CollectionConstraint.AllValuesIn (implements org.biojava.bio.CollectionConstraint)
  - class org.biojava.bio.CollectionConstraint.And (implements org.biojava.bio.CollectionConstraint)
  - class org.biojava.bio.CollectionConstraint.Contains (implements org.biojava.bio.CollectionConstraint)
  - class org.biojava.bio.CollectionConstraint.Or (implements org.biojava.bio.CollectionConstraint)
  - class org.biojava.bio.program.ssaha.CompactedDataStore (implements org.biojava.bio.program.ssaha.DataStore)
  - class org.biojava.bio.program.ssaha.CompactedDataStoreFactory (implements org.biojava.bio.program.ssaha.DataStoreFactory)
  - class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    - class java.awt.Container
      - class javax.swing.JComponent (implements java.io.Serializable)
        - class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
        - class org.biojava.bio.gui.DistributionLogo
        - class javax.swing.JTree (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          - class org.biojava.bio.gui.FeatureTree
        - class org.biojava.bio.gui.sequence.PairwiseSequencePanel (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.PairwiseRenderContext, java.io.Serializable)
        - class org.biojava.bio.gui.sequence.SequencePanel (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.SequenceRenderContext, javax.swing.SwingConstants)
        - class org.biojava.bio.gui.sequence.SequencePoster (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.SequenceRenderContext, javax.swing.SwingConstants)
        - class org.biojava.bio.gui.sequence.TranslatedSequencePanel (implements org.biojava.utils.Changeable, org.biojava.bio.gui.sequence.SequenceRenderContext)
  - class org.biojava.utils.Constants
  - class org.biojava.bio.program.das.DASLink
  - class org.biojava.bio.program.das.DASSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - class org.biojava.bio.program.das.DataSource
    - class org.biojava.bio.program.das.ReferenceServer (implements org.biojava.utils.Changeable)
  - class org.biojava.bio.seq.db.biosql.DBHelper
    - class org.biojava.bio.seq.db.biosql.MySQLDBHelper
    - class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
    - class org.biojava.bio.seq.db.biosql.UnknownDBHelper
  - class org.biojava.bio.seq.db.biosql.DBHelper.DeleteStyle
  - class org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    - class org.biojava.bio.program.blast2html.Blast2HTMLHandler
    - class org.biojava.bio.program.xml.SimpleXMLEmitter
    - class org.biojava.bio.dist.XMLDistributionReader
  - class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory (implements org.biojava.bio.program.blast2html.URLGeneratorFactory)
  - class java.util.Dictionary
    - class java.util.Hashtable (implements java.lang.Cloneable, java.util.Map, java.io.Serializable)
      - class java.util.Properties
        - class org.biojava.utils.TypedProperties
  - class org.biojava.bio.proteomics.Digest
  - class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory (implements org.biojava.bio.dist.DistributionFactory, java.io.Serializable)
  - class org.biojava.bio.dist.DistributionTools
  - class org.biojava.bio.symbol.DNAAmbPack (implements org.biojava.bio.symbol.Packing, java.io.Serializable)
  - class org.biojava.bio.symbol.DNANoAmbPack (implements org.biojava.bio.symbol.Packing, java.io.Serializable)
  - class org.biojava.bio.gui.DNAStyle (implements org.biojava.bio.gui.SymbolStyle)
  - class org.biojava.bio.seq.DNATools
  - class org.biojava.bio.dp.DP
    - class org.biojava.bio.dp.twohead.PairwiseDP (implements java.io.Serializable)
    - class org.biojava.bio.dp.onehead.SingleDP (implements java.io.Serializable)
  - class org.biojava.bio.dp.DP.ReverseIterator (implements java.util.Iterator, java.io.Serializable)
  - class org.biojava.bio.dp.twohead.DPCompiler (implements org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker)
  - class org.biojava.bio.dp.DPFactory.DefaultFactory (implements org.biojava.bio.dp.DPFactory)
  - class org.biojava.bio.dp.twohead.DPInterpreter (implements org.biojava.bio.dp.twohead.CellCalculatorFactory)
  - class org.biojava.bio.dp.twohead.DPInterpreter.Maker (implements org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker)
  - class org.biojava.bio.seq.db.DummySequenceDBInstallation (implements org.biojava.bio.seq.db.SequenceDBInstallation)
  - class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator (implements org.biojava.bio.program.blast2html.DatabaseURLGenerator)
  - class org.biojava.bio.taxa.EbiFormat (implements org.biojava.bio.taxa.TaxonParser)
  - class org.biojava.bio.program.tagvalue.Echo (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - class org.biojava.bio.symbol.Edit (implements java.io.Serializable)
  - class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer (implements org.biojava.bio.program.xff.ElementRecognizer)
  - class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName (implements org.biojava.bio.program.xff.ElementRecognizer)
  - class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - class org.biojava.bio.program.xff.ElementRecognizer.ByNSName (implements org.biojava.bio.program.xff.ElementRecognizer)
  - class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute (implements org.biojava.bio.program.xff.ElementRecognizer)
  - class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute (implements org.biojava.bio.seq.io.game.ElementRecognizer)
  - class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
    - class org.biojava.bio.seq.db.emblcd.AcnumHitReader
    - class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
    - class org.biojava.bio.seq.db.emblcd.DivisionLkpReader
    - class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader
  - class org.biojava.bio.seq.db.EmblCDROMIndexStore (implements org.biojava.bio.seq.db.IndexStore)
  - class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
    - class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
  - class org.biojava.bio.seq.io.EmblLikeFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.seq.io.EmblLikeLocationParser
  - class org.biojava.bio.seq.io.EmblProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.dp.twohead.EmissionCache
  - class java.util.EventObject (implements java.io.Serializable)
    - class org.biojava.utils.ChangeEvent
    - class org.biojava.utils.ParseErrorEvent
    - class org.biojava.bio.gui.sequence.SequenceViewerEvent
    - class org.biojava.stats.svm.TrainingEvent
  - class org.biojava.bio.seq.io.FastaAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.io.FastaFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.utils.xml.FastXMLWriter
  - class org.biojava.bio.seq.Feature.ByLocationComparator (implements java.util.Comparator)
  - class org.biojava.bio.seq.Feature.Template (implements java.io.Serializable)
    - class org.biojava.bio.seq.StrandedFeature.Template
      - class org.biojava.bio.seq.ComponentFeature.Template
      - class org.biojava.bio.seq.FramedFeature.Template
      - class org.biojava.bio.seq.homol.HomologyFeature.Template
      - class org.biojava.bio.seq.RemoteFeature.Template
      - class org.biojava.bio.molbio.RestrictionSite.Template
      - class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  - class org.biojava.bio.seq.FeatureFilter.And (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByAncestor (implements org.biojava.bio.seq.OptimizableFilter, org.biojava.bio.seq.Up)
  - class org.biojava.bio.seq.FeatureFilter.ByAnnotationType (implements org.biojava.bio.seq.OptimizableFilter)
    - class org.biojava.bio.seq.FeatureFilter.AnnotationContains
    - class org.biojava.bio.seq.FeatureFilter.ByAnnotation
    - class org.biojava.bio.seq.FeatureFilter.HasAnnotation
  - class org.biojava.bio.seq.FeatureFilter.ByChild (implements org.biojava.bio.seq.Down, org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByClass (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByComponentName (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByDescendant (implements org.biojava.bio.seq.Down, org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByFeature (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByParent (implements org.biojava.bio.seq.OptimizableFilter, org.biojava.bio.seq.Up)
  - class org.biojava.bio.seq.FeatureFilter.BySequenceName (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.BySource (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByType (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ContainedByLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.FrameFilter (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.Not (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.OnlyChildren (implements org.biojava.bio.seq.ByHierarchy, org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.OnlyDescendants (implements org.biojava.bio.seq.ByHierarchy, org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.Or (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.OverlapsLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.FeatureFilter.StrandFilter (implements org.biojava.bio.seq.OptimizableFilter)
  - class org.biojava.bio.seq.impl.FeatureImpl
  - class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker (implements org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)
  - class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker (implements org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)
  - class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker (implements org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker)
  - class org.biojava.bio.seq.io.FeatureTableParser
  - class org.biojava.bio.seq.FeatureTypes
  - class org.biojava.bio.seq.db.FetchURL
  - class org.biojava.bio.seq.FilterUtils
  - class org.biojava.bio.seq.FilterUtils.DelegatingTransformer (implements org.biojava.bio.seq.FilterUtils.FilterTransformer)
  - class org.biojava.utils.cache.FixedSizeCache (implements org.biojava.utils.cache.Cache)
  - class org.biojava.utils.cache.FixedSizeMap (implements org.biojava.utils.cache.CacheMap)
  - class org.biojava.bio.program.unigene.FlatFileUnigeneFactory (implements org.biojava.bio.program.unigene.UnigeneFactory)
  - class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider (implements org.biojava.directory.SequenceDBProvider)
  - class org.biojava.bio.program.tagvalue.Formats
  - class org.biojava.bio.seq.FramedFeature.ReadingFrame (implements org.biojava.bio.seq.Frame, java.io.Serializable)
  - class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
  - class org.biojava.bio.seq.io.GAMEFormat (implements org.biojava.bio.seq.io.SequenceFormat)
  - class org.biojava.bio.seq.io.GenbankFormat (implements org.biojava.utils.ParseErrorListener, org.biojava.utils.ParseErrorSource, org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.seq.io.GenbankProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.db.GenbankSequenceDB
  - class org.biojava.bio.seq.GeneticCodes
  - class org.biojava.bio.seq.db.GenpeptSequenceDB
  - class org.biojava.bio.seq.distributed.GFFDataSource (implements org.biojava.bio.seq.distributed.DistDataSource)
  - class org.biojava.bio.program.gff.GFFEntrySet
  - class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler (implements org.biojava.bio.program.gff.GFFErrorHandler)
  - class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler (implements org.biojava.bio.program.gff.GFFErrorHandler)
  - class org.biojava.bio.program.gff.GFFFilterer (implements org.biojava.bio.program.gff.GFFDocumentHandler)
  - class org.biojava.bio.program.gff.GFFParser
  - class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter (implements org.biojava.bio.program.gff.GFFRecordFilter)
  - class org.biojava.bio.program.gff.GFFTools
  - class org.biojava.bio.program.gff.GFFWriter (implements org.biojava.bio.program.gff.GFFDocumentHandler)
  - class org.biojava.bio.gui.sequence.HeadlessRenderContext (implements org.biojava.bio.gui.sequence.SequenceRenderContext)
  - class org.biojava.bio.program.ssaha.HitMerger (implements org.biojava.bio.program.ssaha.SearchListener)
  - class org.biojava.bio.program.hmmer.HmmerProfileParser
  - class org.biojava.bio.program.blast2html.HTMLRenderer
  - class org.biojava.bio.seq.db.IDMaker.ByName (implements org.biojava.bio.seq.db.IDMaker, java.io.Serializable)
  - class org.biojava.bio.seq.db.IDMaker.ByURN (implements org.biojava.bio.seq.db.IDMaker, java.io.Serializable)
  - class org.biojava.bio.dist.IgnoreCountsTrainer (implements org.biojava.bio.dist.DistributionTrainer)
  - class org.biojava.bio.gui.sequence.ImageMap.ClientSide (implements org.biojava.bio.gui.sequence.ImageMap, java.io.Serializable)
  - class org.biojava.bio.gui.sequence.ImageMap.HotSpot (implements java.io.Serializable)
  - class org.biojava.bio.gui.sequence.ImageMap.ServerSide (implements org.biojava.bio.gui.sequence.ImageMap, java.io.Serializable)
  - class org.biojava.bio.program.tagvalue.Index2Model
  - class org.biojava.utils.IndexedChangeHub (implements org.biojava.utils.ChangeHub)
  - class org.biojava.utils.IndexedChangeHub.ListenerMemento
  - class org.biojava.bio.program.tagvalue.Indexer (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - class org.biojava.bio.program.tagvalue.Indexer2 (implements org.biojava.bio.program.tagvalue.TagValueListener)
  - class org.biojava.bio.program.indexdb.IndexTools
  - class java.io.InputStream
    - class org.biojava.utils.io.CachingInputStream (implements org.biojava.utils.io.Seekable)
  - class org.biojava.bio.proteomics.IsoelectricPointCalc
  - class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator (implements org.biojava.utils.math.ComputeObject)
  - class org.biojava.utils.JDBCConnectionPool
  - class org.biojava.bio.search.KnuthMorrisPrattSearch
  - class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing (implements org.biojava.bio.gui.sequence.LabelRenderer)
  - class org.biojava.utils.io.LargeBuffer
  - class org.biojava.bio.gui.sequence.LayeredRenderer
  - class org.biojava.bio.seq.impl.LazyFilterFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
  - class org.biojava.utils.lsid.LifeScienceIdentifier (implements java.io.Serializable)
  - class org.biojava.bio.dp.twohead.LightPairDPCursor (implements org.biojava.bio.dp.twohead.PairDPCursor)
  - class org.biojava.stats.svm.LinearKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
  - class org.biojava.bio.gui.sequence.LineInfo
  - class org.biojava.bio.program.tagvalue.LineSplitParser (implements java.lang.Cloneable, org.biojava.bio.program.tagvalue.TagValueParser)
  - class org.biojava.utils.ListTools (implements java.io.Serializable)
  - class org.biojava.bio.symbol.LocationTools
  - class org.biojava.bio.seq.db.LocusLinkParser
  - class org.biojava.bio.program.ssaha.MappedDataStoreFactory (implements org.biojava.bio.program.ssaha.DataStoreFactory)
  - class org.biojava.bio.proteomics.MassCalc
  - class org.biojava.bio.program.Meme
  - class org.biojava.bio.symbol.MotifTools
  - class org.biojava.bio.seq.io.MSFAlignmentFormat (implements org.biojava.bio.seq.io.AlignmentFormat)
  - class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator (implements org.biojava.bio.program.blast2html.DatabaseURLGenerator)
  - class org.biojava.stats.svm.NestedKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
    - class org.biojava.stats.svm.CachingKernel
    - class org.biojava.stats.svm.DiagonalAddKernel
    - class org.biojava.stats.svm.DiagonalCachingKernel
    - class org.biojava.stats.svm.ListSumKernel
    - class org.biojava.stats.svm.NormalizingKernel
    - class org.biojava.stats.svm.PolynomialKernel
    - class org.biojava.stats.svm.RadialBaseKernel
  - class org.biojava.bio.program.ssaha.NIODataStoreFactory (implements org.biojava.bio.program.ssaha.DataStoreFactory)
  - class org.biojava.bio.seq.NucleotideTools
  - class org.biojava.directory.OBDARegistryParser
  - class org.biojava.utils.ObjectUtil
  - class org.biojava.bio.dist.OrderNDistributionFactory (implements org.biojava.bio.dist.DistributionFactory)
  - class org.biojava.bio.seq.io.OrganismParser.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.symbol.PackedSymbolListFactory (implements org.biojava.bio.symbol.SymbolListFactory)
  - class org.biojava.bio.symbol.PackingFactory
  - class org.biojava.bio.dp.twohead.PairDPMatrix (implements org.biojava.bio.dp.DPMatrix, java.io.Serializable)
  - class org.biojava.bio.program.tagvalue.Parser
  - class org.biojava.bio.program.tagvalue.ParserListener
  - class org.biojava.bio.program.PdbToXMLConverter
  - class org.biojava.bio.program.phred.PhredFormat (implements org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.program.phred.PhredTools
  - class org.biojava.bio.gui.PlainBlock (implements org.biojava.bio.gui.BlockPainter)
  - class org.biojava.bio.gui.PlainStyle (implements org.biojava.bio.gui.SymbolStyle)
  - class org.biojava.utils.xml.PrettyXMLWriter (implements org.biojava.utils.xml.XMLWriter)
  - class org.biojava.bio.seq.projection.ProjectedFeature (implements org.biojava.bio.seq.Feature, org.biojava.bio.seq.projection.Projection)
    - class org.biojava.bio.seq.projection.ProjectedStrandedFeature (implements org.biojava.bio.seq.StrandedFeature)
  - class org.biojava.bio.seq.projection.ProjectionEngine
  - class org.biojava.bio.seq.projection.ProjectionEngine.InstantiatorImpl (implements org.biojava.bio.seq.projection.ProjectionEngine.Instantiator)
  - class org.biojava.bio.seq.projection.ProjectionUtils
  - class org.biojava.bio.PropertyConstraint.And (implements org.biojava.bio.PropertyConstraint)
  - class org.biojava.bio.PropertyConstraint.ByAnnotationType (implements org.biojava.bio.PropertyConstraint)
  - class org.biojava.bio.PropertyConstraint.ByClass (implements org.biojava.bio.PropertyConstraint)
  - class org.biojava.bio.PropertyConstraint.Enumeration (implements org.biojava.bio.PropertyConstraint)
  - class org.biojava.bio.PropertyConstraint.ExactValue (implements org.biojava.bio.PropertyConstraint)
  - class org.biojava.bio.PropertyConstraint.Or (implements org.biojava.bio.PropertyConstraint)
  - class org.biojava.bio.proteomics.Protease (implements java.io.Serializable)
  - class org.biojava.bio.proteomics.ProteaseManager
  - class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.ProteinTools
  - class org.biojava.bio.seq.ragbag.RagbagAbstractSequence (implements org.biojava.bio.seq.Sequence)
    - class org.biojava.bio.seq.ragbag.RagbagAssembly
  - class org.biojava.bio.seq.ragbag.RagbagComponentDirectory.EmptyComponentDirectory (implements org.biojava.bio.seq.ragbag.RagbagComponentDirectory)
  - class org.biojava.bio.seq.ragbag.RagbagFeatureTypeCatcher (implements org.biojava.bio.seq.ragbag.RagbagFilterFactory)
  - class org.biojava.bio.seq.ragbag.RagbagFilteredCachedSeqFactory (implements org.biojava.bio.seq.ragbag.RagbagSequenceFactory)
  - class org.biojava.bio.seq.ragbag.RagbagFixedCacheSeqFactory (implements org.biojava.bio.seq.ragbag.RagbagSequenceFactory)
  - class org.biojava.bio.seq.ragbag.RagbagHashedComponentDirectory (implements org.biojava.bio.seq.ragbag.RagbagComponentDirectory)
  - class org.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder (implements org.biojava.bio.seq.io.SequenceBuilder)
  - class org.biojava.bio.seq.ragbag.RagbagMap.MapElement
  - class org.biojava.bio.seq.ragbag.RagbagMap.MapEnum (implements java.util.Enumeration)
  - class org.biojava.bio.seq.ragbag.RagbagSoftRefSeqFactory (implements org.biojava.bio.seq.ragbag.RagbagSequenceFactory)
  - class org.biojava.bio.seq.ragbag.RagbagUncachedSeqFactory (implements org.biojava.bio.seq.ragbag.RagbagSequenceFactory)
  - class java.io.RandomAccessFile (implements java.io.DataInput, java.io.DataOutput)
    - class org.biojava.utils.io.RAF
  - class java.io.Reader
    - class java.io.BufferedReader
      - class org.biojava.utils.io.CountedBufferedReader
    - class org.biojava.utils.io.RandomAccessReader
  - class org.biojava.bio.program.indexdb.Record.Impl (implements org.biojava.bio.program.indexdb.Record)
  - class org.biojava.bio.gui.sequence.RectangularImapRenderer (implements org.biojava.bio.gui.sequence.BeadFeatureRenderer, org.biojava.bio.gui.sequence.ImageMapRenderer, java.io.Serializable)
  - class java.lang.ref.Reference
    - class java.lang.ref.WeakReference
      - class org.biojava.utils.cache.KeyedWeakReference
  - class org.biojava.bio.program.tagvalue.RegexChanger (implements org.biojava.bio.program.tagvalue.ChangeTable.Changer)
  - class org.biojava.bio.program.tagvalue.RegexParser (implements org.biojava.bio.program.tagvalue.TagValueParser)
  - class org.biojava.bio.program.tagvalue.RegexSplitter (implements org.biojava.bio.program.tagvalue.ChangeTable.Splitter)
  - class org.biojava.directory.Registry
  - class org.biojava.directory.RegistryConfiguration.Composite (implements org.biojava.directory.RegistryConfiguration)
  - class org.biojava.directory.RegistryConfiguration.Impl (implements org.biojava.directory.RegistryConfiguration)
  - class org.biojava.bio.seq.RemoteFeature.Region
  - class org.biojava.utils.xml.ResourceEntityResolver (implements org.xml.sax.EntityResolver)
  - class org.biojava.bio.molbio.RestrictionEnzyme (implements java.io.Serializable)
  - class org.biojava.bio.molbio.RestrictionEnzymeManager
  - class org.biojava.bio.molbio.RestrictionMapper (implements org.biojava.bio.seq.SequenceAnnotator)
  - class org.biojava.bio.seq.RNATools
  - class org.biojava.bio.gui.sequence.RulerRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
  - class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor (implements org.xml.sax.ContentHandler)
  - class org.biojava.utils.stax.SAX2StAXAdaptor (implements org.xml.sax.ContentHandler)
  - class org.biojava.bio.dp.ScoreType.NullModel (implements org.biojava.bio.dp.ScoreType)
  - class org.biojava.bio.dp.ScoreType.Odds (implements org.biojava.bio.dp.ScoreType)
  - class org.biojava.bio.dp.ScoreType.Probability (implements org.biojava.bio.dp.ScoreType)
  - class org.biojava.bio.search.SearchContentAdapter (implements org.biojava.bio.search.SearchContentHandler)
  - class org.biojava.bio.search.SearchContentFilter (implements org.biojava.bio.search.SearchContentHandler)
  - class org.biojava.bio.seq.io.SeqAlignReadWrite
  - class org.biojava.bio.seq.io.SeqIOAdapter (implements org.biojava.bio.seq.io.SeqIOListener)
  - class org.biojava.bio.seq.io.SeqIOConstants
  - class org.biojava.bio.seq.io.SeqIOFilter (implements org.biojava.bio.seq.io.SeqIOListener)
  - class org.biojava.bio.seq.io.SeqIOTools
  - class org.biojava.bio.program.ssbind.SeqSimilarityAdapter (implements org.xml.sax.ContentHandler)
  - class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator (implements java.util.Comparator)
  - class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator (implements java.util.Comparator)
  - class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator (implements java.util.Comparator)
  - class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator (implements java.util.Comparator)
  - class org.biojava.bio.seq.io.SequenceBuilderBase (implements org.biojava.bio.seq.io.SequenceBuilder)
    - class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
    - class org.biojava.bio.seq.io.SimpleAssemblyBuilder
    - class org.biojava.bio.seq.io.SimpleSequenceBuilder
    - class org.biojava.bio.seq.io.SmartSequenceBuilder
  - class org.biojava.bio.seq.io.SequenceBuilderFilter (implements org.biojava.bio.seq.io.SequenceBuilder)
    - class org.biojava.bio.seq.io.EmblProcessor (implements org.biojava.utils.ParseErrorSource)
    - class org.biojava.bio.seq.io.FastaDescriptionLineParser
    - class org.biojava.bio.seq.io.GenbankProcessor (implements org.biojava.utils.ParseErrorSource)
      - class org.biojava.bio.seq.io.ProteinRefSeqProcessor
    - class org.biojava.bio.seq.io.OrganismParser
    - class org.biojava.bio.seq.io.SwissprotProcessor (implements org.biojava.utils.ParseErrorSource)
  - class org.biojava.bio.seq.distributed.SequenceDBDataSource (implements org.biojava.bio.seq.distributed.DistDataSource)
  - class org.biojava.bio.gui.sequence.SequencePanel.Border (implements java.io.Serializable, javax.swing.SwingConstants)
  - class org.biojava.bio.gui.sequence.SequencePoster.Border (implements java.io.Serializable, javax.swing.SwingConstants)
  - class org.biojava.bio.gui.sequence.SequenceRenderContext.Border (implements java.io.Serializable, javax.swing.SwingConstants)
  - class org.biojava.bio.program.gff.SequencesAsGFF
  - class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer (implements org.biojava.bio.program.ssaha.SequenceStreamer)
  - class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer (implements org.biojava.bio.program.ssaha.SequenceStreamer)
  - class org.biojava.bio.seq.SequenceTools
  - class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
  - class org.biojava.bio.gui.sequence.SequenceViewerSupport
  - class org.biojava.utils.Services
  - class org.biojava.stats.svm.SigmoidKernel (implements org.biojava.stats.svm.SVMKernel)
  - class org.biojava.bio.alignment.SimpleAlignmentElement (implements org.biojava.bio.alignment.AlignmentElement)
  - class org.biojava.bio.seq.io.agave.SimpleAnnotFilter (implements org.biojava.bio.seq.io.agave.AGAVEAnnotFilter)
    - class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
    - class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
  - class org.biojava.bio.dist.SimpleDistribution.Trainer (implements org.biojava.bio.dist.DistributionTrainer)
  - class org.biojava.bio.dist.SimpleDistributionTrainer (implements org.biojava.bio.dist.DistributionTrainer, java.io.Serializable)
  - class org.biojava.bio.dist.SimpleDistributionTrainerContext (implements org.biojava.bio.dist.DistributionTrainerContext, java.io.Serializable)
    - class org.biojava.bio.dp.SimpleModelTrainer (implements org.biojava.bio.dp.ModelTrainer, java.io.Serializable)
  - class org.biojava.bio.seq.SimpleFeatureRealizer (implements org.biojava.bio.seq.FeatureRealizer, java.io.Serializable)
  - class org.biojava.bio.symbol.SimpleGappedSymbolList.Block (implements java.io.Serializable)
  - class org.biojava.bio.program.gff.SimpleGFFRecord (implements org.biojava.bio.program.gff.GFFRecord)
  - class org.biojava.bio.seq.db.SimpleIndex (implements org.biojava.bio.seq.db.Index)
  - class org.biojava.stats.svm.SimpleItemValue (implements org.biojava.stats.svm.ItemValue)
  - class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver (implements org.biojava.bio.seq.RemoteFeature.Resolver)
  - class org.biojava.bio.seq.db.SimpleSequenceDBInstallation (implements org.biojava.bio.seq.db.SequenceDBInstallation)
  - class org.biojava.bio.seq.impl.SimpleSequenceFactory (implements org.biojava.bio.seq.SequenceFactory, java.io.Serializable)
  - class org.biojava.stats.svm.SimpleSVMTarget (implements org.biojava.stats.svm.SVMTarget)
  - class org.biojava.bio.symbol.SimpleSymbolListFactory (implements org.biojava.bio.symbol.SymbolListFactory)
  - class org.biojava.bio.symbol.SimpleSymbolPropertyTable (implements org.biojava.bio.symbol.SymbolPropertyTable)
  - class org.biojava.bio.gui.SimpleSymbolStyle (implements org.biojava.bio.gui.SymbolStyle)
  - class org.biojava.bio.taxa.SimpleTaxonFactory (implements org.biojava.bio.taxa.TaxonFactory)
  - class org.biojava.utils.SimpleThreadPool (implements org.biojava.utils.ThreadPool)
  - class org.biojava.bio.symbol.SimpleTranslationTable (implements java.io.Serializable, org.biojava.bio.symbol.TranslationTable)
    - class org.biojava.bio.symbol.SimpleReversibleTranslationTable (implements org.biojava.bio.symbol.ReversibleTranslationTable, java.io.Serializable)
  - class org.biojava.bio.dp.SimpleWeightMatrix (implements java.io.Serializable, org.biojava.bio.dp.WeightMatrix)
  - class org.biojava.bio.dp.onehead.SingleDPMatrix (implements org.biojava.bio.dp.DPMatrix, java.io.Serializable)
  - class org.biojava.stats.svm.SMORegressionTrainer
  - class org.biojava.stats.svm.SMOTrainer
  - class org.biojava.utils.cache.SoftReferenceCache (implements org.biojava.utils.cache.Cache)
  - class org.biojava.stats.svm.SparseVector (implements java.io.Serializable)
  - class org.biojava.stats.svm.SparseVector.NormalizingKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
  - class org.biojava.bio.program.unigene.SQLUnigeneFactory (implements org.biojava.bio.program.unigene.UnigeneFactory)
  - class org.biojava.bio.gui.StackedLogoPainter (implements org.biojava.bio.gui.LogoPainter)
  - class org.biojava.utils.StaticMemberPlaceHolder (implements java.io.Serializable)
  - class org.biojava.utils.stax.StAXContentHandlerBase (implements org.biojava.utils.stax.StAXContentHandler)
    - class org.biojava.utils.stax.BooleanElementHandlerBase
    - class org.biojava.utils.stax.ByteElementHandlerBase
    - class org.biojava.utils.stax.CharElementHandlerBase
    - class org.biojava.utils.stax.DoubleElementHandlerBase
    - class org.biojava.bio.program.xff.FeatureHandler
      - class org.biojava.bio.program.xff.StrandedFeatureHandler
    - class org.biojava.utils.stax.FloatElementHandlerBase
    - class org.biojava.utils.stax.IntElementHandlerBase
    - class org.biojava.bio.program.xff.LocationHandlerBase
    - class org.biojava.utils.stax.LongElementHandlerBase
    - class org.biojava.bio.seq.ragbag.RagbagMap
    - class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
    - class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
      - class org.biojava.bio.program.ssbind.AlignmentStAXHandler
      - class org.biojava.bio.program.ssbind.HeaderStAXHandler
      - class org.biojava.bio.program.ssbind.HitStAXHandler
      - class org.biojava.bio.program.ssbind.HSPStAXHandler
      - class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler
    - class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
      - class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
    - class org.biojava.bio.program.sax.blastxml.StAXFeatureHandler
      - class org.biojava.bio.program.sax.blastxml.BlastXMLParser
    - class org.biojava.bio.seq.io.game.StAXFeatureHandler
      - class org.biojava.bio.seq.io.game.GAMEAnnotationHandler (implements org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf)
      - class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler (implements org.biojava.bio.seq.io.game.GAMENameCallbackItf, org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf)
      - class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
      - class org.biojava.bio.seq.io.game.GAMEHandler
    - class org.biojava.bio.seq.io.game12.StAXFeatureHandler
      - class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
      - class org.biojava.bio.seq.io.game12.GAMEAspectHandler
      - class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
      - class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
      - class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
      - class org.biojava.bio.seq.io.game12.GAMEGeneHandler
      - class org.biojava.bio.seq.io.game12.GAMEHandler
      - class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
      - class org.biojava.bio.seq.io.game12.GAMESeqHandler
      - class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
        - class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.SeqRelHandler
      - class org.biojava.bio.seq.io.game12.GAMESpanHandler
    - class org.biojava.bio.seq.io.game.StAXPropertyHandler
      - class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
      - class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
      - class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler
      - class org.biojava.bio.seq.io.game.GAMEGenePropHandler (implements org.biojava.bio.seq.io.game.GAMENameCallbackItf)
      - class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
      - class org.biojava.bio.seq.io.game.GAMESeqPropHandler (implements org.biojava.bio.seq.io.game.GAMENameCallbackItf)
      - class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
      - class org.biojava.bio.seq.io.game.GAMESpanPropHandler
    - class org.biojava.utils.stax.StringElementHandlerBase
      - class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
      - class org.biojava.bio.seq.io.game.GAMENamePropHandler
      - class org.biojava.bio.seq.io.game.GAMETypePropHandler
      - class org.biojava.bio.program.xff.PropDetailHandler
    - class org.biojava.bio.program.xff.XFFFeatureSetHandler
    - class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
  - class org.biojava.bio.seq.io.agave.StAXContentHandlerBase (implements org.biojava.bio.seq.io.agave.StAXContentHandler)
    - class org.biojava.bio.seq.io.agave.StAXFeatureHandler
      - class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler (implements org.biojava.bio.seq.io.agave.SequenceHandler)
      - class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler (implements org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
      - class org.biojava.bio.seq.io.agave.AGAVECdsHandler
      - class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler (implements org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler (implements org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVECompResultHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
      - class org.biojava.bio.seq.io.agave.AGAVEContigHandler (implements org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
      - class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEGeneHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEHandler (implements org.biojava.bio.seq.io.agave.AGAVECallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
      - class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
      - class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
      - class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
      - class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
    - class org.biojava.bio.seq.io.agave.StAXPropertyHandler
      - class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
      - class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf)
      - class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
      - class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf)
  - class org.biojava.bio.program.ssbind.StAXHandlerBinding
  - class org.biojava.bio.gui.sequence.StopRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
  - class org.biojava.bio.seq.StrandedFeature.Strand (implements java.io.Serializable)
  - class org.biojava.bio.seq.StrandParser
  - class org.biojava.bio.seq.io.StreamReader (implements org.biojava.utils.ParseErrorListener, org.biojava.bio.seq.SequenceIterator)
  - class org.biojava.bio.seq.io.StreamWriter
  - class org.biojava.bio.proteomics.StructureTools
  - class org.biojava.bio.gui.sequence.SubPairwiseRenderContext (implements org.biojava.bio.gui.sequence.PairwiseRenderContext)
  - class org.biojava.bio.seq.SubSequence (implements org.biojava.bio.seq.Sequence)
  - class org.biojava.bio.gui.sequence.SubSequenceRenderContext (implements org.biojava.bio.gui.sequence.SequenceRenderContext)
  - class org.biojava.bio.symbol.SuffixTree (implements java.io.Serializable)
  - class org.biojava.bio.symbol.SuffixTree.SuffixNode (implements java.io.Serializable)
  - class org.biojava.stats.svm.tools.SuffixTreeKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
  - class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler (implements java.io.Serializable, org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler)
  - class org.biojava.stats.svm.tools.SVM_Light
  - class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
  - class org.biojava.stats.svm.SVMRegressionModel
  - class org.biojava.bio.seq.io.SwissprotProcessor.Factory (implements org.biojava.bio.seq.io.SequenceBuilderFactory, java.io.Serializable)
  - class org.biojava.bio.seq.db.SwissprotSequenceDB
  - class org.biojava.bio.seq.io.SymbolListCharSequence (implements java.lang.CharSequence)
  - class org.biojava.bio.symbol.SymbolListViews
  - class org.biojava.bio.gui.sequence.SymbolSequenceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
  - class org.biojava.bio.seq.io.SymbolTokenization.TokenType
  - class org.biojava.directory.SystemRegistry
  - class org.biojava.bio.seq.db.TabIndexStore (implements org.biojava.bio.seq.db.IndexStore, java.io.Serializable)
  - class org.biojava.bio.program.tagvalue.TagMapper
  - class org.biojava.bio.program.tagvalue.TagValue
  - class org.biojava.bio.program.tagvalue.TagValueWrapper (implements org.biojava.bio.program.tagvalue.TagValueListener)
    - class org.biojava.bio.program.tagvalue.RegexFieldFinder
    - class org.biojava.bio.program.tagvalue.TagDelegator
    - class org.biojava.bio.program.tagvalue.TagDropper
    - class org.biojava.bio.program.tagvalue.TagRenamer
    - class org.biojava.bio.program.tagvalue.ValueChanger
  - class org.biojava.bio.gui.TextBlock (implements org.biojava.bio.gui.BlockPainter)
  - class org.biojava.bio.gui.TextLogoPainter (implements org.biojava.bio.gui.LogoPainter)
  - class java.lang.Throwable (implements java.io.Serializable)
    - class java.lang.Error
      - class org.biojava.utils.NestedError
        - class org.biojava.bio.BioError
    - class java.lang.Exception
      - class org.biojava.utils.xml.AppException
      - class org.biojava.bio.program.gff.IgnoreRecordException
      - class org.biojava.utils.lsid.LifeScienceIdentifierParseException
      - class org.biojava.utils.NestedException
        - class org.biojava.bio.BioException
          - class org.biojava.bio.taxa.CircularReferenceException
          - class org.biojava.bio.symbol.IllegalAlphabetException
          - class org.biojava.bio.seq.db.IllegalIDException
          - class org.biojava.bio.symbol.IllegalSymbolException
          - class org.biojava.bio.dp.IllegalTransitionException
          - class org.biojava.bio.seq.io.ParseException
          - class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
        - class org.biojava.utils.ChangeVetoException
        - class org.biojava.utils.ParserException
        - class org.biojava.directory.RegistryException
          - class org.biojava.directory.ProviderNotFoundException
      - class java.lang.RuntimeException
        - class org.biojava.utils.NestedRuntimeException
          - class org.biojava.bio.BioRuntimeException
            - class org.biojava.bio.alignment.IllegalAlignmentEditException
  - class org.biojava.stats.svm.tools.Train
  - class org.biojava.bio.dp.TrainerTransition (implements java.io.Serializable)
  - class org.biojava.stats.svm.tools.TrainRegression
  - class org.biojava.bio.dp.Transition (implements java.io.Serializable)
  - class org.biojava.bio.symbol.UkkonenSuffixTree
  - class org.biojava.utils.Unchangeable (implements org.biojava.utils.Changeable)
    - class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB (implements org.biojava.bio.seq.db.SequenceDBLite)
    - class org.biojava.bio.seq.io.CharacterTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
    - class org.biojava.bio.program.das.DASSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
    - class org.biojava.bio.symbol.DoubleAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange (implements org.biojava.bio.symbol.BasisSymbol, java.io.Serializable)
    - class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
    - class org.biojava.bio.seq.db.flat.FlatSequenceDB (implements org.biojava.bio.seq.db.SequenceDBLite)
    - class org.biojava.bio.dist.GapDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
    - class org.biojava.bio.symbol.IntegerAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - class org.biojava.bio.symbol.RelabeledAlignment (implements org.biojava.bio.symbol.Alignment)
    - class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment (implements org.biojava.bio.symbol.Alignment)
    - class org.biojava.bio.dp.SimpleStatePath (implements java.io.Serializable, org.biojava.bio.dp.StatePath)
    - class org.biojava.bio.symbol.SymbolList.EmptySymbolList (implements java.io.Serializable, org.biojava.bio.symbol.SymbolList)
    - class org.biojava.bio.seq.ViewSequence (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence, java.io.Serializable)
      - class org.biojava.bio.seq.CircularView
    - class org.biojava.bio.seq.io.WordTokenization (implements java.io.Serializable, org.biojava.bio.seq.io.SymbolTokenization)
      - class org.biojava.bio.seq.io.CrossProductTokenization
      - class org.biojava.bio.seq.io.DoubleTokenization
      - class org.biojava.bio.seq.io.IntegerTokenization
      - class org.biojava.bio.seq.io.NameTokenization
  - class org.biojava.bio.program.unigene.UnigeneTools
  - class org.biojava.bio.seq.io.agave.UtilHelper
  - class org.biojava.bio.program.ssbind.ViewSequenceFactory
    - class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder (implements org.biojava.bio.search.SearchContentHandler)
    - class org.biojava.bio.program.ssbind.SimilarityPairBuilder (implements org.biojava.bio.search.SearchContentHandler)
  - class org.biojava.utils.cache.WeakCacheMap (implements org.biojava.utils.cache.CacheMap)
  - class org.biojava.bio.taxa.WeakTaxonFactory (implements org.biojava.bio.taxa.TaxonFactory)
  - class org.biojava.bio.dp.WeightMatrixAnnotator (implements org.biojava.bio.seq.SequenceAnnotator, java.io.Serializable)
  - class org.biojava.bio.program.xff.XFFTools
  - class org.biojava.bio.program.xff.XFFWriter
  - class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  - class org.biojava.utils.xml.XMLBeans
  - class org.biojava.utils.xml.XMLDispatcher (implements org.biojava.utils.xml.XMLPeerFactory)
  - class org.biojava.bio.dist.XMLDistributionWriter
  - class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
  - class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  - class org.biojava.bio.dp.XmlMarkovModel
  - class org.biojava.utils.xml.XMLPeerBuilder (implements org.xml.sax.DocumentHandler)
  - class org.biojava.bio.gui.sequence.ZiggyImapRenderer (implements org.biojava.bio.gui.sequence.ImageMapRenderer, java.io.Serializable)

## Interface Hierarchy

- interface org.biojava.utils.ActivityListener
- interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
- interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
- interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVECallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
- interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
- interface org.biojava.bio.alignment.AlignmentElement
- interface org.biojava.bio.seq.io.AlignmentFormat
- interface org.biojava.bio.AnnotationType
- interface org.biojava.utils.xml.AppEntry
- interface org.biojava.bibliography.BibRefQuery
- interface org.biojava.bibliography.BibRefSupport
- interface org.biojava.bio.gui.BlockPainter
- interface org.biojava.utils.cache.Cache
- interface org.biojava.utils.cache.CacheMap
- interface org.biojava.utils.cache.CacheReference
- interface org.biojava.bio.dp.twohead.CellCalculator
- interface org.biojava.bio.dp.twohead.CellCalculatorFactory
- interface org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker
- interface org.biojava.utils.Changeable
  - interface org.biojava.bio.symbol.Alignment
    - interface org.biojava.bio.alignment.ARAlignment
    - interface org.biojava.bio.dp.StatePath
    - interface org.biojava.bio.alignment.UnequalLengthAlignment
  - interface org.biojava.bio.symbol.Alphabet
    - interface org.biojava.bio.symbol.FiniteAlphabet
  - interface org.biojava.bio.symbol.AlphabetIndex
  - interface org.biojava.bio.Annotatable
    - interface org.biojava.bio.symbol.Alphabet
      - interface org.biojava.bio.symbol.FiniteAlphabet
    - interface org.biojava.bio.symbol.AtomicSymbol
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.symbol.BasisSymbol
      - interface org.biojava.bio.symbol.AtomicSymbol
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
        - interface org.biojava.bio.dp.State
          - interface org.biojava.bio.dp.DotState
          - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.seq.ComponentFeature
    - interface org.biojava.bio.dp.DotState
    - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - interface org.biojava.bio.seq.Feature (also extends org.biojava.bio.seq.FeatureHolder)
      - interface org.biojava.bio.seq.ComponentFeature
      - interface org.biojava.bio.seq.FramedFeature
      - interface org.biojava.bio.seq.homol.HomologyFeature
      - interface org.biojava.bio.seq.RemoteFeature
      - interface org.biojava.bio.molbio.RestrictionSite
      - interface org.biojava.bio.seq.homol.SimilarityPairFeature
      - interface org.biojava.bio.seq.StrandedFeature
        - interface org.biojava.bio.seq.ComponentFeature
        - interface org.biojava.bio.seq.FramedFeature
        - interface org.biojava.bio.seq.homol.HomologyFeature
        - interface org.biojava.bio.seq.RemoteFeature
        - interface org.biojava.bio.molbio.RestrictionSite
        - interface org.biojava.bio.seq.homol.SimilarityPairFeature
    - interface org.biojava.bio.seq.FeatureTypes.Repository
    - interface org.biojava.bio.seq.FeatureTypes.Type
    - interface org.biojava.bio.symbol.FiniteAlphabet
    - interface org.biojava.bio.seq.FramedFeature
    - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
    - interface org.biojava.bio.seq.homol.HomologyFeature
    - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.seq.RemoteFeature
    - interface org.biojava.bio.molbio.RestrictionSite
    - interface org.biojava.bio.search.SeqSimilaritySearchHit
    - interface org.biojava.bio.search.SeqSimilaritySearchResult
    - interface org.biojava.bio.search.SeqSimilaritySearchSubHit
    - interface org.biojava.bio.seq.Sequence (also extends org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.SymbolList)
      - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
    - interface org.biojava.bio.seq.homol.SimilarityPairFeature
    - interface org.biojava.bio.dp.State
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.seq.StrandedFeature
      - interface org.biojava.bio.seq.ComponentFeature
      - interface org.biojava.bio.seq.FramedFeature
      - interface org.biojava.bio.seq.homol.HomologyFeature
      - interface org.biojava.bio.seq.RemoteFeature
      - interface org.biojava.bio.molbio.RestrictionSite
      - interface org.biojava.bio.seq.homol.SimilarityPairFeature
    - interface org.biojava.bio.symbol.Symbol
      - interface org.biojava.bio.symbol.AtomicSymbol
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
        - interface org.biojava.bio.dp.State
          - interface org.biojava.bio.dp.DotState
          - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.symbol.BasisSymbol
        - interface org.biojava.bio.symbol.AtomicSymbol
          - interface org.biojava.bio.dp.DotState
          - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
          - interface org.biojava.bio.dp.ModelInState
          - interface org.biojava.bio.dp.State
            - interface org.biojava.bio.dp.DotState
            - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
            - interface org.biojava.bio.dp.ModelInState
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
        - interface org.biojava.bio.dp.State
          - interface org.biojava.bio.dp.DotState
          - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.seq.io.SymbolTokenization
    - interface org.biojava.bio.taxa.Taxon
    - interface org.biojava.bio.program.unigene.UnigeneCluster
  - interface org.biojava.bio.Annotation
  - interface org.biojava.bio.alignment.ARAlignment
  - interface org.biojava.bio.symbol.AtomicSymbol
    - interface org.biojava.bio.dp.DotState
    - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.dp.State
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
  - interface org.biojava.bio.symbol.BasisSymbol
    - interface org.biojava.bio.symbol.AtomicSymbol
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.dp.DotState
    - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.dp.State
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
  - interface org.biojava.bio.seq.ComponentFeature
  - interface org.biojava.bio.dist.Count
  - interface org.biojava.bio.dist.Distribution
    - interface org.biojava.bio.dist.OrderNDistribution
  - interface org.biojava.bio.dp.DotState
  - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
  - interface org.biojava.bio.seq.Feature (also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder)
    - interface org.biojava.bio.seq.ComponentFeature
    - interface org.biojava.bio.seq.FramedFeature
    - interface org.biojava.bio.seq.homol.HomologyFeature
    - interface org.biojava.bio.seq.RemoteFeature
    - interface org.biojava.bio.molbio.RestrictionSite
    - interface org.biojava.bio.seq.homol.SimilarityPairFeature
    - interface org.biojava.bio.seq.StrandedFeature
      - interface org.biojava.bio.seq.ComponentFeature
      - interface org.biojava.bio.seq.FramedFeature
      - interface org.biojava.bio.seq.homol.HomologyFeature
      - interface org.biojava.bio.seq.RemoteFeature
      - interface org.biojava.bio.molbio.RestrictionSite
      - interface org.biojava.bio.seq.homol.SimilarityPairFeature
  - interface org.biojava.bio.seq.FeatureHolder
    - interface org.biojava.bio.seq.ComponentFeature
    - interface org.biojava.bio.seq.Feature (also extends org.biojava.bio.Annotatable)
      - interface org.biojava.bio.seq.ComponentFeature
      - interface org.biojava.bio.seq.FramedFeature
      - interface org.biojava.bio.seq.homol.HomologyFeature
      - interface org.biojava.bio.seq.RemoteFeature
      - interface org.biojava.bio.molbio.RestrictionSite
      - interface org.biojava.bio.seq.homol.SimilarityPairFeature
      - interface org.biojava.bio.seq.StrandedFeature
        - interface org.biojava.bio.seq.ComponentFeature
        - interface org.biojava.bio.seq.FramedFeature
        - interface org.biojava.bio.seq.homol.HomologyFeature
        - interface org.biojava.bio.seq.RemoteFeature
        - interface org.biojava.bio.molbio.RestrictionSite
        - interface org.biojava.bio.seq.homol.SimilarityPairFeature
    - interface org.biojava.bio.seq.FramedFeature
    - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
    - interface org.biojava.bio.seq.homol.HomologyFeature
    - interface org.biojava.bio.seq.RealizingFeatureHolder
    - interface org.biojava.bio.seq.RemoteFeature
    - interface org.biojava.bio.molbio.RestrictionSite
    - interface org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.symbol.SymbolList)
      - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
    - interface org.biojava.bio.seq.homol.SimilarityPairFeature
    - interface org.biojava.bio.seq.StrandedFeature
      - interface org.biojava.bio.seq.ComponentFeature
      - interface org.biojava.bio.seq.FramedFeature
      - interface org.biojava.bio.seq.homol.HomologyFeature
      - interface org.biojava.bio.seq.RemoteFeature
      - interface org.biojava.bio.molbio.RestrictionSite
      - interface org.biojava.bio.seq.homol.SimilarityPairFeature
  - interface org.biojava.bio.seq.FeatureTypes.Repository
  - interface org.biojava.bio.seq.FeatureTypes.Type
  - interface org.biojava.bio.symbol.FiniteAlphabet
  - interface org.biojava.bio.seq.FramedFeature
  - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
  - interface org.biojava.bio.symbol.GappedSymbolList
    - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.seq.Sequence)
  - interface org.biojava.bio.seq.homol.HomologyFeature
  - interface org.biojava.bio.dp.MarkovModel
  - interface org.biojava.bio.dp.ModelInState
  - interface org.biojava.bio.dist.OrderNDistribution
  - interface org.biojava.bio.seq.RealizingFeatureHolder
  - interface org.biojava.bio.seq.RemoteFeature
  - interface org.biojava.bio.molbio.RestrictionSite
  - interface org.biojava.bio.search.SeqSimilaritySearchHit
  - interface org.biojava.bio.search.SeqSimilaritySearchResult
  - interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  - interface org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.SymbolList)
    - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
  - interface org.biojava.bio.seq.db.SequenceDB
  - interface org.biojava.bio.seq.db.SequenceDBLite
    - interface org.biojava.bio.seq.db.SequenceDB
  - interface org.biojava.bio.seq.homol.SimilarityPairFeature
  - interface org.biojava.bio.dp.State
    - interface org.biojava.bio.dp.DotState
    - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
    - interface org.biojava.bio.dp.ModelInState
  - interface org.biojava.bio.dp.StatePath
  - interface org.biojava.bio.seq.StrandedFeature
    - interface org.biojava.bio.seq.ComponentFeature
    - interface org.biojava.bio.seq.FramedFeature
    - interface org.biojava.bio.seq.homol.HomologyFeature
    - interface org.biojava.bio.seq.RemoteFeature
    - interface org.biojava.bio.molbio.RestrictionSite
    - interface org.biojava.bio.seq.homol.SimilarityPairFeature
  - interface org.biojava.bio.symbol.Symbol
    - interface org.biojava.bio.symbol.AtomicSymbol
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.symbol.BasisSymbol
      - interface org.biojava.bio.symbol.AtomicSymbol
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
        - interface org.biojava.bio.dp.State
          - interface org.biojava.bio.dp.DotState
          - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
          - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.dp.DotState
    - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
    - interface org.biojava.bio.dp.ModelInState
    - interface org.biojava.bio.dp.State
      - interface org.biojava.bio.dp.DotState
      - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
      - interface org.biojava.bio.dp.ModelInState
  - interface org.biojava.bio.symbol.SymbolList
    - interface org.biojava.bio.symbol.Alignment
      - interface org.biojava.bio.alignment.ARAlignment
      - interface org.biojava.bio.dp.StatePath
      - interface org.biojava.bio.alignment.UnequalLengthAlignment
    - interface org.biojava.bio.alignment.ARAlignment
    - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList, org.biojava.bio.seq.Sequence)
    - interface org.biojava.bio.symbol.GappedSymbolList
      - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.seq.Sequence)
    - interface org.biojava.bio.seq.Sequence (also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder)
      - interface org.biojava.bio.seq.GappedSequence (also extends org.biojava.bio.symbol.GappedSymbolList)
    - interface org.biojava.bio.dp.StatePath
    - interface org.biojava.bio.alignment.UnequalLengthAlignment
  - interface org.biojava.bio.seq.io.SymbolTokenization
  - interface org.biojava.bio.taxa.Taxon
  - interface org.biojava.bio.alignment.UnequalLengthAlignment
  - interface org.biojava.bio.program.unigene.UnigeneCluster
  - interface org.biojava.bio.program.unigene.UnigeneDB
- interface org.biojava.utils.ChangeHub
- interface org.biojava.bio.program.tagvalue.ChangeTable.Changer
- interface org.biojava.bio.program.tagvalue.ChangeTable.Splitter
- interface org.biojava.bio.chromatogram.Chromatogram
- interface org.biojava.bio.CollectionConstraint
- interface org.biojava.bio.program.blast2html.ColourCommand
- interface org.biojava.utils.Commitable
- interface org.biojava.utils.math.ComputeObject
- interface org.biojava.bio.program.blast2html.DatabaseURLGenerator
- interface java.io.DataInput
  - interface org.biojava.bio.program.abi.ABIFParser.DataAccess (also extends org.biojava.utils.io.Seekable)
- interface org.biojava.bio.program.ssaha.DataStore
- interface org.biojava.bio.program.ssaha.DataStoreFactory
- interface org.biojava.bio.seq.io.agave.DelegationManager
- interface org.biojava.utils.stax.DelegationManager
- interface org.biojava.bio.seq.distributed.DistDataSource
- interface org.biojava.bio.dist.DistributionFactory
- interface org.biojava.bio.dist.DistributionTrainer
- interface org.biojava.bio.dist.DistributionTrainerContext
  - interface org.biojava.bio.dp.ModelTrainer
- interface org.biojava.bio.dp.DPFactory
- interface org.biojava.bio.dp.DPMatrix
- interface org.biojava.bio.alignment.EditableAlignment
- interface org.biojava.bio.program.xff.ElementRecognizer
- interface org.biojava.bio.seq.io.agave.ElementRecognizer
- interface org.biojava.bio.seq.io.game.ElementRecognizer
- interface java.util.EventListener
  - interface org.biojava.utils.candy.CandyFinder
  - interface org.biojava.utils.candy.CandyVocabulary
  - interface org.biojava.utils.ChangeListener
  - interface org.biojava.utils.ParseErrorListener
  - interface java.beans.PropertyChangeListener
    - interface org.biojava.utils.candy.CandyFinder
    - interface org.biojava.utils.candy.CandyVocabulary
  - interface org.biojava.bio.gui.sequence.SequenceViewerListener
  - interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener
  - interface org.biojava.stats.svm.TrainingListener
- interface org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker
- interface org.biojava.bio.seq.FeatureRealizer
- interface org.biojava.bio.gui.sequence.FeatureRenderer
  - interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
  - interface org.biojava.bio.gui.sequence.ImageMapRenderer
- interface org.biojava.bio.seq.FilterUtils.FilterTransformer
- interface org.biojava.bio.seq.Frame
- interface org.biojava.bio.symbol.FuzzyPointLocation.PointResolver
- interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
- interface org.biojava.bio.seq.io.game.GAMENameCallbackItf
- interface org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf
- interface org.biojava.bio.program.gff.GFFDocumentHandler
- interface org.biojava.bio.program.gff.GFFErrorHandler
- interface org.biojava.bio.program.gff.GFFRecord
- interface org.biojava.bio.program.gff.GFFRecordFilter
- interface org.biojava.bio.seq.homol.Homology
- interface org.biojava.bio.seq.homol.HomologyDB
- interface org.biojava.utils.lsid.Identifiable
- interface org.biojava.bio.seq.db.IDMaker
- interface org.biojava.bio.gui.sequence.ImageMap
- interface org.biojava.bio.seq.db.Index
- interface org.biojava.bio.program.indexdb.IndexStore
- interface org.biojava.bio.seq.db.IndexStore
- interface org.biojava.utils.xml.Initializable
- interface org.biojava.stats.svm.ItemValue
- interface org.biojava.bio.gui.sequence.LabelRenderer
- interface org.biojava.bio.symbol.Location
- interface org.biojava.bio.gui.LogoContext
- interface org.biojava.bio.gui.LogoPainter
- interface org.biojava.bio.gui.sequence.OverlayMarker
- interface org.biojava.bio.symbol.Packing
- interface org.biojava.bio.dp.twohead.PairDPCursor
- interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer
- interface org.biojava.utils.ParseErrorSource
- interface org.biojava.bio.seq.projection.Projection
- interface org.biojava.bio.seq.projection.ProjectionContext
- interface org.biojava.bio.seq.projection.ProjectionEngine.Instantiator
- interface org.biojava.bio.PropertyConstraint
- interface org.biojava.bio.program.phred.Qualitative
- interface org.biojava.bio.alignment.QualitativeAlignment
- interface org.biojava.bio.seq.ragbag.RagbagComponentDirectory
- interface org.biojava.bio.seq.ragbag.RagbagFileParserFactory
- interface org.biojava.bio.seq.ragbag.RagbagFilterFactory
- interface org.biojava.bio.seq.ragbag.RagbagSequenceFactory
- interface org.biojava.bio.program.indexdb.Record
- interface org.biojava.directory.RegistryConfiguration
- interface org.biojava.bio.seq.RemoteFeature.Resolver
- interface org.biojava.bio.dp.ScoreType
- interface org.biojava.bio.search.SearchContentHandler
  - interface org.biojava.bio.search.SearchBuilder
- interface org.biojava.bio.program.ssaha.SearchListener
- interface org.biojava.utils.io.Seekable
  - interface org.biojava.bio.program.abi.ABIFParser.DataAccess (also extends java.io.DataInput)
- interface org.biojava.bio.seq.io.SeqIOListener
  - interface org.biojava.bio.seq.io.SeqFileFormer
  - interface org.biojava.bio.seq.io.SequenceBuilder
- interface org.biojava.bio.search.SeqSimilaritySearcher
- interface org.biojava.bio.seq.SequenceAnnotator
- interface org.biojava.bio.seq.io.SequenceBuilderFactory
- interface org.biojava.bio.seq.db.SequenceDBInstallation
- interface org.biojava.directory.SequenceDBProvider
- interface org.biojava.bio.seq.SequenceFactory
- interface org.biojava.bio.seq.io.SequenceFormat
- interface org.biojava.bio.seq.io.agave.SequenceHandler
- interface org.biojava.bio.seq.SequenceIterator
- interface org.biojava.bio.gui.sequence.SequenceRenderer
- interface org.biojava.bio.program.ssaha.SequenceStreamer
- interface java.io.Serializable
  - interface org.biojava.bio.seq.FeatureFilter
    - interface org.biojava.bio.seq.OptimizableFilter
  - interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
  - interface org.biojava.bio.seq.OptimizableFilter
- interface org.biojava.bio.seq.io.agave.StAXContentHandler
- interface org.biojava.utils.stax.StAXContentHandler
  - interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler
  - interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
  - interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler
- interface org.biojava.bio.program.ssbind.StAXHandlerFactory
- interface org.biojava.bio.seq.io.agave.StAXHandlerFactory
- interface org.biojava.bio.seq.io.game.StAXHandlerFactory
- interface org.biojava.bio.seq.io.game12.StAXHandlerFactory
- interface org.biojava.bio.dp.StoppingCriteria
- interface org.biojava.bio.seq.io.StreamParser
- interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler
- interface org.biojava.stats.svm.SVMClassifierModel
- interface org.biojava.stats.svm.SVMKernel
- interface org.biojava.stats.svm.SVMTarget
- interface javax.swing.SwingConstants
  - interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  - interface org.biojava.bio.gui.sequence.SequenceRenderContext
    - interface org.biojava.bio.gui.sequence.PairwiseRenderContext
- interface org.biojava.bio.symbol.SymbolListFactory
- interface org.biojava.bio.symbol.SymbolPropertyTable
- interface org.biojava.bio.seq.io.SymbolReader
- interface org.biojava.bio.gui.SymbolStyle
- interface org.biojava.bio.program.tagvalue.TagValueContext
- interface org.biojava.bio.program.tagvalue.TagValueListener
- interface org.biojava.bio.program.tagvalue.TagValueParser
- interface org.biojava.bio.taxa.TaxonFactory
- interface org.biojava.bio.taxa.TaxonParser
- interface org.biojava.utils.ThreadPool
- interface org.biojava.bio.dp.Trainable
  - interface org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State)
- interface org.biojava.bio.dp.TrainingAlgorithm
- interface org.biojava.stats.svm.TrainingContext
- interface org.biojava.bio.dp.TransitionTrainer
- interface org.biojava.bio.symbol.TranslationTable
  - interface org.biojava.bio.symbol.ReversibleTranslationTable
- interface org.biojava.bio.program.unigene.UnigeneFactory
- interface org.biojava.utils.net.URLFactory
- interface org.biojava.bio.program.blast2html.URLGeneratorFactory
- interface org.biojava.bio.dp.WeightMatrix
- interface org.biojava.bio.program.xff.XFFHelper
- interface org.biojava.bio.program.xff.XFFPartHandlerFactory
- interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory
- interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory
- interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter
- interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter
- interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory
- interface org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter
- interface org.biojava.utils.xml.XMLPeerFactory
- interface org.biojava.utils.xml.XMLWritable
- interface org.biojava.utils.xml.XMLWriter