Here is a list of all class members with links to the classes they belong to:

- a -

• a : ContigJoin
• a_ : ScoreMaker
• addHit() : PackedHitStore , HitListVector , CustomHitStore , HitListRepeated
• addMatch() : MatchStoreImp , MatchStore
• addMatch_ : MatchPolicy
• addReader() : SequenceReaderMulti
• addValue() : CommandLineArg , CommandLineArgString , CommandLineArgInt , CommandLineArgBool
• addWord() : SequenceEncoder , WordSequence
• AlignInfo() : AlignInfo
• alignment_ : TraceBackerBasic , TraceBacker3D
• allocate() : AllocatorLocal< T > , Allocator< PositionPacked > , AllocatorLocal< T > , AllocatorLocal< PositionInHitList > , AllocatorLocal< PositionInDatabase > , Allocator< PositionInHitList > , Allocator< T > , Allocator< PositionInHitList > arrayAllocator , Allocator< HitType > , AllocatorLocal< PositionPacked >
• allocateAndZero() : Allocator< PositionInHitList > arrayAllocator , Allocator< PositionPacked > , AllocatorLocal< T > , AllocatorLocal< PositionInHitList > , AllocatorLocal< PositionInDatabase > , Allocator< PositionInHitList > , Allocator< T > , Allocator< HitType > , AllocatorLocal< PositionPacked >
• allocateHitList() : HashTableTranslated , matchWord , HashTableView< T, SUBCLASS > , HashTableGeneric
• Allocator() : AllocatorLocal< PositionPacked > , Allocator< PositionInHitList > , Allocator< HitType > , Allocator< PositionPacked > , AllocatorLocal< T > , AllocatorLocal< PositionInHitList > , AllocatorLocal< PositionInDatabase > , Allocator< T > , Allocator< PositionInHitList > arrayAllocator
• AllocatorLocal() : AllocatorLocal< PositionInDatabase > , AllocatorLocal< T > , AllocatorLocal< PositionInHitList > , AllocatorLocal< PositionPacked >
• allReaders_ : SequenceReaderMulti
• allSeqsRead_ : SeqReaderInfo
• allSequencesRead_ : SequenceReader
• areAllSequencesRead() : SequenceReader
• Array2D() : Array2D< T > , Array2D< ScoreType > , Array2D< T >
• Array3D() : Array3D< ScoreType > , Array3D< T >

---