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ssaha Class Hierarchy
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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
Generated on Fri Dec 21 13:15:29 2007 for ssaha by
1.5.2