ssaha Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

• AdapterFactory
• AlignInfo
• Alignment
• Allocator< T >
  • AllocatorLocal< T >
• Allocator< HitType >
• Array2D< T >
• Array3D< T >
• BaseGenerator
• CellFiller
• CellFiller3D
• ColumnFiller3D
• ColumnFillerBasic
• CombineSort< C1, C2, C3 >
• CommandLineArg
  • CommandLineArgBool
  • CommandLineArgInt
  • CommandLineArgString
• ContigHitOnRead
• ContigJoin
• Handshake
• HashFunctor
• HashTableFactory
• HashTableGeneric
  • HashTableTranslated
    • HashTableTranslatedPeek
  • HashTableView< T, SUBCLASS >
  • HashTableView< PositionInDatabase, HashTable >
    • HashTable
      • HashTableFred
      • HashTableTest
  • HashTableView< PositionPacked, HashTablePacked >
    • HashTablePacked
      • HashTableComponent
      • HashTablePackedProtein
        • HashTablePackedCustom
• HitInfo
• HitListRepeated
• HitListVector
  • CustomHitStore
• ifstreamSSAHA
• LessThanDiff
• LessThanQuery
• LessThanSubject
• MachineInfo
• MakeIntoWord
• Match
  • MatchImp
  • MatchRemote
• MatchAdder
  • MatchAdderImp
    • MatchAdderCodonCodon
    • MatchAdderCodonProtein
    • MatchAdderProteinCodon
• MatchAlgorithm
  • MatchAlgorithmGapped
  • MatchAlgorithmUngapped
• MatchAligner
  • MatchAlignerDNA
  • MatchAlignerProtein
  • MatchAlignerTranslated
    • MatchAlignerTranslatedDNA
    • MatchAlignerTranslatedProtein
• MatchHeader
• MatchInfo
• MatchPolicy
  • MatchPolicyDNADNA
  • MatchPolicyDNAProtein
  • MatchPolicyDNATranslated
  • MatchPolicyProteinProtein
  • MatchPolicyProteinTranslated
• MatchStore
  • MatchStoreImp
  • MatchStoreRemote
• MatchTask
  • CombineTask< TASK1, TASK2 >
  • CombineTaskVirtual
  • MatchTaskAlign
  • MatchTaskPrint
  • MatchTaskPrintReverse
  • MatchTaskPrintTabbed
  • MatchTaskPrintTabbedReverse
  • MatchTaskServer
  • MatchTaskSort< SORTER >
  • MatchTaskTest
• NameReader
  • NameReaderIndex
  • NameReaderLocal
• NullBuffer
• ofstreamSSAHA
• PackedHitStore
• PathMatrix< PATH_TYPE >
• PositionInDatabase
• PrintFromWord
  • printBase
  • printResidue
• QueryHeader
• QueryManager
• QueryParameterStruct
• RadixSorter
• ReadHitOnContig
• ReadInfo
• RepeatedHit
• ScoreMaker
• SeqReaderInfo
• SequenceAdapter
  • SequenceAdapterWithOverlap
• SequenceEncoder
  • SequenceEncoderCodon
  • SequenceEncoderDNA
  • SequenceEncoderProtein
• SequenceHeader
• SequenceReaderMode
  • SequenceReaderModeFlagReplace
  • SequenceReaderModeIgnore
  • SequenceReaderModeReplace
  • SequenceReaderModeReport
  • SequenceReaderModeReportReplace
• SequenceReaderPrinter
  • SequenceReaderNamePrinter
  • SequenceReaderSideInfoPrinter
  • SequenceReaderSourcePrinter
• SequenceReaderState
  • SequenceReaderFileState
  • SequenceReaderFilterState
  • SequenceReaderMultiState
• SocketInterface
• SortByDiff
• SortByMatch
• SortByMatchSize
• SortByPercentMatch
• SortByQueryStart
• SortBySubjectName
• SortNull
• SourceReader
  • SequenceReader
    • SequenceReaderFile
      • SequenceReaderFasta
        • SequenceReaderFastaProtein
      • SequenceReaderFastq
        • SequenceReaderFastqProtein
    • SequenceReaderFilter
    • SequenceReaderLocal
    • SequenceReaderMulti
    • SequenceReaderStringBase
      • SequenceReaderStringDNA
      • SequenceReaderStringProtein
  • SourceReaderDummy
  • SourceReaderIndex
• SourceReader::SeqIndexInfo
• SSAHAException
  • NetworkException
    • BrokenSocketException
  • NumberOutOfRange
• SSAHAHit
• StaticScoreTable
• StringHash
• Timer
• TopList
• TraceBacker3D
• TraceBackerBasic
• WordSequence
• WordSequenceShifted

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