mems::GenericMatchList< MatchPtrType > Class Template Reference

#include <MatchList.h>

Inheritance diagram for mems::GenericMatchList< MatchPtrType >:

[legend]List of all members.

Public Member Functions
void	Clear ()
	Deletes the genome::gnSequence, SortedMerList, and Match objects associated with this GenericMatchList.
void	CreateMemorySMLs (uint mer_size, std::ostream *log_stream, int seed_rank=0)
	Loads sequences to align from a Multi-FastA file and constructs a SML for each sequence entry in the file.
	GenericMatchList (const GenericMatchList &ml)
	GenericMatchList ()
void	LengthFilter (gnSeqI length)
	Removes all matches that shorter than the specified length.
void	LoadSMLs (uint mer_size, std::ostream *log_stream, int seed_rank=0)
	Attempts to load SMLs designated by the elements of the sml_filename vector.
void	MultiplicityFilter (unsigned mult)
	Removes all matches that have a multiplicity lower than the specified level.
GenericMatchList &	operator= (const GenericMatchList &ml)
Static Public Member Functions
uint	GetDefaultMerSize (const std::vector< genome::gnSequence * > &seq_table)
	Calculates a default search mer size for the given set of sequences.
Public Attributes
std::vector< std::string >	seq_filename
	The file names of the sequence data, may be empty or null.
std::vector< genome::gnSequence * >	seq_table
	The actual sequences associated with the matches stored in this list.
std::vector< std::string >	sml_filename
	The file names of the sorted mer list for each sequence, may be empty or null.
std::vector< SortedMerList * >	sml_table
	The sorted mer list associated with each sequence, may be empty or null.

template<typename MatchPtrType>
class mems::GenericMatchList< MatchPtrType >

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Constructor & Destructor Documentation

template<typename MatchPtrType> mems::GenericMatchList< MatchPtrType >::GenericMatchList (   )  [inline]

Definition at line 36 of file MatchList.h.

template<typename MatchPtrType> mems::GenericMatchList< MatchPtrType >::GenericMatchList (  const GenericMatchList< MatchPtrType > &  ml  )

Definition at line 145 of file MatchList.h.

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Member Function Documentation

template<typename MatchPtrType> void mems::GenericMatchList< MatchPtrType >::Clear (   )

Deletes the genome::gnSequence, SortedMerList, and Match objects associated with this GenericMatchList. Definition at line 430 of file MatchList.h. References mems::GenericMatchList< MatchPtrType >::sml_filename, mems::GenericMatchList< MatchPtrType >::sml_table, and uint.

template<typename MatchPtrType> void mems::GenericMatchList< MatchPtrType >::CreateMemorySMLs (  uint  mer_size, std::ostream *  log_stream, int  seed_rank = 0 )

Loads sequences to align from a Multi-FastA file and constructs a SML for each sequence entry in the file. The genome::gnSequence and SortedMerList objects are created on the heap and are not deallocated when this class is destroyed. They should be manually destroyed when no longer in use. Parameters: mer_size  The seed size to use when constructing the sorted mer lists log_stream  An output stream to log messages to. If NULL no logging is done load_smls  Specifies whether sorted mer lists should be created for each sequence entry Definition at line 400 of file MatchList.h. References mems::MemorySML::Create(), mems::GenericMatchList< MatchPtrType >::GetDefaultMerSize(), getSeed(), mems::GenericMatchList< MatchPtrType >::sml_table, uint, and mems::uint64.

template<typename MatchPtrType> uint mems::GenericMatchList< MatchPtrType >::GetDefaultMerSize (  const std::vector< genome::gnSequence * > &  seq_table  )  [static]

Calculates a default search mer size for the given set of sequences. Parameters: seq_table  The vector of sequences to calculate a default mer size for Definition at line 344 of file MatchList.h. References getDefaultSeedWeight(), and uint. Referenced by mems::GenericMatchList< MatchPtrType >::CreateMemorySMLs(), mems::RepeatMatchList::LoadSMLs(), and mems::GenericMatchList< MatchPtrType >::LoadSMLs().

template<typename MatchPtrType> void mems::GenericMatchList< MatchPtrType >::LengthFilter (  gnSeqI  length  )

Removes all matches that shorter than the specified length. Parameters: length  The minimum length Definition at line 644 of file MatchList.h. Referenced by mems::ProgressiveAligner::pairwiseAnchorSearch(), mems::Aligner::Recursion(), and mems::SearchLCBGaps().

template<typename MatchPtrType> void mems::GenericMatchList< MatchPtrType >::LoadSMLs (  uint  mer_size, std::ostream *  log_stream, int  seed_rank = 0 )

Attempts to load SMLs designated by the elements of the sml_filename vector. This method will create the sorted mer lists if they do not exist. The DNAFileSML objects are created on the heap and are not deallocated when this class is destroyed. They should be manually destroyed when no longer in use. Parameters: seed_rank  The rank of the seed to use, 0-2 are ranked spaced seeds, other options include CODING_SEED and SOLID_SEED Definition at line 262 of file MatchList.h. References mems::GenericMatchList< MatchPtrType >::GetDefaultMerSize(), getSeed(), mems::FileSML::LoadFile(), mems::SortedMerList::Seed(), mems::GenericMatchList< MatchPtrType >::sml_filename, mems::GenericMatchList< MatchPtrType >::sml_table, uint, and mems::uint64.

template<typename MatchPtrType> void mems::GenericMatchList< MatchPtrType >::MultiplicityFilter (  unsigned  mult  )

Removes all matches that have a multiplicity lower than the specified level. Parameters: mult  The multiplicity filter threshold Definition at line 629 of file MatchList.h. References uint. Referenced by mems::Aligner::align(), mems::ProgressiveAligner::CreatePairwiseBPDistance(), mems::Aligner::Recursion(), mems::SearchLCBGaps(), and mems::Aligner::SearchWithinLCB().

template<typename MatchPtrType> GenericMatchList< MatchPtrType > & mems::GenericMatchList< MatchPtrType >::operator= (  const GenericMatchList< MatchPtrType > &  ml  )

Definition at line 150 of file MatchList.h. References mems::GenericMatchList< MatchPtrType >::seq_filename, mems::GenericMatchList< MatchPtrType >::seq_table, mems::GenericMatchList< MatchPtrType >::sml_filename, and mems::GenericMatchList< MatchPtrType >::sml_table.

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Member Data Documentation

template<typename MatchPtrType> std::vector<std::string> mems::GenericMatchList< MatchPtrType >::seq_filename

The file names of the sequence data, may be empty or null. Definition at line 108 of file MatchList.h. Referenced by mems::Aligner::align(), mems::MemHash::FindMatchesFromPosition(), mems::ProgressiveAligner::getPairwiseMatches(), mems::GenericMatchList< MatchPtrType >::operator=(), mems::ReadList(), mems::Aligner::RecursiveAnchorSearch(), and mems::WriteList().

template<typename MatchPtrType> std::vector<genome::gnSequence*> mems::GenericMatchList< MatchPtrType >::seq_table

The actual sequences associated with the matches stored in this list. Should not be empty or null. Definition at line 110 of file MatchList.h. Referenced by mems::Aligner::align(), mems::Aligner::AlignLCB(), mems::AlignLCBInParallel(), mems::ProgressiveAligner::alignProfileToProfile(), mems::ProgressiveAligner::CreatePairwiseBPDistance(), mems::DistanceMatrix(), mems::MemHash::FindMatches(), mems::MemHash::FindMatchesFromPosition(), mems::GetLCBCoverage(), mems::MemHash::GetMatchList(), mems::ProgressiveAligner::getPairwiseMatches(), mems::GenericMatchList< MatchPtrType >::operator=(), mems::ProgressiveAligner::pairwiseAnchorSearch(), mems::ReadList(), mems::ProgressiveAligner::recurseOnPairs(), mems::Aligner::Recursion(), mems::Aligner::RecursiveAnchorSearch(), mems::SearchLCBGaps(), and mems::WriteList().

template<typename MatchPtrType> std::vector<std::string> mems::GenericMatchList< MatchPtrType >::sml_filename

The file names of the sorted mer list for each sequence, may be empty or null. Parameters: filter_spec  The specification of the intersection filter, true designates match must exist in that sequence. filter_spec must contain one boolean entry for every sequence. Definition at line 107 of file MatchList.h. Referenced by mems::GenericMatchList< MatchPtrType >::Clear(), mems::GenericMatchList< MatchPtrType >::LoadSMLs(), and mems::GenericMatchList< MatchPtrType >::operator=().

template<typename MatchPtrType> std::vector<SortedMerList*> mems::GenericMatchList< MatchPtrType >::sml_table

The sorted mer list associated with each sequence, may be empty or null. Definition at line 109 of file MatchList.h. Referenced by mems::GenericMatchList< MatchPtrType >::Clear(), mems::GenericMatchList< MatchPtrType >::CreateMemorySMLs(), mems::MemHash::FindMatchesFromPosition(), mems::MemHash::GetMatchList(), mems::GenericMatchList< MatchPtrType >::LoadSMLs(), mems::GenericMatchList< MatchPtrType >::operator=(), mems::ProgressiveAligner::pairwiseAnchorSearch(), mems::Aligner::Recursion(), and mems::SearchLCBGaps().

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The documentation for this class was generated from the following file:

• libMems/MatchList.h

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