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

- 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 >
• adjs : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer
• align() : mems::ProgressiveAligner, mems::Aligner
• Align() : mems::MuscleInterface, mems::GappedAligner, mems::ClustalInterface
• align_length : mems::AbstractGappedAlignment< AbstractMatchImpl >
• align_matrix : mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >
• alignedSeqsSize() : mems::gnAlignedSequences
• alignedSequenceFileName : mems::gnAlignedSequences
• alignedSequences : mems::gnAlignedSequences
• Aligner() : mems::Aligner
• AlignLCB() : mems::Aligner
• alignment_tree : mems::ProgressiveAligner
• 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
• all_id_remaps : mems::EvenFasterSumOfPairsBreakpointScorer
• Allocate() : mems::SlotAllocator< T >
• allocated : mems::MemHash
• allocated_aln : mems::ClustalInterface
• allocator : mems::MemHash
• alpha_map : mems::MatchFinder
• alpha_map_size : mems::MatchFinder
• alphabet_bits : mems::SMLHeader, mems::MatchFinder, mems::SMLHeader_s
• ambiguity_tolerance : mems::MatchFinder
• AmbiguityTolerance() : mems::MatchFinder
• AncestralScoring : mems::ProgressiveAligner
• AncestralSumOfPairsScoring : mems::ProgressiveAligner
• applyScoreDifference() : mems::EvenFasterSumOfPairsBreakpointScorer
• assignFileName() : mems::gnAlignedSequences

- b -

• back() : PhyloTree< T >
• backbone_filename : mems::GenericIntervalList< MatchType >
• BadSize() : Matrix< T >::BadSize
• base() : mems::FileSML
• base_number : mems::sort_buf_s
• BasicDNATable() : mems::SortedMerList
• bb_cols : mems::bb_entry_s
• bb_seq : mems::bb_entry_s
• bcount : mems::CompactGappedAlignment< BaseType >
• BigCreate() : mems::FileSML
• bin : mems::sort_buf_s
• binary_seq_len : mems::SortedMerList
• bogus_scores : mems::EvenFasterSumOfPairsBreakpointScorer
• BoundsViolation() : Matrix< T >::BoundsViolation
• bp_count : mems::SimpleBreakpointScorer
• bp_dist_estimate_score : mems::ProgressiveAligner
• bp_dist_scale : mems::ProgressiveAligner
• bp_distance : mems::ProgressiveAligner
• bp_penalty : mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer
• bp_weights : mems::EvenFasterSumOfPairsBreakpointScorer
• breakpoint_penalty : mems::ProgressiveAligner
• bsearch() : mems::SortedMerList
• buf : mems::sort_buf_s, mems::iodevice_s, mems::_aIORec
• bufpos : mems::seqbuf_s
• bufs : mems::seqbuf_s, mems::bin_s, mems::working_set_s
• buildConsensus() : mems::gnAlignedSequences
• busy : mems::_aFILE

- c -

• c1_siv : mems::SuperInterval
• c2_siv : mems::SuperInterval
• 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 >
• children : TreeNode
• children_aligned : mems::AlignmentTreeNode
• circular : mems::SMLHeader, mems::SMLHeader_s
• 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 >
• clustal_score_cutoff : mems::ClustalInterface
• ClustalInterface() : mems::ClustalInterface
• collapseIdenticalSequences() : mems::gnAlignedSequences
• collinear : mems::SimpleBreakpointScorer
• collinear_genomes : mems::Aligner
• cols() : Matrix< T >
• comp : mems::CgaBsComp< CompType >
• CompactGappedAlignment() : mems::CompactGappedAlignment< BaseType >
• computeAvgAncestralMatchScores() : mems::ProgressiveAligner
• computeInternalNodeDistances() : mems::ProgressiveAligner
• concatenateAlignedSequences() : mems::gnAlignedSequences
• CondenseGapColumns() : mems::CompactGappedAlignment< BaseType >
• consensus : mems::gnAlignedSequences
• conservation_dist_scale : mems::ProgressiveAligner
• conservation_distance : mems::ProgressiveAligner
• conservation_weights : mems::EvenFasterSumOfPairsBreakpointScorer
• 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 >
• count : mems::_aIORec
• 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
• cur_leftend : mems::AlnProgressTracker
• cur_min_coverage : mems::Aligner
• cur_position : mems::sort_buf_s
• cur_ptr_offsets : mems::sort_buf_s
• currently_recursing : mems::Aligner

- d -

• data : mems::SlotAllocator< T >, mems::SeedOccurrenceList, genome::gnRAWSequence
• data_ : Matrix< T >
• debug : mems::ProgressiveAligner, mems::Aligner
• deleted_tracking_matches : mems::EvenFasterSumOfPairsBreakpointScorer
• DenseAbstractMatch() : mems::DenseAbstractMatch< MAX_SEQS >
• Description() : mems::SortedMerList
• description : mems::SMLHeader, mems::SMLHeader_s
• determineBaseIndex() : mems::gnAlignedSequences
• dev : mems::seqbuf_s, mems::bin_s, mems::device_s, mems::sort_buf_s
• device : mems::buffer_s
• devname : mems::device_s
• distance : TreeNode
• distance_matrix : mems::ClustalInterface
• divisor : mems::sort_buf_s
• 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
• ExtantSumOfPairsScoring : mems::ProgressiveAligner
• extend_lcbs : mems::Aligner
• Extended() : mems::MatchHashEntry
• extended : mems::MatchHashEntry
• ExtendEnd() : mems::UngappedLocalAlignment< AbstractMatchImpl >
• ExtendMatch() : mems::MatchFinder
• ExtendStart() : mems::UngappedLocalAlignment< AbstractMatchImpl >
• extra_muscle_arguments : mems::MuscleInterface
• extractAlignment() : mems::ProgressiveAligner
• extractVariableSites() : mems::gnAlignedSequences

- f -

• file : mems::seqbuf_s, mems::bin_s, mems::buffer_s
• filename : genome::gnRAWSequence, mems::FileSML
• fileop : mems::buffer_s
• filep_high : mems::_aFILE
• filep_low : mems::_aFILE
• 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
• first_time : mems::EvenFasterSumOfPairsBreakpointScorer
• FirstStart() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• fixed_seq_ids : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
• fixed_starts : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
• FixLeftEnds() : mems::ProgressiveAligner
• fname : mems::bin_s
• FormatVersion() : mems::FileSML, mems::DNAFileSML
• forward : mems::AbstractMatch
• Free() : mems::UngappedLocalAlignment< AbstractMatchImpl >, mems::SlotAllocator< T >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::MatchHashEntry, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >, mems::AbstractMatch
• free_list : mems::SlotAllocator< T >
• frequency_type : mems::SeedOccurrenceList
• FromSeq() : mems::RepeatMatch
• full_impact_list : mems::EvenFasterSumOfPairsBreakpointScorer

- g -

• gal : mems::Aligner
• gap_extend : mems::PairwiseScoringScheme
• gap_mh : mems::Aligner
• gap_open : mems::PairwiseScoringScheme
• gapped_alignment : mems::Aligner
• 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
• head : mems::buffer_list_s
• header : mems::SortedMerList
• histogram : mems::sort_buf_s
• histogram_size : mems::sort_buf_s
• HybridAbstractMatch() : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >

- i -

• id : mems::SMLHeader, mems::idmer, mems::SMLHeader_s
• indexPositions : mems::gnAlignedSequences
• init() : Matrix< T >
• input_guide_tree_fname : mems::ProgressiveAligner
• input_pos : mems::buffer_s
• internal_lcb_removed_count : mems::EvenFasterSumOfPairsBreakpointScorer
• internal_lcb_score_diff : mems::EvenFasterSumOfPairsBreakpointScorer
• 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
• inverted : mems::PairwiseMatchAdapter
• io_pos : mems::buffer_s
• io_size : mems::buffer_s
• 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
• iter : mems::PlacementMatch
• iv : mems::bb_entry_s
• IvTrackerComp() : mems::IvTrackerComp

- k -

• key : mems::sml_s, mems::record_s

- l -

• label : mems::LabeledMem
• LabeledMemComparator() : mems::LabeledMemComparator
• LabelSort() : mems::LabelSort< PairType >
• last : mems::buffer_s, mems::_aIORec
• LCB() : mems::LCB
• lcb_id : mems::LCB, mems::TrackingLCB< MatchType >
• lcb_ids : mems::EvenFasterSumOfPairsBreakpointScorer
• LCB_minimum_density : mems::Aligner
• LCB_minimum_range : mems::Aligner
• LCBLeftComparator() : mems::LCBLeftComparator
• LCBLeftEndComp() : mems::LCBLeftEndComp
• LcbScoringScheme : mems::ProgressiveAligner
• left_adjacency : mems::LCB, mems::TrackingLCB< MatchType >
• left_col : mems::HssCols
• left_end : mems::SuperInterval, mems::LCB, mems::TrackingLCB< MatchType >
• 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
• leftend : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >
• leftI : mems::Island
• leftJ : mems::Island
• 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
• little_endian : mems::SMLHeader, mems::SMLHeader_s
• LoadFile() : mems::MemHash, mems::FileSML
• LoadSequences() : mems::RepeatMatchList
• LoadSMLs() : mems::RepeatMatchList, mems::GenericMatchList< MatchPtrType >
• LoadSource() : genome::gnRAWSequence
• localToGlobal() : genome::gnRAWSequence
• localToSource() : genome::gnRAWSequence
• log_stream : mems::MatchFinder
• LogProgress() : mems::MatchFinder
• lrc_zeros : mems::EvenFasterSumOfPairsBreakpointScorer
• lsd_zeros : mems::EvenFasterSumOfPairsBreakpointScorer

- m -

• m : mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter
• m_collision_count : mems::MemHash
• m_enumeration_tolerance : mems::MemHash
• m_extended : mems::MatchHashEntry
• m_length : mems::UngappedLocalAlignment< AbstractMatchImpl >
• m_mem_count : mems::MemHash
• m_mersize : mems::MatchHashEntry
• m_multiplicity : mems::DenseAbstractMatch< MAX_SEQS >
• m_offset : mems::MatchHashEntry
• m_progress : mems::MatchFinder
• m_repeat_tolerance : mems::MemHash
• m_seq : mems::GenericMatchSeqManipulator< MatchType >, mems::LCBLeftComparator, mems::PlacementMatchComparator, mems::LabeledMemComparator, mems::MatchLeftEndComparator, mems::SSC< MatchType >, mems::SingleStartComparator< MatchType >, mems::MatchStartComparator< MatchType >, mems::AbstractMatchSingleStartComparator< MatchType >, mems::AbstractMatchStartComparator< MatchType >
• m_seq_count : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >
• m_seq_id : mems::RepeatMatch
• Marble() : mems::GenericInterval< GappedBaseImpl >
• mask_size : mems::SortedMerList
• MaskedMemHash() : mems::MaskedMemHash
• match_id : mems::LcbTrackingMatch< MatchType >
• match_log : mems::MemHash
• matches : mems::GenericInterval< GappedBaseImpl >, mems::TrackingLCB< MatchType >
• MatchFinder() : mems::MatchFinder
• MatchHashEntry() : mems::MatchHashEntry
• MatchLeftEndComparator() : mems::MatchLeftEndComparator
• MatchProjectionAdapter() : mems::MatchProjectionAdapter
• MatchStartComparator() : mems::MatchStartComparator< MatchType >
• matrix : mems::PairwiseScoringScheme
• Matrix() : Matrix< T >
• max_alignment_length : mems::GappedAligner
• max_extension_iters : mems::Aligner
• max_gapped_alignment_length : mems::ProgressiveAligner
• mem : mems::PlacementMatch, mems::LabeledMem
• mem_table : mems::MemHash
• mem_table_count : mems::MemHash
• MemCollisionCount() : mems::MemHash
• MemCount() : mems::MemHash
• MemHash() : mems::MemHash
• MemoryMinimum() : mems::FileSML
• MemorySML() : mems::MemorySML
• MemTableCount() : mems::MemHash
• MemType : mems::MatchHashEntry
• mer : mems::bmer, mems::idmer
• mer_mask : mems::SortedMerList
• mer_size : mems::MatchFinder
• MerCompare() : mems::MerCompare
• Merge() : mems::SortedMerList, mems::MemorySML, mems::FileSML
• merge() : genome::gnRAWSequence
• mergeContigs() : genome::gnRAWSequence
• mers_processed : mems::MatchFinder
• MerSize() : mems::MatchHashEntry
• mhecomp : mems::MemHash
• min_breakpoint_penalty : mems::ProgressiveAligner, mems::EvenFasterSumOfPairsBreakpointScorer
• min_flank_size : mems::ClustalInterface
• min_recursive_gap_length : mems::Aligner
• min_weight : mems::GreedyRemovalScorer
• mode : mems::_aFILE
• 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
• msc : mems::SearchCacheComparator
• 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 >
• muscle_arguments : mems::MuscleInterface
• muscle_cmdline : mems::MuscleInterface
• muscle_path : mems::MuscleInterface
• MuscleInterface() : mems::MuscleInterface
• my_del_lcbs : mems::EvenFasterSumOfPairsBreakpointScorer

- n -

• n1_des : mems::EvenFasterSumOfPairsBreakpointScorer
• n2_des : mems::EvenFasterSumOfPairsBreakpointScorer
• n_elems : mems::SlotAllocator< T >
• name : TreeNode
• names : mems::gnAlignedSequences
• nbufs : mems::working_set_s
• ncols_ : Matrix< T >
• next : mems::buffer_s, mems::_aIORec
• nitems : mems::buffer_list_s
• NO_SEQ : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
• node_match : mems::LcbTrackingMatch< MatchType >
• node_sequence_map : mems::ProgressiveAligner
• nodes : PhyloTree< T >
• nrecs : mems::bin_s
• nrows_ : Matrix< T >
• num : mems::record_s
• NumericMatrix() : NumericMatrix< T >
• numrecs : mems::buffer_s
• nway_mh : mems::Aligner

- o -

• Offset() : mems::MatchHashEntry
• offset_lessthan() : mems::MatchHashEntry
• offset_stream : mems::MatchFinder
• op : mems::iodevice_s, mems::_aFILE
• OpenForWriting() : mems::FileSML
• operation : mems::buffer_s, mems::_aIORec
• 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::UngappedLocalAlignment< AbstractMatchImpl >, mems::GenericInterval< GappedBaseImpl >, mems::GappedAlignment
• 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::GenericInterval< GappedBaseImpl >, mems::GappedAlignment
• operator[]() : mems::SortedMerList, PhyloTree< T >, mems::MemorySML, genome::gnRAWSequence, mems::gnAlignedSequences, mems::FileSML, mems::AbstractMatch
• ordering : mems::AlignmentTreeNode
• orient : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >
• Orientation() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• orientation : mems::AbstractMatch
• original_match : mems::LcbTrackingMatch< MatchType >
• original_ml : mems::ProgressiveAligner
• output() : mems::gnAlignedSequences
• output_guide_tree_fname : mems::ProgressiveAligner
• outputClustalW() : mems::gnAlignedSequences
• outputCodon() : mems::gnAlignedSequences
• outputMega() : mems::gnAlignedSequences
• outputMSF() : mems::gnAlignedSequences
• outputNexus() : mems::gnAlignedSequences
• outputPhylip() : mems::gnAlignedSequences
• outputWithConsensus() : mems::gnAlignedSequences

- p -

• pairwise_adjacencies : mems::EvenFasterSumOfPairsBreakpointScorer
• pairwise_lcb_count : mems::EvenFasterSumOfPairsBreakpointScorer
• pairwise_lcb_score : mems::EvenFasterSumOfPairsBreakpointScorer
• pairwiseAnchorSearch() : mems::ProgressiveAligner
• PairwiseMatchAdapter() : mems::PairwiseMatchAdapter
• PairwiseMatchFinder() : mems::PairwiseMatchFinder
• pairwiseScoreTrackingMatches() : mems::ProgressiveAligner
• PairwiseScoringScheme() : mems::PairwiseScoringScheme
• parent_siv : mems::SuperInterval
• parents : TreeNode
• parents_aligned : mems::AlignmentTreeNode
• ParseMusclePath() : mems::MuscleInterface
• path : mems::device_s
• payload : mems::record_s
• permutation_filename : mems::Aligner
• permutation_weight : mems::Aligner
• PhyloTree() : PhyloTree< T >
• PlacementMatchComparator() : mems::PlacementMatchComparator
• pos : mems::sml_s, mems::_aIORec
• position : mems::bmer, mems::idmer
• positions : mems::MemorySML, mems::gnAlignedSequences
• prev_progress : mems::AlnProgressTracker
• 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
• queuehead : mems::_aFILE
• queuetail : mems::_aFILE

- r -

• radix_tmp : mems::sort_buf_s
• 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 >
• rec_ptrs : mems::sort_buf_s
• recs : mems::buffer_s
• recurseOnPairs() : mems::ProgressiveAligner
• Recursion() : mems::Aligner
• recursive : mems::Aligner
• RecursiveAnchorSearch() : mems::Aligner
• recursiveApplyAncestralBreakpoints() : mems::ProgressiveAligner
• reference_iv : mems::SuperInterval
• Refine() : mems::MuscleInterface
• refine : mems::ProgressiveAligner
• refineAlignment() : mems::ProgressiveAligner
• refined : mems::AlignmentTreeNode
• 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
• reverse : mems::AbstractMatch
• right_adjacency : mems::LCB, mems::TrackingLCB< MatchType >
• right_col : mems::HssCols
• right_end : mems::LCB, mems::TrackingLCB< MatchType >
• RightEnd() : mems::AbstractMatch
• rightI : mems::Island
• rightJ : mems::Island
• root : PhyloTree< T >
• rows() : Matrix< T >

- s -

• sar : mems::MerCompare
• sar_table : mems::MatchFinder
• sardata : mems::FileSML
• sarfile : mems::FileSML
• sarray_start_offset : mems::FileSML
• score() : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer
• scores : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer
• scoring_scheme : mems::ProgressiveAligner
• search_cache : mems::Aligner
• SearchCacheComparator() : mems::SearchCacheComparator
• SearchRange() : mems::MatchFinder
• SearchWithinLCB() : mems::Aligner
• Seed() : mems::SortedMerList
• seed : mems::SMLHeader, mems::MatchHashEntry, mems::SMLHeader_s
• seed_length : mems::SMLHeader, mems::SMLHeader_s
• seed_mask : mems::SortedMerList
• seed_weight : mems::SMLHeader, mems::SMLHeader_s
• SeedLength() : mems::SortedMerList
• SeedOccurrenceList() : mems::SeedOccurrenceList
• SeedWeight() : mems::SortedMerList
• seq : mems::gnAlignedSequences, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter
• seq_coords : mems::FileSML
• seq_count : mems::MatchFinder, mems::Aligner
• seq_filename : mems::GenericMatchList< MatchPtrType >, mems::GenericIntervalList< MatchType >
• seq_ids : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
• seq_mask : mems::MaskedMemHash
• seq_pos : mems::seqbuf_s
• seq_table : mems::GenericMatchList< MatchPtrType >, mems::MatchFinder, mems::GenericIntervalList< MatchType >
• SeqCount() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• seqI : mems::HssCols, mems::Island
• seqI_count : mems::EvenFasterSumOfPairsBreakpointScorer
• seqI_first : mems::EvenFasterSumOfPairsBreakpointScorer
• seqI_last : mems::EvenFasterSumOfPairsBreakpointScorer
• SeqId() : mems::RepeatMatch
• seqJ : mems::HssCols, mems::Island
• seqJ_count : mems::EvenFasterSumOfPairsBreakpointScorer
• seqJ_first : mems::EvenFasterSumOfPairsBreakpointScorer
• seqJ_last : mems::EvenFasterSumOfPairsBreakpointScorer
• SeqPosToColumn() : mems::CompactGappedAlignment< BaseType >
• SeqToIndex() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
• sequence : mems::SortedMerList, mems::AlignmentTreeNode
• sequenceNameInList() : mems::gnAlignedSequences
• sequences : 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 >
• sml_filename : mems::GenericMatchList< MatchPtrType >
• sml_table : mems::GenericMatchList< MatchPtrType >
• SMLLength() : mems::SortedMerList
• smoothFrequencies() : mems::SeedOccurrenceList
• sol_list : mems::ProgressiveAligner
• sort_state : mems::sort_buf_s
• SortedMerList() : mems::SortedMerList
• SparseAbstractMatch() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >
• Split() : mems::GappedAlignment
• splitContig() : genome::gnRAWSequence
• ssc : mems::LabelSort< PairType >, mems::IvTrackerComp, mems::LCBLeftEndComp
• 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
• starts : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
• state : mems::sort_buf_s, mems::iodevice_s
• StealMatches() : mems::GenericInterval< GappedBaseImpl >
• strict_start_lessthan_ptr() : mems::MatchHashEntry
• subseq() : genome::gnRAWSequence
• subst_scoring : mems::ProgressiveAligner
• 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 -

• table_size : mems::MemHash
• TableSize() : mems::MemHash
• tail_free : mems::SlotAllocator< T >
• tm : mems::PairwiseMatchAdapter
• tm_lcb_id_array : mems::EvenFasterSumOfPairsBreakpointScorer
• tm_score_array : mems::EvenFasterSumOfPairsBreakpointScorer
• tmp_paths : mems::FileSML
• tmpfile : mems::SeedOccurrenceList
• to_be_deleted : mems::LCB, mems::TrackingLCB< MatchType >
• ToArray() : genome::gnRAWSequence
• toclose : mems::_aFILE
• ToString() : genome::gnRAWSequence
• total_len : mems::AlnProgressTracker
• total_mers : mems::MatchFinder
• total_weight : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer
• totalrecs : mems::buffer_s
• tracking_matches : mems::EvenFasterSumOfPairsBreakpointScorer
• TrackingLCB() : mems::TrackingLCB< MatchType >
• translate() : mems::SortedMerList, mems::CompactGappedAlignment< BaseType >
• translate32() : mems::SortedMerList
• translateGappedCoordinates() : mems::ProgressiveAligner
• translation_table : mems::SMLHeader, mems::SMLHeader_s
• TreeNode() : TreeNode

- u -

• undefined : mems::AbstractMatch
• undoScoreDifference() : mems::EvenFasterSumOfPairsBreakpointScorer
• UngappedLocalAlignment() : mems::UngappedLocalAlignment< AbstractMatchImpl >
• unique_mers : mems::SMLHeader, mems::SMLHeader_s
• UniqueMerCount() : mems::SortedMerList, mems::FileSML
• use_seed_families : mems::ProgressiveAligner
• use_weight_scaling : mems::ProgressiveAligner
• UsedSeq() : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >, mems::AbstractMatch
• using_cache_db : mems::ProgressiveAligner
• using_lsd : mems::EvenFasterSumOfPairsBreakpointScorer

- 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
• version : mems::SMLHeader, mems::SMLHeader_s

- w -

• weight : PhyloTree< T >, mems::LCB, mems::TrackingLCB< MatchType >
• word_size : mems::SMLHeader, mems::SMLHeader_s
• 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

---