ssaha Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

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

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