libMems Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
mems::_aFILE
mems::_aIORec
mems::AbsolutComparator< T >
mems::AbstractGappedAlignment< AbstractMatchImpl >
mems::AbstractMatchAbstractMatch 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::AlignerUsed 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::AlignmentTreeNodeA 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::DNAFileSMLThe seed pattern for DNA SMLs must be palindromic
mems::DNAMemorySMLThe 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::gnAlignedSequencesGnAlignedSequences allows for the manipulation of aligned sequence data
genome::gnRAWSequenceGnRAWSequence 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::IslandA class to represent an island in an alignment
mems::IvTrackerComp
mems::LabeledMemA mem labeled with a number
mems::LabeledMemComparatorCompares Matches labeled with a number
mems::LabelSort< PairType >
mems::LCBThis class is used to track relationships between LCBs during the LCB determination process
mems::LCBIDComparator
mems::LCBLeftComparatorCompares LCBs
mems::LCBLeftEndComp
mems::LcbTrackingMatch< MatchType >A wrapper that maps a match among extant sequences to a match among ancestral and extant seqs
mems::MaskedMemHashFinds matches that meet a particular sequence mask, e.g
mems::MatchFinderThis pure virtual class implements a general framework for finding exactly matching mers
mems::MatchHashEntryThe Match class stores the location of an equal size (inexact or exactly) matching region between several sequences
mems::MatchLeftEndComparator
mems::MatchProjectionAdapterMatchProjectionAdapter 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::MemHashMemHash implements an algorithm for finding exact matches of a certain minimal length in several sequences
mems::MemorySMLThe 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::PairwiseMatchAdapterPairwiseMatchAdapter is a wrapper around an AbstractMatch that effectively projects a multi-match to a pairwise match
mems::PairwiseMatchFinderFinds all pairwise matches with unique seeds among a group of sequences
mems::PairwiseScoringScheme
mems::ParallelMemHashWhen built without OpenMP, the ParallelMemHash is just a stub wrapper around MemHash
PhyloTree< T >
mems::PlacementMatchA match with an associated list iterator
mems::PlacementMatchComparatorCompares Matches
mems::ProgressiveAlignerComputes multiple genome alignments using a progressive alignment algorithm
mems::record_s
mems::RepeatHashFinds repeats within a single sequence
mems::RepeatMatchThe Match class stores the location of an equal size (inexact or exactly) matching region between several sequences
mems::RepeatMatchList
mems::SearchCacheComparatorUsed for search cache lookups
mems::SeedOccurrenceList
mems::seqbuf_s
mems::SimpleBreakpointScorerA 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::SortedMerListA 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::SuperIntervalA 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

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