## Hierarchy For All Packages

Package Hierarchies:
  annodb, biosql, blastxml, CircLocTest, das, dist, dp, eventbasedparsing, game, gff, indexing, nativeapps, performance, process, prot, search, seq, seqviewer, ssaha, ssbind, structure, symbol, tagvalue, unigene, xff

## Class Hierarchy

- java.lang.Object
  - performance.AlignProteins
  - seqviewer.BeadDemo
  - eventbasedparsing.Blast2HTML
  - eventbasedparsing.BlastLike2XML
  - nativeapps.BlastLike2XML
  - blastxml.BlastParser
  - seqviewer.CircularEmblViewer
  - CircLocTest.CircularLocationTester
  - java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    - java.awt.Container
      - java.awt.Window (implements javax.accessibility.Accessible)
        - java.awt.Frame (implements java.awt.MenuContainer)
          - javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - CircLocTest.TestFrame
            - performance.UserDisplay
  - ssaha.CreateDNAFastaHashTable
  - ssaha.CreateDNAFastaHashTableCompact
  - ssaha.CreateDNAFastaHashTableLarge
  - ssaha.CreateEmblHashTable
  - ssaha.CreateEmblHashTableLarge
  - indexing.CreateFAIndex
  - indexing.CreateIndex
  - annodb.CreateIndexDB
  - indexing.CreateSPIndex
  - unigene.CreateUnigeneFlat
  - dp.Dice
  - biosql.DummyFromGFF
  - ssbind.Echoer (implements org.biojava.bio.search.SearchContentHandler)
  - gff.EmblToGffFasta
  - seqviewer.EmblViewer
  - seqviewer.EmblViewer2
  - eventbasedparsing.Fasta2XML
  - seqviewer.FastBeadDemo
  - seq.FetchSeq
  - seqviewer.GappedViewer
  - seq.GCContent
  - gff.GenbankToGffFasta
  - gff.GFFCompare
  - gff.GFFFilter
  - gff.GFFMask
  - gff.GFFToFeatures
  - tagvalue.Grep
  - tagvalue.Index
  - search.IndexFastaDB
  - biosql.LargeSequenceTest
  - indexing.ListIDs
  - structure.LoadStructure
  - symbol.MatrixValue
  - seq.MotifFinder2
  - dp.PairwiseAlignment
  - tagvalue.Parse
  - tagvalue.ParseEmbl
  - unigene.ParseLibInfo
  - tagvalue.ParseSwissprot
  - unigene.ParseUnigene
  - symbol.PatternDemo
  - dp.PatternFinder
  - eventbasedparsing.Pdb2XML
  - nativeapps.Pdb2XML
  - structure.PDBView
  - structure.PhiPsiCalculation
  - tagvalue.PrintFormat
  - ssbind.ProcessBlastReport
  - process.ProcessToolsTest
  - performance.ReadFasta
  - performance.ReadFastaX
  - performance.ReadFastaX2
  - indexing.ReadRaw
  - indexing.ReadRawSecondary
  - ssaha.ResultPrinter (implements org.biojava.bio.program.ssaha.SearchListener)
  - performance.ReverseComplement
  - seq.ReverseComplement
  - org.biojava.bio.search.SearchContentAdapter (implements org.biojava.bio.search.SearchContentHandler)
    - ssbind.CountHits
    - ssbind.CountSubHits
    - ssbind.ListQueries
    - ssbind.ListSubjects
    - ssbind.PropertyEchoer
  - org.biojava.bio.search.SearchContentFilter (implements org.biojava.bio.search.SearchContentHandler)
    - ssbind.AlignmentBuilder
    - ssbind.SubHitBuilder
    - ssbind.SubHitFilter
      - ssbind.FilterByValue
  - dp.SearchProfile
  - unigene.SearchUnigeneFlat
  - biosql.SeqDumper
  - biosql.SeqEMBL
  - biosql.SeqGFF
  - org.biojava.bio.seq.io.SeqIOAdapter (implements org.biojava.bio.seq.io.SeqIOListener)
    - game.SeqIOTatler
  - biosql.SequenceTest
  - seq.SimpleAssemblyTest
  - performance.SmithWatermanExample
  - ssaha.SSAHA
  - ssaha.SSAHALarge
  - ssaha.SSAHASeq
  - ssaha.SSAHASeqLarge
  - structure.SuperimposeStructures
  - gff.SwissprotToGffFasta
  - symbol.TestAlphabetIndexers
  - symbol.TestAmbiguity
  - das.TestDAS
  - das.TestDASG
  - das.TestDASH
  - prot.TestDigestIO
  - dist.TestDistribution
  - das.TestDSN
  - seq.TestEmbl
  - seq.TestEmbl2
  - game.TestGAME
  - symbol.TestGappedSymbolList
  - seq.TestGenbank
  - symbol.TestIndexedIntegers
  - symbol.TestLocation
  - dist.TestOrderNAlphabet
  - dist.TestOrderNDistribution
  - symbol.TestOrderNSymbolList
  - seq.TestRefSeqPrt
  - symbol.TestSimpleAlignment
  - seq.TestSubSequence
  - seq.TestSwissprot
  - seq.TestTranslation
  - symbol.TestWindowedSymbolList
  - xff.TestXFFStreaming
  - dist.Tools
  - symbol.Tools
  - seqviewer.TraceViewer
  - eventbasedparsing.TutorialEx1
  - seq.UniProtDemo
  - biosql.UploadFlat
  - dp.ViterbiAlign
  - symbol.WindowCount
  - gff.XFF2GFF

## Interface Hierarchy

- symbol.TestLocation.BooleanBinaryOp
- symbol.TestLocation.LocationBinaryOp