| mems::_aFILE | |
| mems::_aIORec | |
| mems::AbsolutComparator< T > | |
| mems::AbstractGappedAlignment< AbstractMatchImpl > | |
| mems::AbstractMatch | AbstractMatch is a pure virtual base class that defines an interface for both gapped and ungapped alignments among several sequences or several regions of the same sequence |
| mems::AbstractMatchSingleStartComparator< MatchType > | |
| mems::AbstractMatchStartComparator< MatchType > | |
| mems::Aligner | Used to find locally colinear blocks (LCBs) and do recursive alignments on the blocks To create an alignment one need only use the align method |
| mems::AlignmentTreeNode | A class that stores alignment-related information as a node in a phylogenetic tree |
| mems::AlnProgressTracker | |
| mems::bb_entry_s | |
| mems::bin_s | |
| mems::bmer | |
| mems::buffer_list_s | |
| mems::buffer_s | |
| mems::CgaBsComp< CompType > | |
| mems::ClustalInterface | |
| mems::CompactGappedAlignment< BaseType > | The CompactGappedAlignment stores a gapped alignment as a bit-vector Rather than using one byte per aligned position, this class uses one bit, making particularly space efficient |
| mems::DenseAbstractMatch< MAX_SEQS > | The DenseAbstractMatch implements the AbstractMatch interface in a way that is most efficient when Multiplicity and SeqCount are identical or nearly so |
| mems::device_s | |
| mems::DNAFileSML | The seed pattern for DNA SMLs must be palindromic |
| mems::DNAMemorySML | The DNAMemorySML is an implementation of sorted mer lists which creates and stores the sorted mer list entirely in memory |
| mems::EvenFasterSumOfPairsBreakpointScorer | |
| mems::FileSML | |
| mems::GappedAligner | |
| mems::GappedAlignment | |
| mems::GenericInterval< GappedBaseImpl > | |
| mems::GenericIntervalList< MatchType > | This class represents a set Intervals, each of which is a collinear aligned region There are functions to read and write an GenericIntervalList |
| mems::GenericMatchList< MatchPtrType > | |
| mems::GenericMatchSeqManipulator< MatchType > | |
| mems::gnAlignedSequences | GnAlignedSequences allows for the manipulation of aligned sequence data |
| genome::gnRAWSequence | GnRAWSequence is a bastardization of gnSequence that creates a lightweight wrapper around a memory-mapped file of raw sequence data |
| mems::GreedyRemovalScorer | |
| mems::HssCols | |
| mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc > | The HybridAbstractMatch implements the AbstractMatch interface in a way that allows matches with a large SeqCount and low Multiplicity to be stored efficiently |
| mems::idmer | |
| mems::iodevice_s | |
| mems::Island | A class to represent an island in an alignment |
| mems::IvTrackerComp | |
| mems::LabeledMem | A mem labeled with a number |
| mems::LabeledMemComparator | Compares Matches labeled with a number |
| mems::LabelSort< PairType > | |
| mems::LCB | This class is used to track relationships between LCBs during the LCB determination process |
| mems::LCBIDComparator | |
| mems::LCBLeftComparator | Compares LCBs |
| mems::LCBLeftEndComp | |
| mems::LcbTrackingMatch< MatchType > | A wrapper that maps a match among extant sequences to a match among ancestral and extant seqs |
| mems::MaskedMemHash | Finds matches that meet a particular sequence mask, e.g |
| mems::MatchFinder | This pure virtual class implements a general framework for finding exactly matching mers |
| mems::MatchHashEntry | The Match class stores the location of an equal size (inexact or exactly) matching region between several sequences |
| mems::MatchLeftEndComparator | |
| mems::MatchProjectionAdapter | MatchProjectionAdapter is a wrapper around an AbstractMatch that effectively projects a multi-match to a subset match |
| mems::MatchStartComparator< MatchType > | |
| Matrix< T > | |
| Matrix< T >::BadSize | |
| Matrix< T >::BoundsViolation | |
| mems::MemHash | MemHash implements an algorithm for finding exact matches of a certain minimal length in several sequences |
| mems::MemorySML | The MemorySML is an implementation of sorted mer lists which creates and stores the sorted mer list entirely in memory |
| mems::MerCompare | |
| mems::MheCompare | |
| mems::MoveScoreHeapComparator | |
| mems::MuscleInterface | |
| NumericMatrix< T > | |
| mems::PairwiseMatchAdapter | PairwiseMatchAdapter is a wrapper around an AbstractMatch that effectively projects a multi-match to a pairwise match |
| mems::PairwiseMatchFinder | Finds all pairwise matches with unique seeds among a group of sequences |
| mems::PairwiseScoringScheme | |
| mems::ParallelMemHash | When built without OpenMP, the ParallelMemHash is just a stub wrapper around MemHash |
| PhyloTree< T > | |
| mems::PlacementMatch | A match with an associated list iterator |
| mems::PlacementMatchComparator | Compares Matches |
| mems::ProgressiveAligner | Computes multiple genome alignments using a progressive alignment algorithm |
| mems::record_s | |
| mems::RepeatHash | Finds repeats within a single sequence |
| mems::RepeatMatch | The Match class stores the location of an equal size (inexact or exactly) matching region between several sequences |
| mems::RepeatMatchList | |
| mems::SearchCacheComparator | Used for search cache lookups |
| mems::SeedOccurrenceList | |
| mems::seqbuf_s | |
| mems::SimpleBreakpointScorer | A breakpoint scorer that applies a fixed penalty for each breakpoint that exists in a set of two or more sequences |
| mems::SingleStartComparator< MatchType > | |
| mems::SlotAllocator< T > | This class allocates memory according to the slot allocation scheme for fixed size objects |
| mems::sml_s | |
| mems::SMLHeader | |
| mems::SMLHeader_s | |
| mems::sort_buf_s | |
| mems::SortedMerList | A base class which defines an interface common to all sorted mer lists |
| mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc > | The SparseAbstractMatch implements the AbstractMatch interface in a way that allows matches with a large SeqCount and low Multiplicity to be stored efficiently |
| mems::SSC< MatchType > | |
| mems::SuperInterval | A class that stores an alignment and coordinate mapping between collinear segments of an ancestral genome and two descendant genomes |
| mems::SuperIntervalManipulator | |
| mems::SuperIntervalPtrComp | |
| mems::TrackingLCB< MatchType > | This class is used to track relationships between LCBs during the LCB determination process |
| TreeNode | |
| mems::UngappedLocalAlignment< AbstractMatchImpl > | The UngappedLocalAlignment class stores the location of an equal size (inexact or exactly) matching region between several sequences |
| mems::working_set_s |
1.3.6