- a -

• AbstractGappedAlignment() : mems::AbstractGappedAlignment< AbstractMatchImpl >
• AbstractMatchSingleStartComparator() : mems::AbstractMatchSingleStartComparator< MatchType >
• AbstractMatchStartComparator() : mems::AbstractMatchStartComparator< MatchType >
• add() : mems::GenericInterval< GappedBaseImpl >
• addAllSegments() : mems::gnAlignedSequences
• addAllSegmentsReplaceGaps() : mems::gnAlignedSequences
• AddCopy() : mems::SuperIntervalManipulator, mems::GenericMatchSeqManipulator< MatchType >
• addFeature() : genome::gnRAWSequence
• AddHashEntry() : mems::MemHash
• addHeader() : genome::gnRAWSequence
• AddSequence() : mems::MatchFinder
• addSequence() : mems::gnAlignedSequences
• addUnalignedRegions() : mems::GenericInterval< GappedBaseImpl >
• align() : mems::ProgressiveAligner, mems::Aligner
• Align() : mems::MuscleInterface, mems::GappedAligner, mems::ClustalInterface
• alignedSeqsSize() : mems::gnAlignedSequences
• Aligner() : mems::Aligner
• AlignLCB() : mems::Aligner
• AlignmentLength() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::AbstractMatch, mems::AbstractGappedAlignment< AbstractMatchImpl >
• AlignmentTreeNode() : mems::AlignmentTreeNode
• alignNodes() : mems::ProgressiveAligner
• alignPP() : mems::ProgressiveAligner
• alignProfileToProfile() : mems::ProgressiveAligner
• Allocate() : mems::SlotAllocator< T >
• AmbiguityTolerance() : mems::MatchFinder
• applyScoreDifference() : mems::EvenFasterSumOfPairsBreakpointScorer
• assignFileName() : mems::gnAlignedSequences

- b -

• back() : PhyloTree< T >
• BadSize() : Matrix< T >::BadSize
• base() : mems::FileSML
• BasicDNATable() : mems::SortedMerList
• BigCreate() : mems::FileSML
• BoundsViolation() : Matrix< T >::BoundsViolation
• bsearch() : mems::SortedMerList
• buildConsensus() : mems::gnAlignedSequences

- c -

• CalculateAlignmentLength() : mems::GenericInterval< GappedBaseImpl >
• CalculateMaxMerSize() : mems::SortedMerList, mems::DNAFileSML
• CalculateOffset() : mems::MatchHashEntry, mems::GenericInterval< GappedBaseImpl >
• CallClustal() : mems::ClustalInterface
• CallMuscle() : mems::MuscleInterface
• CallMuscleFast() : mems::MuscleInterface
• CgaBsComp() : mems::CgaBsComp< CompType >
• clear() : PhyloTree< T >
• Clear() : mems::SortedMerList, mems::MemorySML, mems::MemHash, mems::GenericMatchList< MatchPtrType >, mems::MatchFinder, mems::GenericIntervalList< MatchType >, mems::FileSML
• ClearCommandLine() : mems::MuscleInterface
• ClearSequences() : mems::MemHash
• Clone() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::RepeatHash, mems::ParallelMemHash, mems::PairwiseMatchFinder, mems::PairwiseMatchAdapter, mems::MemorySML, mems::MemHash, mems::MatchProjectionAdapter, mems::MatchHashEntry, mems::MaskedMemHash, mems::GenericInterval< GappedBaseImpl >, genome::gnRAWSequence, mems::GappedAlignment, mems::FileSML, mems::DNAMemorySML, mems::DNAFileSML, mems::DenseAbstractMatch< MAX_SEQS >, mems::CompactGappedAlignment< BaseType >
• ClustalInterface() : mems::ClustalInterface
• collapseIdenticalSequences() : mems::gnAlignedSequences
• cols() : Matrix< T >
• CompactGappedAlignment() : mems::CompactGappedAlignment< BaseType >
• computeAvgAncestralMatchScores() : mems::ProgressiveAligner
• computeInternalNodeDistances() : mems::ProgressiveAligner
• concatenateAlignedSequences() : mems::gnAlignedSequences
• CondenseGapColumns() : mems::CompactGappedAlignment< BaseType >
• consistencyCheck() : mems::Aligner
• construct() : mems::SeedOccurrenceList
• constructClustalWAlignedSequenceList() : mems::gnAlignedSequences
• constructFromClustalW() : mems::gnAlignedSequences
• constructFromMega() : mems::gnAlignedSequences
• constructFromMSF() : mems::gnAlignedSequences
• constructFromNexus() : mems::gnAlignedSequences
• constructFromPhylip() : mems::gnAlignedSequences
• constructFromRelaxedNexus() : mems::gnAlignedSequences
• constructLcbTrackingMatches() : mems::ProgressiveAligner
• constructMegaAlignedSequenceList() : mems::gnAlignedSequences
• constructMSFAlignedSequenceList() : mems::gnAlignedSequences
• constructNexusAlignedSequenceList() : mems::gnAlignedSequences
• constructPhylipAlignedSequenceList() : mems::gnAlignedSequences
• ConstructSuperIntervalFromMSA() : mems::ProgressiveAligner
• Contains() : mems::MatchHashEntry
• contig() : genome::gnRAWSequence
• contigByBase() : genome::gnRAWSequence
• contigByName() : genome::gnRAWSequence
• contigIndexByBase() : genome::gnRAWSequence
• contigIndexByName() : genome::gnRAWSequence
• contigLength() : genome::gnRAWSequence
• contigListLength() : genome::gnRAWSequence
• contigListSize() : genome::gnRAWSequence
• contigName() : genome::gnRAWSequence
• contigStart() : genome::gnRAWSequence
• coordinates() : mems::gnAlignedSequences
• Copy() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::MatchHashEntry, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• copyRange() : mems::CompactGappedAlignment< BaseType >
• Create() : mems::SortedMerList, mems::MemorySML, mems::FileSML
• create_bitcount() : mems::CompactGappedAlignment< BaseType >
• createAncestralOrdering() : mems::ProgressiveAligner
• CreateBasicDNATable() : mems::SortedMerList
• CreateMatches() : mems::RepeatHash, mems::MemHash
• CreateMemorySMLs() : mems::GenericMatchList< MatchPtrType >
• CreatePairwiseBPDistance() : mems::ProgressiveAligner
• CreateProteinTable() : mems::SortedMerList
• CreateTree() : mems::MuscleInterface
• CropEnd() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• CropEndCoords() : mems::GappedAlignment
• CropLeft() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::SuperInterval, mems::SuperIntervalManipulator, mems::GenericMatchSeqManipulator< MatchType >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• CropRight() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::SuperInterval, mems::SuperIntervalManipulator, mems::GenericMatchSeqManipulator< MatchType >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• CropStart() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• CropStartCoords() : mems::GappedAlignment

- d -

• DenseAbstractMatch() : mems::DenseAbstractMatch< MAX_SEQS >
• Description() : mems::SortedMerList
• determineBaseIndex() : mems::gnAlignedSequences
• dmCreate() : mems::FileSML
• DNAFileSML() : mems::DNAFileSML
• DNAMemorySML() : mems::DNAMemorySML
• doGappedAlignment() : mems::ProgressiveAligner
• DoSomethingCool() : mems::Aligner

- e -

• End() : mems::AbstractMatch
• end_to_start_compare() : mems::MatchHashEntry
• EnumerateMatches() : mems::RepeatHash, mems::PairwiseMatchFinder, mems::MemHash, mems::MatchFinder
• EvenFasterSumOfPairsBreakpointScorer() : mems::EvenFasterSumOfPairsBreakpointScorer
• Extended() : mems::MatchHashEntry
• ExtendEnd() : mems::UngappedLocalAlignment< AbstractMatchImpl >
• ExtendMatch() : mems::MatchFinder
• ExtendStart() : mems::UngappedLocalAlignment< AbstractMatchImpl >
• extractAlignment() : mems::ProgressiveAligner
• extractVariableSites() : mems::gnAlignedSequences

- f -

• FileSML() : mems::FileSML
• FillDnaSeedSML() : mems::SortedMerList
• FillDnaSML() : mems::SortedMerList
• FillSML() : mems::SortedMerList, mems::DNAMemorySML, mems::DNAFileSML
• Find() : mems::SortedMerList
• find() : genome::gnRAWSequence
• FindAll() : mems::SortedMerList
• FindMatches() : mems::MemHash
• FindMatchesFromPosition() : mems::MemHash
• FindMatchPos() : mems::GenericInterval< GappedBaseImpl >
• FindMatchSeeds() : mems::MatchFinder
• FindMer() : mems::SortedMerList
• FindSubsets() : mems::MatchFinder, mems::MaskedMemHash
• FirstStart() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• FixLeftEnds() : mems::ProgressiveAligner
• FormatVersion() : mems::FileSML, mems::DNAFileSML
• Free() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::SlotAllocator< T >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::MatchHashEntry, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• FromSeq() : mems::RepeatMatch

- g -

• GappedAligner() : mems::GappedAligner
• GappedAlignment() : mems::GappedAlignment
• GenericInterval() : mems::GenericInterval< GappedBaseImpl >
• GenericIntervalList() : mems::GenericIntervalList< MatchType >
• GenericMatchList() : mems::GenericMatchList< MatchPtrType >
• GenericMatchSeqManipulator() : mems::GenericMatchSeqManipulator< MatchType >
• getAlignedChildren() : mems::ProgressiveAligner
• getAlignedSegment() : mems::gnAlignedSequences
• getAlignedSequenceFileName() : mems::gnAlignedSequences
• GetAlignedSequences() : mems::GenericInterval< GappedBaseImpl >
• GetAlignment() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• getAlignment() : mems::ProgressiveAligner
• getAncestralMatches() : mems::ProgressiveAligner
• GetBestLCB() : mems::Aligner
• getBpDistEstimateMinScore() : mems::ProgressiveAligner
• GetBreakpoint() : mems::MatchFinder
• getBreakpointDistanceScale() : mems::ProgressiveAligner
• getBrokenFeatures() : genome::gnRAWSequence
• GetBSequence() : mems::SortedMerList
• getClustalInterface() : mems::ClustalInterface
• getCodons() : mems::gnAlignedSequences
• GetColumn() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• GetColumnAndMatch() : mems::GenericInterval< GappedBaseImpl >
• getConservationDistanceScale() : mems::ProgressiveAligner
• getContainedFeatures() : genome::gnRAWSequence
• GetDefaultMerSize() : mems::GenericMatchList< MatchPtrType >
• GetDnaMer() : mems::SortedMerList
• GetDnaSeedMer() : mems::SortedMerList
• GetEnumerationTolerance() : mems::MemHash
• GetExtraMuscleArguments() : mems::MuscleInterface
• getFeature() : genome::gnRAWSequence
• getFeatureListLength() : genome::gnRAWSequence
• getFrequency() : mems::SeedOccurrenceList
• GetHeader() : mems::SortedMerList
• getHeader() : genome::gnRAWSequence
• getHeaderListLength() : genome::gnRAWSequence
• getHeight() : PhyloTree< T >
• GetID() : mems::SortedMerList
• getIntersectingFeatures() : genome::gnRAWSequence
• getLcbScoringScheme() : mems::ProgressiveAligner
• GetMatches() : mems::GenericInterval< GappedBaseImpl >
• GetMatchList() : mems::MemHash
• getMaxNewMoveCount() : mems::EvenFasterSumOfPairsBreakpointScorer
• GetMer() : mems::SortedMerList, mems::DNAMemorySML, mems::DNAFileSML
• GetMerMask() : mems::SortedMerList
• GetMerMaskSize() : mems::SortedMerList
• getMoveCount() : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer
• getMuscleInterface() : mems::MuscleInterface
• GetNeededMemory() : mems::FileSML, mems::DNAFileSML
• getPairwiseMatches() : mems::ProgressiveAligner
• getPath() : mems::ProgressiveAligner
• GetProgress() : mems::MatchFinder
• GetRepeatTolerance() : mems::MemHash
• getRepresentativeAncestralMatches() : mems::ProgressiveAligner
• getResults() : mems::EvenFasterSumOfPairsBreakpointScorer
• GetSar() : mems::RepeatHash, mems::MatchFinder
• GetSeedMask() : mems::SortedMerList
• GetSeedMer() : mems::SortedMerList, mems::DNAMemorySML, mems::DNAFileSML
• GetSeqC() : genome::gnRAWSequence
• GetSlotAllocator() : mems::SlotAllocator< T >
• getSupportedFormats() : mems::gnAlignedSequences
• getTempPath() : mems::FileSML
• getTempPathCount() : mems::FileSML
• getUsedCoordinates() : mems::FileSML
• getUseLcbWeightScaling() : mems::ProgressiveAligner
• getUseSeedFamilies() : mems::ProgressiveAligner
• globalToLocal() : genome::gnRAWSequence
• globalToSource() : genome::gnRAWSequence
• gnAlignedSequences() : mems::gnAlignedSequences
• gnRAWSequence() : genome::gnRAWSequence
• GreedyRemovalScorer() : mems::GreedyRemovalScorer
• guideTreeLoaded() : mems::ClustalInterface

- h -

• HashMatch() : mems::RepeatHash, mems::MemHash, mems::MatchFinder, mems::MaskedMemHash
• HybridAbstractMatch() : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >

- i -

• init() : Matrix< T >
• Invert() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::GappedAlignment, mems::DenseAbstractMatch< MAX_SEQS >, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• IsCircular() : mems::SortedMerList
• isCircular() : genome::gnRAWSequence
• IsGap() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• isReverseComplement() : genome::gnRAWSequence
• isSupportedFormat() : mems::gnAlignedSequences
• isValid() : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer
• IvTrackerComp() : mems::IvTrackerComp

- l -

• LabeledMemComparator() : mems::LabeledMemComparator
• LabelSort() : mems::LabelSort< PairType >
• LCB() : mems::LCB
• LCBLeftComparator() : mems::LCBLeftComparator
• LCBLeftEndComp() : mems::LCBLeftEndComp
• LeftEnd() : mems::SuperInterval, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::SuperIntervalManipulator, mems::GenericMatchSeqManipulator< MatchType >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• length() : genome::gnRAWSequence, mems::SuperInterval, mems::SMLHeader, mems::SMLHeader_s, mems::AbstractGappedAlignment< AbstractMatchImpl >
• Length() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::SuperInterval, mems::SortedMerList, mems::SuperIntervalManipulator, mems::GenericMatchSeqManipulator< MatchType >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::AbstractMatch, mems::AbstractGappedAlignment< AbstractMatchImpl >
• LengthFilter() : mems::GenericMatchList< MatchPtrType >
• linkSuperIntervals() : mems::ProgressiveAligner
• LoadFile() : mems::MemHash, mems::FileSML
• LoadSequences() : mems::RepeatMatchList
• LoadSMLs() : mems::RepeatMatchList, mems::GenericMatchList< MatchPtrType >
• LoadSource() : genome::gnRAWSequence
• localToGlobal() : genome::gnRAWSequence
• localToSource() : genome::gnRAWSequence
• LogProgress() : mems::MatchFinder

- m -

• Marble() : mems::GenericInterval< GappedBaseImpl >
• MaskedMemHash() : mems::MaskedMemHash
• MatchFinder() : mems::MatchFinder
• MatchHashEntry() : mems::MatchHashEntry
• MatchLeftEndComparator() : mems::MatchLeftEndComparator
• MatchProjectionAdapter() : mems::MatchProjectionAdapter
• MatchStartComparator() : mems::MatchStartComparator< MatchType >
• Matrix() : Matrix< T >
• MemCollisionCount() : mems::MemHash
• MemCount() : mems::MemHash
• MemHash() : mems::MemHash
• MemoryMinimum() : mems::FileSML
• MemorySML() : mems::MemorySML
• MemTableCount() : mems::MemHash
• MerCompare() : mems::MerCompare
• Merge() : mems::SortedMerList, mems::MemorySML, mems::FileSML
• merge() : genome::gnRAWSequence
• mergeContigs() : genome::gnRAWSequence
• MerSize() : mems::MatchHashEntry
• Move() : mems::UngappedLocalAlignment< AbstractMatchImpl >
• MoveEnd() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• MoveStart() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::GenericInterval< GappedBaseImpl >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• Multiplicity() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::MatchFinder, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• MultiplicityFilter() : mems::GenericMatchList< MatchPtrType >
• MuscleInterface() : mems::MuscleInterface

- n -

• NumericMatrix() : NumericMatrix< T >

- o -

• Offset() : mems::MatchHashEntry
• offset_lessthan() : mems::MatchHashEntry
• OpenForWriting() : mems::FileSML
• operator *() : NumericMatrix< T >
• operator *=() : NumericMatrix< T >
• operator()() : mems::MerCompare, mems::AbsolutComparator< T >, mems::CgaBsComp< CompType >, mems::SuperIntervalPtrComp, Matrix< T >, mems::MheCompare, mems::LCBIDComparator, mems::LCBLeftComparator, mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer, mems::LabelSort< PairType >, mems::MoveScoreHeapComparator, mems::IvTrackerComp, mems::SearchCacheComparator, mems::PlacementMatchComparator, mems::LabeledMemComparator, mems::LCBLeftEndComp, mems::MatchLeftEndComparator, mems::SSC< MatchType >, mems::SingleStartComparator< MatchType >, mems::MatchStartComparator< MatchType >, mems::AbstractMatchSingleStartComparator< MatchType >, mems::AbstractMatchStartComparator< MatchType >
• operator+() : NumericMatrix< T >
• operator+=() : NumericMatrix< T >, genome::gnRAWSequence
• operator-() : NumericMatrix< T >
• operator-=() : NumericMatrix< T >
• operator/() : NumericMatrix< T >
• operator/=() : NumericMatrix< T >
• operator<() : mems::SuperInterval
• operator=() : mems::SuperInterval, mems::PairwiseScoringScheme, mems::SortedMerList, mems::SlotAllocator< T >, mems::SeedOccurrenceList, mems::ProgressiveAligner, PhyloTree< T >, NumericMatrix< T >, mems::MuscleInterface, mems::MemorySML, mems::MemHash, Matrix< T >, mems::MatchProjectionAdapter, mems::GenericMatchList< MatchPtrType >, mems::MatchHashEntry, mems::MaskedMemHash, mems::GenericIntervalList< MatchType >, mems::GenericInterval< GappedBaseImpl >, mems::TrackingLCB< MatchType >, mems::GappedAligner, mems::FileSML, mems::DNAMemorySML, mems::DNAFileSML, mems::ClustalInterface, mems::Aligner, mems::SSC< MatchType >, mems::SingleStartComparator< MatchType >, mems::MatchStartComparator< MatchType >, mems::AbstractMatchSingleStartComparator< MatchType >, mems::AbstractMatchStartComparator< MatchType >, mems::ParallelMemHash
• operator==() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::MatchHashEntry, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >
• operator[]() : mems::SortedMerList, PhyloTree< T >, mems::MemorySML, genome::gnRAWSequence, mems::gnAlignedSequences, mems::FileSML, mems::AbstractMatch
• Orientation() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• output() : mems::gnAlignedSequences
• outputClustalW() : mems::gnAlignedSequences
• outputCodon() : mems::gnAlignedSequences
• outputMega() : mems::gnAlignedSequences
• outputMSF() : mems::gnAlignedSequences
• outputNexus() : mems::gnAlignedSequences
• outputPhylip() : mems::gnAlignedSequences
• outputWithConsensus() : mems::gnAlignedSequences

- p -

• pairwiseAnchorSearch() : mems::ProgressiveAligner
• PairwiseMatchAdapter() : mems::PairwiseMatchAdapter
• PairwiseMatchFinder() : mems::PairwiseMatchFinder
• pairwiseScoreTrackingMatches() : mems::ProgressiveAligner
• PairwiseScoringScheme() : mems::PairwiseScoringScheme
• ParseMusclePath() : mems::MuscleInterface
• PhyloTree() : PhyloTree< T >
• PlacementMatchComparator() : mems::PlacementMatchComparator
• print() : Matrix< T >
• PrintDistribution() : mems::MemHash
• ProfileAlign() : mems::MuscleInterface
• ProfileAlignFast() : mems::MuscleInterface
• ProgressiveAligner() : mems::ProgressiveAligner
• propagateDescendantBreakpoints() : mems::ProgressiveAligner
• ProteinTable() : mems::SortedMerList
• Purge() : mems::SlotAllocator< T >
• push_back() : PhyloTree< T >

- q -

• quadratic_li() : mems::MemHash

- r -

• RadixSort() : mems::FileSML
• Read() : mems::SortedMerList, mems::MemorySML, mems::FileSML
• read() : Matrix< T >
• readClustalWAlignment() : mems::gnAlignedSequences
• ReadList() : mems::RepeatMatchList, mems::GenericIntervalList< MatchType >
• readMegaAlignment() : mems::gnAlignedSequences
• readMSFAlignment() : mems::gnAlignedSequences
• readNexusAlignment() : mems::gnAlignedSequences
• readPhylipAlignment() : mems::gnAlignedSequences
• readRelaxedNexusAlignment() : mems::gnAlignedSequences
• ReadStandardAlignment() : mems::GenericIntervalList< MatchType >
• ReadStandardAlignmentCompact() : mems::GenericIntervalList< MatchType >
• readTree() : PhyloTree< T >
• recurseOnPairs() : mems::ProgressiveAligner
• Recursion() : mems::Aligner
• RecursiveAnchorSearch() : mems::Aligner
• recursiveApplyAncestralBreakpoints() : mems::ProgressiveAligner
• Refine() : mems::MuscleInterface
• refineAlignment() : mems::ProgressiveAligner
• RefineFast() : mems::MuscleInterface
• registerTempPath() : mems::FileSML
• remove() : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer
• removeAlignedSeq() : mems::gnAlignedSequences
• removeAllSegments() : mems::gnAlignedSequences
• removeFeature() : genome::gnRAWSequence
• removeHeader() : genome::gnRAWSequence
• RepeatMatch() : mems::RepeatMatch
• RepeatMatchList() : mems::RepeatMatchList
• resize() : PhyloTree< T >
• RevCompMer() : mems::SortedMerList
• RightEnd() : mems::AbstractMatch
• rows() : Matrix< T >

- s -

• score() : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer
• SearchCacheComparator() : mems::SearchCacheComparator
• SearchRange() : mems::MatchFinder
• SearchWithinLCB() : mems::Aligner
• Seed() : mems::SortedMerList
• SeedLength() : mems::SortedMerList
• SeedOccurrenceList() : mems::SeedOccurrenceList
• SeedWeight() : mems::SortedMerList
• seq() : mems::gnAlignedSequences, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter
• SeqCount() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• SeqId() : mems::RepeatMatch
• SeqPosToColumn() : mems::CompactGappedAlignment< BaseType >
• SeqToIndex() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
• sequenceNameInList() : mems::gnAlignedSequences
• SetAlignment() : mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractGappedAlignment< AbstractMatchImpl >
• SetAlignmentLength() : mems::AbstractGappedAlignment< AbstractMatchImpl >
• SetAmbiguityTolerance() : mems::MatchFinder
• setBpDistEstimateMinScore() : mems::ProgressiveAligner
• setBreakpointDistanceScale() : mems::ProgressiveAligner
• setBreakpointPenalty() : mems::ProgressiveAligner
• setCircular() : genome::gnRAWSequence
• setCollinear() : mems::ProgressiveAligner
• setConservationDistanceScale() : mems::ProgressiveAligner
• setContigName() : genome::gnRAWSequence
• SetDescription() : mems::SortedMerList, mems::FileSML
• SetDirection() : mems::MemHash
• SetDistanceMatrix() : mems::ClustalInterface
• SetEnumerationTolerance() : mems::MemHash
• SetExtended() : mems::MatchHashEntry
• SetExtraMuscleArguments() : mems::MuscleInterface
• SetGappedAligner() : mems::Aligner
• setGappedAlignment() : mems::ProgressiveAligner
• setGuideTree() : mems::ClustalInterface
• SetID() : mems::SortedMerList, mems::FileSML
• setInputGuideTreeFileName() : mems::ProgressiveAligner
• setLcbScoringScheme() : mems::ProgressiveAligner
• SetLeftEnd() : mems::SuperInterval, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• SetLength() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::SuperInterval, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::AbstractMatch, mems::AbstractGappedAlignment< AbstractMatchImpl >
• SetMask() : mems::MaskedMemHash
• SetMatches() : mems::GenericInterval< GappedBaseImpl >
• SetMatchesTemp() : mems::GenericInterval< GappedBaseImpl >
• SetMatchLog() : mems::MemHash
• setMatrix() : mems::PairwiseScoringScheme
• SetMaxAlignmentLength() : mems::GappedAligner
• SetMaxExtensionIterations() : mems::Aligner
• SetMaxGappedAlignmentLength() : mems::ProgressiveAligner, mems::Aligner
• SetMerMaskSize() : mems::SortedMerList
• SetMinFlankSize() : mems::ClustalInterface
• setMinimumBreakpointPenalty() : mems::ProgressiveAligner
• SetMinRecursionGapLength() : mems::Aligner
• SetMuscleArguments() : mems::MuscleInterface
• SetMusclePath() : mems::MuscleInterface
• SetOffset() : mems::MatchHashEntry
• SetOffsetLog() : mems::MatchFinder
• SetOrientation() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• setOutputGuideTreeFileName() : mems::ProgressiveAligner
• setPairwiseMatches() : mems::ProgressiveAligner
• setPairwiseScoringScheme() : mems::ProgressiveAligner
• SetPermutationOutput() : mems::Aligner
• SetRecursive() : mems::Aligner
• setRefinement() : mems::ProgressiveAligner
• SetRepeatTolerance() : mems::MemHash
• setReverseComplement() : genome::gnRAWSequence
• SetSequence() : mems::SortedMerList
• SetStart() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• SetTableSize() : mems::MemHash
• SetUseCacheDb() : mems::ProgressiveAligner
• setUseLcbWeightScaling() : mems::ProgressiveAligner
• setUseSeedFamilies() : mems::ProgressiveAligner
• ShiftWords() : mems::SortedMerList
• SimpleBreakpointScorer() : mems::SimpleBreakpointScorer
• SingleStartComparator() : mems::SingleStartComparator< MatchType >
• size() : PhyloTree< T >, genome::gnRAWSequence, mems::working_set_s, mems::_aIORec
• SlotAllocator() : mems::SlotAllocator< T >
• SMLLength() : mems::SortedMerList
• smoothFrequencies() : mems::SeedOccurrenceList
• SortedMerList() : mems::SortedMerList
• SparseAbstractMatch() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >
• Split() : mems::GappedAlignment
• splitContig() : genome::gnRAWSequence
• SSC() : mems::SSC< MatchType >
• Start() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• start_compare() : mems::MatchHashEntry
• start_lessthan() : mems::MatchHashEntry
• start_lessthan_ptr() : mems::MatchHashEntry
• StealMatches() : mems::GenericInterval< GappedBaseImpl >
• strict_start_lessthan_ptr() : mems::MatchHashEntry
• subseq() : genome::gnRAWSequence
• SuperInterval() : mems::SuperInterval
• swap() : mems::SuperInterval, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, PhyloTree< T >, mems::GenericInterval< GappedBaseImpl >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractGappedAlignment< AbstractMatchImpl >

- t -

• TableSize() : mems::MemHash
• ToArray() : genome::gnRAWSequence
• ToString() : genome::gnRAWSequence
• TrackingLCB() : mems::TrackingLCB< MatchType >
• translate() : mems::SortedMerList, mems::CompactGappedAlignment< BaseType >
• translate32() : mems::SortedMerList
• translateGappedCoordinates() : mems::ProgressiveAligner
• TreeNode() : TreeNode

- u -

• undoScoreDifference() : mems::EvenFasterSumOfPairsBreakpointScorer
• UngappedLocalAlignment() : mems::UngappedLocalAlignment< AbstractMatchImpl >
• UniqueMerCount() : mems::SortedMerList, mems::FileSML
• UsedSeq() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch

- v -

• validate() : mems::EvenFasterSumOfPairsBreakpointScorer, mems::CompactGappedAlignment< BaseType >
• validate_bitcount() : mems::CompactGappedAlignment< BaseType >
• ValidateMatches() : mems::GenericInterval< GappedBaseImpl >
• validatePairwiseIntervals() : mems::ProgressiveAligner
• ValidateSelf() : mems::SuperInterval
• validateSuperIntervals() : mems::ProgressiveAligner

- w -

• WriteAlignedSequences() : mems::GenericIntervalList< MatchType >
• WriteFile() : mems::MemHash
• WriteHeader() : mems::FileSML
• WriteList() : mems::RepeatMatchList, mems::GenericIntervalList< MatchType >
• WritePermutation() : mems::Aligner
• WriteStandardAlignment() : mems::GenericIntervalList< MatchType >
• writeTree() : PhyloTree< T >

- ~ -

• ~ClustalInterface() : mems::ClustalInterface
• ~DNAFileSML() : mems::DNAFileSML
• ~GenericInterval() : mems::GenericInterval< GappedBaseImpl >
• ~GenericIntervalList() : mems::GenericIntervalList< MatchType >
• ~gnAlignedSequences() : mems::gnAlignedSequences
• ~LabeledMemComparator() : mems::LabeledMemComparator
• ~MaskedMemHash() : mems::MaskedMemHash
• ~MatchFinder() : mems::MatchFinder
• ~MatchProjectionAdapter() : mems::MatchProjectionAdapter
• ~Matrix() : Matrix< T >
• ~MemHash() : mems::MemHash
• ~MemorySML() : mems::MemorySML
• ~MuscleInterface() : mems::MuscleInterface
• ~NumericMatrix() : NumericMatrix< T >
• ~PairwiseMatchFinder() : mems::PairwiseMatchFinder
• ~PhyloTree() : PhyloTree< T >
• ~PlacementMatchComparator() : mems::PlacementMatchComparator
• ~ProgressiveAligner() : mems::ProgressiveAligner
• ~RepeatMatch() : mems::RepeatMatch
• ~SeedOccurrenceList() : mems::SeedOccurrenceList
• ~SlotAllocator() : mems::SlotAllocator< T >
• ~SortedMerList() : mems::SortedMerList
• ~SuperInterval() : mems::SuperInterval

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