## Hierarchy For All Packages

Package Hierarchies:
  GNOME, org.acedb, org.acedb.seq, org.acedb.socket, org.acedb.staticobj, org.Biocorba.Seqcore, org.biojava.bio, org.biojava.bio.dist, org.biojava.bio.dp, org.biojava.bio.gui, org.biojava.bio.gui.sequence, org.biojava.bio.program, org.biojava.bio.program.gff, org.biojava.bio.search, org.biojava.bio.seq, org.biojava.bio.seq.db, org.biojava.bio.seq.io, org.biojava.bio.symbol, org.biojava.bridge.Biocorba.Seqcore, org.biojava.bridge.GNOME, org.biojava.stats.svm, org.biojava.stats.svm.tools, org.biojava.utils, org.biojava.utils.contract, org.biojava.utils.xml

## Class Hierarchy

- class java.lang.Object
  - class org.biojava.bio.symbol.AbstractAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet)
    - class org.biojava.bio.symbol.SimpleAlphabet (implements java.io.Serializable)
  - class org.biojava.bio.dist.AbstractDistribution (implements org.biojava.bio.dist.Distribution)
    - class org.biojava.bio.dist.DNADistribution (implements java.io.Serializable)
    - class org.biojava.bio.dist.PairDistribution (implements java.io.Serializable)
    - class org.biojava.bio.dist.SimpleDistribution (implements java.io.Serializable)
    - 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.SimpleFeatureHolder
  - 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.symbol.AbstractSymbolList (implements org.biojava.bio.symbol.SymbolList)
    - class org.biojava.bio.symbol.GappedSymbolList (implements java.io.Serializable)
    - class org.biojava.bio.symbol.OrderNSymbolList (implements java.io.Serializable)
    - class org.biojava.bio.symbol.ReverseSymbolList (implements java.io.Serializable)
    - class org.biojava.bio.symbol.SimpleAlignment (implements org.biojava.bio.symbol.Alignment, java.io.Serializable)
    - class org.biojava.bio.symbol.SimpleSymbolList (implements java.io.Serializable)
    - class org.biojava.bio.symbol.TranslatedSymbolList (implements org.biojava.bio.symbol.SymbolList)
    - class org.biojava.bio.symbol.WindowedSymbolList (implements java.io.Serializable)
  - 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.acedb.Ace
  - class org.acedb.seq.AceAnnotation (implements org.biojava.bio.Annotation)
  - class org.acedb.AcePerlParser
  - class org.acedb.seq.AceSequence (implements org.biojava.bio.seq.Sequence)
  - class org.acedb.seq.AceSequenceDB (implements org.biojava.bio.seq.db.SequenceDB)
  - class org.acedb.AceURL
  - class org.acedb.AceUtils
  - class org.biojava.bio.symbol.AllTokensAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
  - class org.biojava.bio.symbol.Alphabet.EmptyAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
  - class org.biojava.bio.symbol.AlphabetManager
  - class org.biojava.bio.symbol.AlphabetManager.ListWrapper
  - class org.biojava.bio.seq.db.AnnotatedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
  - class org.biojava.bio.Annotation.EmptyAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
  - class org.Biocorba.Seqcore.AnonymousSeqHelper
  - class org.Biocorba.Seqcore.AnonymousSeqHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.biojava.bio.gui.BarLogoPainter (implements org.biojava.bio.gui.LogoPainter)
  - class org.biojava.bio.gui.sequence.BasicFeatureRenderer (implements org.biojava.bio.gui.sequence.FeatureRenderer)
  - class org.biojava.bio.seq.db.CachingSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
  - class org.biojava.stats.svm.tools.ClassifierExample
  - class org.biojava.stats.svm.tools.Classify
  - class org.biojava.bio.dist.ComplementaryDistribution (implements org.biojava.bio.dist.Distribution, java.io.Serializable)
  - 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 org.biojava.bio.gui.SequencePanel (implements javax.swing.SwingConstants)
  - class org.biojava.bio.symbol.CompoundLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
  - class org.biojava.utils.contract.Contract
  - class org.biojava.bio.symbol.CrossProductSymbolNameParser (implements java.io.Serializable, org.biojava.bio.symbol.SymbolParser)
  - class org.biojava.bio.seq.io.DefaultDescriptionReader (implements org.biojava.bio.seq.io.FastaDescriptionReader, java.io.Serializable)
  - 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.dist.DistributionFactory.DefaultDistributionFactory (implements org.biojava.bio.dist.DistributionFactory, 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.symbol.DoubleAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
  - class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
  - class org.biojava.bio.dp.DP
    - class org.biojava.bio.dp.PairwiseDP (implements java.io.Serializable)
  - class org.biojava.bio.dp.DP.ReverseIterator (implements java.util.Iterator, java.io.Serializable)
  - class org.biojava.bio.dp.DPFactory
  - class org.biojava.bio.seq.io.EmblFormat (implements org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.Biocorba.Seqcore.EndOfStreamHelper
  - class org.Biocorba.Seqcore.EndOfStreamHolder (implements org.omg.CORBA.portable.Streamable)
  - class java.util.EventObject (implements java.io.Serializable)
    - class org.biojava.bio.dp.ModelChangeEvent
      - class org.biojava.bio.dp.TransitionEvent
    - class org.biojava.stats.svm.TrainingEvent
  - class org.biojava.bio.seq.io.FastaFormat (implements org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.seq.Feature.Template (implements java.io.Serializable)
    - class org.biojava.bio.seq.StrandedFeature.Template
  - class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter (implements org.biojava.bio.seq.Feature)
  - class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer (implements java.beans.PropertyChangeListener, org.biojava.bio.gui.sequence.SequenceRenderer)
  - class org.biojava.bio.seq.FeatureFilter.AcceptAllFilter (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.And (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.BySource (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.ByType (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.ContainedByLocation (implements org.biojava.bio.seq.FeatureFilter)
  - class org.biojava.bio.seq.FeatureFilter.Not (implements org.biojava.bio.seq.FeatureFilter)
  - 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.FeatureFilter)
  - class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder (implements org.biojava.bio.seq.FeatureHolder)
  - class org.biojava.bio.symbol.FixedWidthParser (implements java.io.Serializable, org.biojava.bio.symbol.SymbolParser)
  - class org.biojava.bio.dist.GapDistribution (implements org.biojava.bio.dist.Distribution)
  - class org.biojava.bio.seq.io.GenbankFormat (implements org.biojava.bio.seq.io.SequenceFormat, java.io.Serializable)
  - class org.biojava.bio.seq.GeneticCode
  - 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.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.GFFWriter (implements org.biojava.bio.program.gff.GFFDocumentHandler)
  - class org.biojava.bio.seq.db.HashSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, java.io.Serializable)
  - 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.seq.db.IndexedSequenceDB (implements org.biojava.bio.seq.db.SequenceDB, 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.stats.svm.LinearKernel (implements java.io.Serializable, org.biojava.stats.svm.SVMKernel)
  - class org.biojava.bio.symbol.Location.EmptyLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
  - class org.biojava.bio.symbol.Location.LocationComparator (implements java.util.Comparator, java.io.Serializable)
  - class org.biojava.bio.program.Meme
  - class org.biojava.bio.dp.ModelView (implements org.biojava.bio.dp.MarkovModel)
  - class org.biojava.bio.dp.ModelView.ViewTransitionTrainer (implements java.io.Serializable, org.biojava.bio.dp.TransitionTrainer)
  - class org.biojava.bio.symbol.NameParser (implements java.io.Serializable, org.biojava.bio.symbol.SymbolParser)
  - class org.Biocorba.Seqcore.NameValueSet (implements org.omg.CORBA.portable.IDLEntity)
  - class org.Biocorba.Seqcore.NameValueSetHelper
  - class org.Biocorba.Seqcore.NameValueSetHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.NameValueSetListHelper
  - class org.Biocorba.Seqcore.NameValueSetListHolder (implements org.omg.CORBA.portable.Streamable)
  - 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.omg.CORBA.portable.ObjectImpl (implements org.omg.CORBA.Object)
    - class org.Biocorba.Seqcore._AnonymousSeqStub (implements org.Biocorba.Seqcore.AnonymousSeq)
    - class org.Biocorba.Seqcore._PrimarySeqDBStub (implements org.Biocorba.Seqcore.PrimarySeqDB)
    - class org.Biocorba.Seqcore._PrimarySeqIteratorStub (implements org.Biocorba.Seqcore.PrimarySeqIterator)
    - class org.Biocorba.Seqcore._PrimarySeqStub (implements org.Biocorba.Seqcore.PrimarySeq)
    - class org.Biocorba.Seqcore._SeqDBStub (implements org.Biocorba.Seqcore.SeqDB)
    - class org.Biocorba.Seqcore._SeqFeatureIteratorStub (implements org.Biocorba.Seqcore.SeqFeatureIterator)
    - class org.Biocorba.Seqcore._SeqFeatureStub (implements org.Biocorba.Seqcore.SeqFeature)
    - class org.Biocorba.Seqcore._SeqStub (implements org.Biocorba.Seqcore.Seq)
    - class GNOME._UnknownStub (implements GNOME.Unknown)
    - class org.omg.CORBA.DynamicImplementation
      - class org.Biocorba.Seqcore._AnonymousSeqImplBase (implements org.Biocorba.Seqcore.AnonymousSeq)
        - class org.Biocorba.Seqcore._AnonymousSeq_Tie
      - class org.Biocorba.Seqcore._PrimarySeqDBImplBase (implements org.Biocorba.Seqcore.PrimarySeqDB)
        - class org.Biocorba.Seqcore._PrimarySeqDB_Tie
      - class org.Biocorba.Seqcore._PrimarySeqImplBase (implements org.Biocorba.Seqcore.PrimarySeq)
        - class org.Biocorba.Seqcore._PrimarySeq_Tie
      - class org.Biocorba.Seqcore._PrimarySeqIteratorImplBase (implements org.Biocorba.Seqcore.PrimarySeqIterator)
        - class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
      - class org.Biocorba.Seqcore._SeqDBImplBase (implements org.Biocorba.Seqcore.SeqDB)
        - class org.Biocorba.Seqcore._SeqDB_Tie
      - class org.Biocorba.Seqcore._SeqFeatureImplBase (implements org.Biocorba.Seqcore.SeqFeature)
        - class org.Biocorba.Seqcore._SeqFeature_Tie
      - class org.Biocorba.Seqcore._SeqFeatureIteratorImplBase (implements org.Biocorba.Seqcore.SeqFeatureIterator)
        - class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
      - class org.Biocorba.Seqcore._SeqImplBase (implements org.Biocorba.Seqcore.Seq)
        - class org.Biocorba.Seqcore._Seq_Tie
      - class GNOME._UnknownImplBase (implements GNOME.Unknown)
        - class GNOME._Unknown_Tie
  - class org.biojava.utils.ObjectUtil
  - class org.Biocorba.Seqcore.OutOfRangeHelper
  - class org.Biocorba.Seqcore.OutOfRangeHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.biojava.bio.OverlayAnnotation (implements org.biojava.bio.Annotation)
  - class org.biojava.bio.dp.PairDPMatrix (implements org.biojava.bio.dp.DPMatrix, java.io.Serializable)
  - class org.biojava.bio.gui.PlainStyle (implements org.biojava.bio.gui.SymbolStyle)
  - class org.biojava.bio.symbol.PointLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
  - class org.Biocorba.Seqcore.primaryidListHelper
  - class org.Biocorba.Seqcore.primaryidListHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.PrimarySeqDBHelper
  - class org.Biocorba.Seqcore.PrimarySeqDBHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.PrimarySeqHelper
  - class org.Biocorba.Seqcore.PrimarySeqHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
  - class org.Biocorba.Seqcore.PrimarySeqIteratorHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.biojava.bio.seq.ProteinTools
  - class org.biojava.bio.symbol.RangeLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
  - class org.Biocorba.Seqcore.RequestTooLargeHelper
  - class org.Biocorba.Seqcore.RequestTooLargeHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.SeqDBHelper
  - class org.Biocorba.Seqcore.SeqDBHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.SeqFeatureHelper
  - class org.Biocorba.Seqcore.SeqFeatureHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
  - class org.Biocorba.Seqcore.SeqFeatureIteratorHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.SeqFeatureListHelper
  - class org.Biocorba.Seqcore.SeqFeatureListHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.SeqHelper
  - class org.Biocorba.Seqcore.SeqHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.Biocorba.Seqcore.SeqType (implements org.omg.CORBA.portable.IDLEntity)
  - class org.Biocorba.Seqcore.SeqTypeHelper
  - class org.Biocorba.Seqcore.SeqTypeHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter (implements org.biojava.bio.seq.db.SequenceDB)
  - class org.biojava.bridge.Biocorba.Seqcore.SequenceIteratorAdapter (implements org.biojava.bio.seq.SequenceIterator)
  - class org.biojava.bio.gui.SequencePanel.Border (implements java.io.Serializable, javax.swing.SwingConstants)
  - class org.biojava.bio.program.gff.SequencesAsGFF
  - class org.biojava.stats.svm.SigmoidKernel (implements org.biojava.stats.svm.SVMKernel)
  - class org.biojava.bio.SimpleAnnotation (implements org.biojava.bio.Annotation, java.io.Serializable)
  - class org.biojava.bio.symbol.SimpleAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol)
    - 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.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.dp.SimpleEmissionState (implements org.biojava.bio.dp.EmissionState, java.io.Serializable)
    - class org.biojava.bio.dp.MagicalState
  - class org.biojava.bio.seq.io.SimpleFeatureBuilder (implements org.biojava.bio.seq.io.FeatureBuilder, java.io.Serializable)
  - class org.biojava.bio.seq.SimpleFeatureRealizer (implements org.biojava.bio.seq.FeatureRealizer, java.io.Serializable)
  - class org.biojava.bio.program.gff.SimpleGFFRecord (implements org.biojava.bio.program.gff.GFFRecord)
  - class org.biojava.stats.svm.SimpleItemValue (implements org.biojava.stats.svm.ItemValue)
  - class org.biojava.bio.dp.SimpleMarkovModel (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
    - class org.biojava.bio.dp.ProfileHMM
  - class org.biojava.bio.search.SimpleSeqSimilaritySearchHit (implements java.lang.Cloneable, org.biojava.bio.search.SeqSimilaritySearchHit)
  - class org.biojava.bio.search.SimpleSeqSimilaritySearchResult (implements java.lang.Cloneable, org.biojava.bio.search.SeqSimilaritySearchResult)
  - class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit (implements java.lang.Cloneable, org.biojava.bio.search.SeqSimilaritySearchSubHit)
  - class org.biojava.bio.seq.SimpleSequence (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence)
  - class org.biojava.bio.seq.db.SimpleSequenceDBInstallation (implements org.biojava.bio.seq.db.SequenceDBInstallation)
  - class org.biojava.bio.seq.SimpleSequenceFactory (implements org.biojava.bio.seq.SequenceFactory, java.io.Serializable)
  - class org.biojava.bio.dp.SimpleStatePath (implements java.io.Serializable, org.biojava.bio.dp.StatePath)
  - class org.biojava.stats.svm.SimpleSVMTarget (implements org.biojava.stats.svm.SVMTarget)
  - class org.biojava.bio.symbol.SimpleSymbol (implements java.io.Serializable, org.biojava.bio.symbol.Symbol)
  - class org.biojava.bio.gui.SimpleSymbolStyle (implements org.biojava.bio.gui.SymbolStyle)
  - class org.biojava.bio.dp.SimpleTransitionTrainer (implements java.io.Serializable, org.biojava.bio.dp.TransitionTrainer)
  - class org.biojava.bio.symbol.SimpleTranslationTable (implements java.io.Serializable, org.biojava.bio.symbol.TranslationTable)
  - class org.biojava.bio.dp.SimpleWeightMatrix (implements java.io.Serializable, org.biojava.bio.dp.WeightMatrix)
  - class org.biojava.bio.symbol.SingletonAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
  - class org.biojava.stats.svm.SMORegressionTrainer
  - class org.biojava.stats.svm.SMOTrainer
  - class org.acedb.socket.SocketDriver (implements org.acedb.Driver)
  - class org.acedb.socket.SocketResultSet (implements org.acedb.AceSet)
  - 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.acedb.staticobj.StaticAceNode (implements org.acedb.AceNode)
    - class org.acedb.staticobj.StaticAceObject (implements org.acedb.AceObject)
    - class org.acedb.staticobj.StaticDateValue (implements org.acedb.DateValue)
    - class org.acedb.staticobj.StaticFloatValue (implements org.acedb.FloatValue)
    - class org.acedb.staticobj.StaticIntValue (implements org.acedb.IntValue)
    - class org.acedb.staticobj.StaticModelNode (implements org.acedb.ModelNode)
      - class org.acedb.staticobj.StaticModelInclude (implements org.acedb.ModelInclude)
      - class org.acedb.staticobj.StaticModelReference (implements org.acedb.ModelReference)
      - class org.acedb.staticobj.StaticModelType (implements org.acedb.ModelType)
    - class org.acedb.staticobj.StaticReference (implements org.acedb.Reference)
    - class org.acedb.staticobj.StaticStringValue (implements org.acedb.StringValue)
  - class org.acedb.staticobj.StaticAceSet (implements org.acedb.AceSet)
  - class org.biojava.utils.StaticMemberPlaceHolder (implements java.io.Serializable)
  - class org.biojava.bio.seq.StrandedFeature.Strand (implements java.io.Serializable)
  - class org.biojava.bio.seq.io.StreamReader (implements org.biojava.bio.seq.SequenceIterator)
  - class org.biojava.bio.seq.io.StreamReader.Context
  - class org.biojava.bio.seq.io.StreamWriter
  - class org.Biocorba.Seqcore.stringListHelper
  - class org.Biocorba.Seqcore.stringListHolder (implements org.omg.CORBA.portable.Streamable)
  - 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.symbol.SymbolList.EmptySymbolList (implements java.io.Serializable, org.biojava.bio.symbol.SymbolList)
  - class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter (implements org.biojava.bio.symbol.SymbolList)
    - class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter (implements org.biojava.bio.seq.Sequence)
  - class org.biojava.bio.gui.sequence.SymbolSequenceRenderer (implements org.biojava.bio.gui.sequence.SequenceRenderer)
  - 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.bio.BioError
        - class org.acedb.AceError
    - class java.lang.Exception
      - class org.biojava.bio.BioException
        - class org.acedb.AceException
          - class org.acedb.AceURLException
        - class org.biojava.bio.symbol.IllegalAlphabetException
        - class org.biojava.bio.symbol.IllegalSymbolException
        - class org.biojava.bio.dp.IllegalTransitionException
      - class org.biojava.bio.program.gff.IgnoreRecordException
      - class org.biojava.bio.dp.ModelVetoException
      - class org.biojava.utils.ParserException
      - class java.lang.RuntimeException
        - class org.biojava.utils.contract.AssertionFailedException
        - class java.lang.IllegalArgumentException
          - class org.biojava.utils.contract.PreconditionNotMetException
        - class org.biojava.utils.contract.PostconditionNotMetException
      - class org.omg.CORBA.UserException (implements org.omg.CORBA.portable.IDLEntity)
        - class org.Biocorba.Seqcore.EndOfStream (implements org.omg.CORBA.portable.IDLEntity)
        - class org.Biocorba.Seqcore.OutOfRange (implements org.omg.CORBA.portable.IDLEntity)
        - class org.Biocorba.Seqcore.RequestTooLarge (implements org.omg.CORBA.portable.IDLEntity)
        - class org.Biocorba.Seqcore.UnableToProcess (implements org.omg.CORBA.portable.IDLEntity)
  - class org.biojava.bio.symbol.TokenParser (implements java.io.Serializable, org.biojava.bio.symbol.SymbolParser)
  - 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.Biocorba.Seqcore.UnableToProcessHelper
  - class org.Biocorba.Seqcore.UnableToProcessHolder (implements org.omg.CORBA.portable.Streamable)
  - class GNOME.UnknownHelper
  - class GNOME.UnknownHolder (implements org.omg.CORBA.portable.Streamable)
  - class org.biojava.bridge.GNOME.UnknownImpl (implements GNOME._Unknown_Operations)
    - class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl (implements org.Biocorba.Seqcore._AnonymousSeq_Operations)
      - class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl (implements org.Biocorba.Seqcore._PrimarySeq_Operations)
        - class org.biojava.bridge.Biocorba.Seqcore.SeqImpl (implements org.Biocorba.Seqcore._Seq_Operations)
    - class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl (implements org.Biocorba.Seqcore._PrimarySeqDB_Operations)
      - class org.biojava.bridge.Biocorba.Seqcore.SeqDBImpl (implements org.Biocorba.Seqcore._SeqDB_Operations)
    - class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqIteratorImpl (implements org.Biocorba.Seqcore._PrimarySeqIterator_Operations)
    - class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl (implements org.Biocorba.Seqcore._SeqFeature_Operations)
    - class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureIteratorImpl (implements org.Biocorba.Seqcore._SeqFeatureIterator_Operations)
  - class java.net.URLStreamHandler
    - class org.acedb.Handler
  - class org.biojava.bio.seq.ViewSequence (implements org.biojava.bio.seq.RealizingFeatureHolder, org.biojava.bio.seq.Sequence)
  - class org.biojava.bio.dp.WeightMatrixAnnotator (implements org.biojava.bio.seq.SequenceAnnotator, java.io.Serializable)
  - class org.biojava.bio.dp.WMAsMM (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
  - class org.biojava.utils.xml.XMLDispatcher (implements org.biojava.utils.xml.XMLPeerFactory)
  - class org.biojava.bio.dp.XmlMarkovModel
  - class org.biojava.utils.xml.XMLPeerBuilder (implements org.xml.sax.DocumentHandler)

## Interface Hierarchy

- interface GNOME._Unknown_Operations
  - interface org.Biocorba.Seqcore._AnonymousSeq_Operations
    - interface org.Biocorba.Seqcore._PrimarySeq_Operations
      - interface org.Biocorba.Seqcore._Seq_Operations
  - interface org.Biocorba.Seqcore._PrimarySeqDB_Operations
    - interface org.Biocorba.Seqcore._SeqDB_Operations
  - interface org.Biocorba.Seqcore._PrimarySeqIterator_Operations
  - interface org.Biocorba.Seqcore._SeqFeature_Operations
  - interface org.Biocorba.Seqcore._SeqFeatureIterator_Operations
- interface org.acedb.AceSet
  - interface org.acedb.AceNode
    - interface org.acedb.AceElement
    - interface org.acedb.AceObject
    - interface org.acedb.AceValue
    - interface org.acedb.DateValue
    - interface org.acedb.FloatValue
    - interface org.acedb.IntValue
    - interface org.acedb.ModelNode
      - interface org.acedb.ModelInclude
      - interface org.acedb.ModelReference
      - interface org.acedb.ModelType
    - interface org.acedb.Reference
    - interface org.acedb.StringValue
- interface org.biojava.bio.seq.io.AlignmentFormat
- interface org.biojava.bio.Annotatable
  - interface org.biojava.bio.symbol.Alphabet
    - interface org.biojava.bio.symbol.CrossProductAlphabet
    - interface org.biojava.bio.symbol.FiniteAlphabet
  - interface org.biojava.bio.seq.Feature(also extends org.biojava.bio.seq.FeatureHolder)
    - interface org.biojava.bio.seq.StrandedFeature
  - interface org.biojava.bio.seq.Sequence(also extends org.biojava.bio.seq.FeatureHolder, org.biojava.bio.symbol.SymbolList)
  - interface org.biojava.bio.symbol.Symbol
    - interface org.biojava.bio.symbol.AtomicSymbol
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState(also extends org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState(also extends org.biojava.bio.dp.Trainable)
    - interface org.biojava.bio.symbol.CrossProductSymbol
- interface org.biojava.bio.Annotation
- interface java.lang.Cloneable
  - interface org.biojava.bio.search.SeqSimilaritySearcher
  - interface org.biojava.bio.search.SeqSimilaritySearchHit
  - interface org.biojava.bio.search.SeqSimilaritySearchResult
  - interface org.biojava.bio.search.SeqSimilaritySearchSubHit
- interface org.acedb.Connection
- interface org.acedb.Database
- interface org.biojava.bio.dist.Distribution
- 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.DPMatrix
- interface org.acedb.Driver
- interface java.util.EventListener
  - interface org.biojava.stats.svm.TrainingListener
- interface org.biojava.bio.seq.io.FastaDescriptionReader
- interface org.biojava.bio.seq.io.FeatureBuilder
- interface org.biojava.bio.seq.FeatureHolder
  - interface org.biojava.bio.seq.Feature(also extends org.biojava.bio.Annotatable)
    - interface org.biojava.bio.seq.StrandedFeature
  - interface org.biojava.bio.seq.RealizingFeatureHolder
  - interface org.biojava.bio.seq.Sequence(also extends org.biojava.bio.Annotatable, org.biojava.bio.symbol.SymbolList)
- interface org.biojava.bio.seq.FeatureRealizer
- interface org.biojava.bio.gui.sequence.FeatureRenderer
- 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.db.IDMaker
- interface org.biojava.stats.svm.ItemValue
- interface org.biojava.bio.symbol.Location
- interface org.biojava.bio.gui.LogoPainter
- interface org.omg.CORBA.Object
  - interface org.Biocorba.Seqcore.AnonymousSeq(also extends org.omg.CORBA.portable.IDLEntity, GNOME.Unknown)
    - interface org.Biocorba.Seqcore.PrimarySeq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
  - interface org.Biocorba.Seqcore.PrimarySeq(also extends org.Biocorba.Seqcore.AnonymousSeq, org.omg.CORBA.portable.IDLEntity)
    - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
  - interface org.Biocorba.Seqcore.PrimarySeqDB(also extends org.omg.CORBA.portable.IDLEntity, GNOME.Unknown)
    - interface org.Biocorba.Seqcore.SeqDB(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
  - interface org.Biocorba.Seqcore.PrimarySeqIterator(also extends org.omg.CORBA.portable.IDLEntity, GNOME.Unknown)
  - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.portable.IDLEntity, org.Biocorba.Seqcore.PrimarySeq)
  - interface org.Biocorba.Seqcore.SeqDB(also extends org.omg.CORBA.portable.IDLEntity, org.Biocorba.Seqcore.PrimarySeqDB)
  - interface org.Biocorba.Seqcore.SeqFeature(also extends org.omg.CORBA.portable.IDLEntity, GNOME.Unknown)
  - interface org.Biocorba.Seqcore.SeqFeatureIterator(also extends org.omg.CORBA.portable.IDLEntity, GNOME.Unknown)
  - interface GNOME.Unknown(also extends org.omg.CORBA.portable.IDLEntity)
    - interface org.Biocorba.Seqcore.AnonymousSeq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.PrimarySeq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
        - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
    - interface org.Biocorba.Seqcore.PrimarySeqDB(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.SeqDB(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
    - interface org.Biocorba.Seqcore.PrimarySeqIterator(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
    - interface org.Biocorba.Seqcore.SeqFeature(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
    - interface org.Biocorba.Seqcore.SeqFeatureIterator(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
- interface org.biojava.bio.seq.SequenceAnnotator
- interface org.biojava.bio.seq.db.SequenceDB
- interface org.biojava.bio.seq.db.SequenceDBInstallation
- interface org.biojava.bio.seq.SequenceFactory
- interface org.biojava.bio.seq.io.SequenceFormat
- interface org.biojava.bio.seq.SequenceIterator
- interface org.biojava.bio.gui.sequence.SequenceRenderer
- interface java.io.Serializable
  - interface org.biojava.bio.seq.FeatureFilter
  - interface org.omg.CORBA.portable.IDLEntity
    - interface org.Biocorba.Seqcore.AnonymousSeq(also extends org.omg.CORBA.Object, GNOME.Unknown)
      - interface org.Biocorba.Seqcore.PrimarySeq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
        - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
    - interface org.Biocorba.Seqcore.PrimarySeq(also extends org.Biocorba.Seqcore.AnonymousSeq, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
    - interface org.Biocorba.Seqcore.PrimarySeqDB(also extends org.omg.CORBA.Object, GNOME.Unknown)
      - interface org.Biocorba.Seqcore.SeqDB(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
    - interface org.Biocorba.Seqcore.PrimarySeqIterator(also extends org.omg.CORBA.Object, GNOME.Unknown)
    - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.Object, org.Biocorba.Seqcore.PrimarySeq)
    - interface org.Biocorba.Seqcore.SeqDB(also extends org.omg.CORBA.Object, org.Biocorba.Seqcore.PrimarySeqDB)
    - interface org.Biocorba.Seqcore.SeqFeature(also extends org.omg.CORBA.Object, GNOME.Unknown)
    - interface org.Biocorba.Seqcore.SeqFeatureIterator(also extends org.omg.CORBA.Object, GNOME.Unknown)
    - interface GNOME.Unknown(also extends org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.AnonymousSeq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
        - interface org.Biocorba.Seqcore.PrimarySeq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
          - interface org.Biocorba.Seqcore.Seq(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.PrimarySeqDB(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
        - interface org.Biocorba.Seqcore.SeqDB(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.PrimarySeqIterator(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.SeqFeature(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
      - interface org.Biocorba.Seqcore.SeqFeatureIterator(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
- interface org.biojava.bio.dp.StoppingCriteria
- 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 org.biojava.bio.symbol.SymbolList
  - interface org.biojava.bio.symbol.Alignment
    - interface org.biojava.bio.dp.StatePath
  - interface org.biojava.bio.seq.Sequence(also extends org.biojava.bio.Annotatable, org.biojava.bio.seq.FeatureHolder)
- interface org.biojava.bio.symbol.SymbolParser
- interface org.biojava.bio.gui.SymbolStyle
- interface org.biojava.bio.dp.Trainable
  - interface org.biojava.bio.dp.EmissionState(also extends org.biojava.bio.dp.State)
  - interface org.biojava.bio.dp.MarkovModel
  - interface org.biojava.bio.dp.ModelInState(also extends org.biojava.bio.dp.State)
- interface org.biojava.bio.dp.TrainingAlgorithm
- interface org.biojava.stats.svm.TrainingContext
- interface org.biojava.bio.dp.TransitionListener
- interface org.biojava.bio.dp.TransitionTrainer
- interface org.biojava.bio.symbol.TranslationTable
- interface org.biojava.bio.dp.WeightMatrix
- interface org.biojava.utils.xml.XMLPeerFactory