mems::ProgressiveAligner Class Reference

Computes multiple genome alignments using a progressive alignment algorithm. More...

#include <ProgressiveAligner.h>

Inheritance diagram for mems::ProgressiveAligner:

[legend]Collaboration diagram for mems::ProgressiveAligner:

[legend]List of all members.

Public Types
enum	LcbScoringScheme { AncestralScoring, AncestralSumOfPairsScoring, ExtantSumOfPairsScoring }
Public Member Functions
void	align (std::vector< genome::gnSequence * > &seq_table, mems::IntervalList &interval_list)
void	alignNodes (node_id_t node1, node_id_t node2, node_id_t ancestor)
	align the sequences at the designated pair of alignment tree nodes
void	alignPP (mems::IntervalList &prof1, mems::IntervalList &prof2, mems::IntervalList &interval_list)
void	alignProfileToProfile (node_id_t node1, node_id_t node2, node_id_t ancestor)
	constructs an alignment of node1 and node2 at their ancestor
void	computeAvgAncestralMatchScores (std::vector< TrackingMatch > &tracking_matches, std::vector< node_id_t > &node1_descendants, std::vector< node_id_t > &node2_descendants, boost::multi_array< double, 3 > &tm_score_array)
void	computeInternalNodeDistances (boost::multi_array< double, 2 > &bp_dist_mat, boost::multi_array< double, 2 > &cons_dist_mat, std::vector< node_id_t > &node1_descendants, std::vector< node_id_t > &node2_descendants)
void	constructLcbTrackingMatches (node_id_t ancestral_node, std::vector< mems::AbstractMatch * > &ancestral_matches, std::vector< mems::LcbTrackingMatch< mems::AbstractMatch * > > &tracking_matches)
void	ConstructSuperIntervalFromMSA (node_id_t ancestor, size_t ans_siv, mems::GappedAlignment &gal)
void	createAncestralOrdering (std::vector< mems::Interval * > &interval_list, std::vector< SuperInterval > &ancestral_sequence)
void	CreatePairwiseBPDistance (boost::multi_array< double, 2 > &bp_distmat)
void	doGappedAlignment (node_id_t ancestor, bool profile_aln)
void	extractAlignment (node_id_t ancestor, size_t super_iv, mems::CompactGappedAlignment<> &cga)
void	extractAlignment (node_id_t ancestor, size_t super_iv, mems::GappedAlignment &gal)
void	FixLeftEnds (node_id_t ancestor)
void	getAlignedChildren (node_id_t node, std::vector< node_id_t > &descendants)
	determine which extant sequences have been aligned at a given node
void	getAncestralMatches (const std::vector< node_id_t > node1_seqs, const std::vector< node_id_t > node2_seqs, node_id_t node1, node_id_t node2, node_id_t ancestor, std::vector< mems::AbstractMatch * > &ancestral_matches)
double	getBpDistEstimateMinScore (void)
double	getBreakpointDistanceScale (void)
double	getConservationDistanceScale (void)
LcbScoringScheme	getLcbScoringScheme (void)
void	getPairwiseMatches (const std::vector< node_id_t > &node1_seqs, const std::vector< node_id_t > &node2_seqs, Matrix< mems::MatchList > &pairwise_matches)
void	getPath (node_id_t first_n, node_id_t last_n, std::vector< node_id_t > &path)
	determine which extant sequences have been aligned at a given node
void	getRepresentativeAncestralMatches (const std::vector< node_id_t > node1_seqs, const std::vector< node_id_t > node2_seqs, node_id_t node1, node_id_t node2, node_id_t ancestor, std::vector< mems::AbstractMatch * > &ancestral_matches)
bool	getUseLcbWeightScaling (void)
bool	getUseSeedFamilies (void)
void	linkSuperIntervals (node_id_t node1, uint seqI, node_id_t ancestor)
ProgressiveAligner &	operator= (const ProgressiveAligner &al)
void	pairwiseAnchorSearch (mems::MatchList &r_list, mems::Match *r_begin, mems::Match *r_end, const mems::AbstractMatch *iv, uint oseqI, uint oseqJ)
void	pairwiseScoreTrackingMatches (std::vector< mems::TrackingMatch > &tracking_matches, std::vector< node_id_t > &node1_descendants, std::vector< node_id_t > &node2_descendants, boost::multi_array< double, 3 > &tm_score_array)
	ProgressiveAligner (const ProgressiveAligner &al)
	ProgressiveAligner (uint seq_count)
	Constructs an aligner for the specified number of sequences.
template<class MatchType> void	propagateDescendantBreakpoints (node_id_t node1, uint seqI, std::vector< MatchType * > &iv_list)
template<class GappedAlignmentType> void	recurseOnPairs (const std::vector< node_id_t > &node1_seqs, const std::vector< node_id_t > &node2_seqs, const GappedAlignmentType &iv, Matrix< mems::MatchList > &matches, Matrix< std::vector< mems::search_cache_t > > &search_cache_db, Matrix< std::vector< mems::search_cache_t > > &new_cache_db, boost::multi_array< std::vector< std::vector< int64 > >, 2 > &iv_regions)
void	recursiveApplyAncestralBreakpoints (node_id_t ancestor)
void	refineAlignment (mems::GappedAlignment &gal, node_id_t ancestor, bool profile_aln, AlnProgressTracker &apt)
void	setBpDistEstimateMinScore (double min_score)
void	setBreakpointDistanceScale (double bp_dist_scale)
void	setBreakpointPenalty (double bp_penalty)
	sets the breakpoint penalty
void	setCollinear (boolean collinear)
	assume all genomes are collinear when set to true
void	setConservationDistanceScale (double conservation_dist_scale)
void	setGappedAlignment (bool do_gapped_alignment)
	Set whether iterative refinement using MUSCLE should be performed (true/false).
void	setInputGuideTreeFileName (std::string &fname)
	use a precomputed guide tree stored in the given file
void	setLcbScoringScheme (LcbScoringScheme scheme)
	set LCB the scoring scheme
void	SetMaxGappedAlignmentLength (size_t len)
	set the max length (in columns) of alignments passed to MUSCLE
void	setMinimumBreakpointPenalty (double min_bp_penalty)
	sets the the minimum breakpoint penalty after scaling
void	setOutputGuideTreeFileName (std::string &fname)
	write the guide tree stored to the given file
void	setPairwiseMatches (mems::MatchList &pair_ml)
	use a list of precomputed matches instead of computing them
void	setPairwiseScoringScheme (const mems::PairwiseScoringScheme &pss)
void	setRefinement (bool refine)
	Set whether iterative refinement using MUSCLE should be performed (true/false).
void	SetUseCacheDb (bool cbd)
	set whether a cache database should be used to speed up recursive anchor search
void	setUseLcbWeightScaling (bool use_weight_scaling)
void	setUseSeedFamilies (bool use_seed_families)
void	translateGappedCoordinates (std::vector< mems::AbstractMatch * > &ml, uint seqI, node_id_t extant, node_id_t ancestor)
bool	validatePairwiseIntervals (node_id_t node1, node_id_t node2, std::vector< mems::Interval * > &pair_iv)
bool	validateSuperIntervals (node_id_t node1, node_id_t node2, node_id_t ancestor)
	~ProgressiveAligner ()
Protected Member Functions
void	getAlignment (mems::IntervalList &interval_list)
Protected Attributes
PhyloTree< AlignmentTreeNode >	alignment_tree
double	bp_dist_estimate_score
	the minimum LCB score to use when estimating BP distance
double	bp_dist_scale
boost::multi_array< double, 2 >	bp_distance
	pairwise breakpoint distances
double	breakpoint_penalty
double	conservation_dist_scale
boost::multi_array< double, 2 >	conservation_distance
	pairwise genome conservation distances
boolean	debug
	Flag for debugging output.
std::string	input_guide_tree_fname
size_t	max_gapped_alignment_length
double	min_breakpoint_penalty
std::vector< uint >	node_sequence_map
mems::MatchList	original_ml
	The list of matches calculated among all sequences.
std::string	output_guide_tree_fname
boolean	refine
LcbScoringScheme	scoring_scheme
std::vector< SeedOccurrenceList >	sol_list
mems::PairwiseScoringScheme	subst_scoring
bool	use_seed_families
bool	use_weight_scaling
bool	using_cache_db

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Detailed Description

Computes multiple genome alignments using a progressive alignment algorithm.

Definition at line 53 of file ProgressiveAligner.h.

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Member Enumeration Documentation

enum mems::ProgressiveAligner::LcbScoringScheme

Enumeration values: AncestralScoring  AncestralSumOfPairsScoring  ExtantSumOfPairsScoring  Definition at line 90 of file ProgressiveAligner.h. Referenced by getLcbScoringScheme().

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Constructor & Destructor Documentation

mems::ProgressiveAligner::ProgressiveAligner (  uint  seq_count  )

Constructs an aligner for the specified number of sequences. Parameters: seq_count  The number of sequences that will be aligned with this Aligner Definition at line 134 of file ProgressiveAligner.cpp. References max_gapped_alignment_length, mems::max_window_size, and uint.

mems::ProgressiveAligner::ProgressiveAligner (  const ProgressiveAligner &  al  )

mems::ProgressiveAligner::~ProgressiveAligner (   )  [inline]

Definition at line 243 of file ProgressiveAligner.h. References original_ml.

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Member Function Documentation

void mems::ProgressiveAligner::align (  std::vector< genome::gnSequence * > &  seq_table, mems::IntervalList &  interval_list )

Definition at line 3741 of file ProgressiveAligner.cpp. References mems::debug_aligner.

void mems::ProgressiveAligner::alignNodes (  node_id_t  node1, node_id_t  node2, node_id_t  ancestor )

align the sequences at the designated pair of alignment tree nodes Definition at line 2905 of file ProgressiveAligner.cpp. References alignment_tree, alignProfileToProfile(), and mems::markAligned(). Referenced by getAlignment().

void mems::ProgressiveAligner::alignPP (  mems::IntervalList &  prof1, mems::IntervalList &  prof2, mems::IntervalList &  interval_list )

Definition at line 3531 of file ProgressiveAligner.cpp. References CreateTempFileName(), mems::MuscleInterface::CreateTree(), mems::debug_aligner, mems::DistanceMatrix(), mems::EliminateOverlaps_v2(), mems::getDefaultBpDistEstimateMinScore(), mems::getDefaultBreakpointPenalty(), mems::makeAlignmentTree(), mems::MatchList, node_id_t, mems::print2d_matrix(), PhyloTree< AlignmentTreeNode >::readTree(), registerFileToDelete(), PhyloTree< AlignmentTreeNode >::size(), and uint.

void mems::ProgressiveAligner::alignProfileToProfile (  node_id_t  node1, node_id_t  node2, node_id_t  ancestor )

constructs an alignment of node1 and node2 at their ancestor < the node id's of extant sequences below node 1 < the node id's of extant sequences below node 2 A cache of regions that were searched in the previous round of recursion Definition at line 1997 of file ProgressiveAligner.cpp. References mems::addUnalignedIntervals_v2(), mems::cachecomp(), mems::computeID(), mems::computeLCBAdjacencies_v3(), mems::ComputeLCBs_v2(), mems::GenericInterval< GappedBaseImpl >::Copy(), mems::countUnrefined(), mems::dbg_count, mems::debug_aligner, mems::debug_me, mems::EliminateOverlaps_v2(), mems::filterMatches_v2(), mems::GetAlignment(), getDescendants(), mems::GenericInterval< GappedBaseImpl >::GetMatches(), mems::getPairwiseLCBs(), mems::EvenFasterSumOfPairsBreakpointScorer::getResults(), mems::greedyBreakpointElimination_v4(), mems::greedySearch(), mems::IdentifyBreakpoints(), mems::initTrackingMatchLCBTracking(), mems::Interval, mems::SparseAbstractMatch<>::LeftEnd(), mems::markAsRefined(), mems::MatchList, mems::mergeUnalignedIntervals(), mems::multFilter(), mems::PairwiseLCBMatrix, mems::print2d_matrix(), printMemUsage(), mems::search_cache_t, mems::SearchLCBGaps(), mems::GenericMatchList< MatchPtrType >::seq_table, mems::SparseAbstractMatch<>::SeqCount(), mems::SimpleGetLCBCoverage(), and uint. Referenced by alignNodes().

void mems::ProgressiveAligner::computeAvgAncestralMatchScores (  std::vector< TrackingMatch > &  tracking_matches, std::vector< node_id_t > &  node1_descendants, std::vector< node_id_t > &  node2_descendants, boost::multi_array< double, 3 > &  tm_score_array )

Definition at line 1796 of file ProgressiveAligner.cpp. References getAlignedChildren(), node_id_t, and uint. Referenced by pairwiseScoreTrackingMatches().

void mems::ProgressiveAligner::computeInternalNodeDistances (  boost::multi_array< double, 2 > &  bp_dist_mat, boost::multi_array< double, 2 > &  cons_dist_mat, std::vector< node_id_t > &  node1_descendants, std::vector< node_id_t > &  node2_descendants )

Definition at line 1856 of file ProgressiveAligner.cpp. References bp_distance, conservation_distance, getAlignedChildren(), node_id_t, node_sequence_map, and uint.

void mems::ProgressiveAligner::constructLcbTrackingMatches (  node_id_t  ancestral_node, std::vector< mems::AbstractMatch * > &  ancestral_matches, std::vector< mems::LcbTrackingMatch< mems::AbstractMatch * > > &  tracking_matches )

Definition at line 1537 of file ProgressiveAligner.cpp. References alignment_tree, mems::bitset_t, mems::CompactGappedAlignment< BaseType >::Copy(), mems::CompactGappedAlignment< BaseType >::copyRange(), mems::debugging_cltm, mems::CompactGappedAlignment< BaseType >::GetAlignment(), mems::CompactGappedAlignment< BaseType >::Invert(), mems::LcbTrackingMatch< MatchType >::match_id, node_id_t, mems::LcbTrackingMatch< MatchType >::node_match, node_sequence_map, mems::LcbTrackingMatch< MatchType >::original_match, propagateDescendantBreakpoints(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), mems::TrackingMatch, mems::CompactGappedAlignment< BaseType >::translate(), and uint.

void mems::ProgressiveAligner::ConstructSuperIntervalFromMSA (  node_id_t  ancestor, size_t  ans_siv, mems::GappedAlignment &  gal )

Definition at line 1384 of file ProgressiveAligner.cpp. References alignment_tree, mems::bitset_t, mems::CompactGappedAlignment< BaseType >::Copy(), getAlignedChildren(), mems::GetAlignment(), mems::Interval, mems::CompactGappedAlignment< BaseType >::Invert(), node_id_t, node_sequence_map, mems::propagateInvert(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), PhyloTree< AlignmentTreeNode >::size(), and uint. Referenced by doGappedAlignment().

void mems::ProgressiveAligner::createAncestralOrdering (  std::vector< mems::Interval * > &  interval_list, std::vector< SuperInterval > &  ancestral_sequence )

Definition at line 2703 of file ProgressiveAligner.cpp. References mems::debug_aligner, and uint.

void mems::ProgressiveAligner::CreatePairwiseBPDistance (  boost::multi_array< double, 2 > &  bp_distmat  )

Definition at line 3335 of file ProgressiveAligner.cpp. References mems::computeLCBAdjacencies_v3(), mems::ComputeLCBs_v2(), mems::EliminateOverlaps_v2(), mems::filterMatches_v2(), mems::getDefaultBreakpointMax(), mems::GetPairwiseAnchorScore(), mems::greedyBreakpointElimination_v4(), mems::IdentifyBreakpoints(), mems::MatchList, mems::GenericMatchList< MatchPtrType >::MultiplicityFilter(), mems::GenericMatchList< MatchPtrType >::seq_table, and uint.

void mems::ProgressiveAligner::doGappedAlignment (  node_id_t  ancestor, bool  profile_aln )

Definition at line 1207 of file ProgressiveAligner.cpp. References alignment_tree, mems::AbstractGappedAlignment< SparseAbstractMatch<> >::AlignmentLength(), ConstructSuperIntervalFromMSA(), mems::AlnProgressTracker::cur_leftend, mems::debug_aligner, extractAlignment(), FixLeftEnds(), mems::SparseAbstractMatch<>::Multiplicity(), node_id_t, mems::AlnProgressTracker::prev_progress, printMemUsage(), mems::printProgress(), refineAlignment(), PhyloTree< AlignmentTreeNode >::size(), mems::AlnProgressTracker::total_len, uint, and validateSuperIntervals(). Referenced by getAlignment().

void mems::ProgressiveAligner::extractAlignment (  node_id_t  ancestor, size_t  super_iv, mems::CompactGappedAlignment<> &  cga )

Definition at line 3205 of file ProgressiveAligner.cpp. References alignment_tree, mems::CompactGappedAlignment< BaseType >::Copy(), mems::UngappedLocalAlignment< AbstractMatchImpl >::Copy(), mems::CompactGappedAlignment< BaseType >::Free(), mems::CompactGappedAlignment< BaseType >::GetAlignment(), mems::SuperInterval::LeftEnd(), mems::SuperInterval::Length(), mems::Match, node_id_t, node_sequence_map, mems::CompactGappedAlignment< BaseType >::SetAlignment(), mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), PhyloTree< AlignmentTreeNode >::size(), translateGappedCoordinates(), and uint.

void mems::ProgressiveAligner::extractAlignment (  node_id_t  ancestor, size_t  super_iv, mems::GappedAlignment &  gal )

Definition at line 3188 of file ProgressiveAligner.cpp. References mems::GetAlignment(). Referenced by doGappedAlignment(), and getAlignment().

void mems::ProgressiveAligner::FixLeftEnds (  node_id_t  ancestor  )

Definition at line 1257 of file ProgressiveAligner.cpp. References alignment_tree, mems::SuperInterval::LeftEnd(), mems::SuperInterval::Length(), node_id_t, PhyloTree< AlignmentTreeNode >::size(), uint, and mems::CompactGappedAlignment< BaseType >::validate(). Referenced by doGappedAlignment().

void mems::ProgressiveAligner::getAlignedChildren (  node_id_t  node, std::vector< node_id_t > &  descendants )

determine which extant sequences have been aligned at a given node Definition at line 160 of file ProgressiveAligner.cpp. References alignment_tree, node_id_t, mems::progress_msgs, PhyloTree< AlignmentTreeNode >::size(), and uint. Referenced by computeAvgAncestralMatchScores(), computeInternalNodeDistances(), ConstructSuperIntervalFromMSA(), and refineAlignment().

void mems::ProgressiveAligner::getAlignment (  mems::IntervalList &  interval_list  )  [protected]

Definition at line 3689 of file ProgressiveAligner.cpp. References alignment_tree, alignNodes(), mems::chooseNextAlignmentPair(), doGappedAlignment(), extractAlignment(), mems::Interval, node_id_t, refine, PhyloTree< AlignmentTreeNode >::root, and PhyloTree< AlignmentTreeNode >::size().

void mems::ProgressiveAligner::getAncestralMatches (  const std::vector< node_id_t >  node1_seqs, const std::vector< node_id_t >  node2_seqs, node_id_t  node1, node_id_t  node2, node_id_t  ancestor, std::vector< mems::AbstractMatch * > &  ancestral_matches )

Definition at line 888 of file ProgressiveAligner.cpp. References mems::UngappedLocalAlignment< AbstractMatchImpl >::Copy(), mems::EliminateOverlaps_v2(), mems::Match, node_id_t, node_sequence_map, original_ml, mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), translateGappedCoordinates(), and uint.

double mems::ProgressiveAligner::getBpDistEstimateMinScore (  void   )  [inline]

Definition at line 114 of file ProgressiveAligner.h. References bp_dist_estimate_score.

double mems::ProgressiveAligner::getBreakpointDistanceScale (  void   )  [inline]

Definition at line 108 of file ProgressiveAligner.h. References bp_dist_scale.

double mems::ProgressiveAligner::getConservationDistanceScale (  void   )  [inline]

Definition at line 111 of file ProgressiveAligner.h. References conservation_dist_scale.

LcbScoringScheme mems::ProgressiveAligner::getLcbScoringScheme (  void   )  [inline]

Definition at line 99 of file ProgressiveAligner.h. References LcbScoringScheme, and scoring_scheme.

void mems::ProgressiveAligner::getPairwiseMatches (  const std::vector< node_id_t > &  node1_seqs, const std::vector< node_id_t > &  node2_seqs, Matrix< mems::MatchList > &  pairwise_matches )

Definition at line 932 of file ProgressiveAligner.cpp. References mems::UngappedLocalAlignment< AbstractMatchImpl >::Copy(), mems::Match, node_sequence_map, original_ml, mems::GenericMatchList< MatchPtrType >::seq_filename, mems::GenericMatchList< MatchPtrType >::seq_table, mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), and uint.

void mems::ProgressiveAligner::getPath (  node_id_t  first_n, node_id_t  last_n, std::vector< node_id_t > &  path )

determine which extant sequences have been aligned at a given node Definition at line 186 of file ProgressiveAligner.cpp. References alignment_tree, node_id_t, PhyloTree< AlignmentTreeNode >::size(), and uint. Referenced by translateGappedCoordinates().

void mems::ProgressiveAligner::getRepresentativeAncestralMatches (  const std::vector< node_id_t >  node1_seqs, const std::vector< node_id_t >  node2_seqs, node_id_t  node1, node_id_t  node2, node_id_t  ancestor, std::vector< mems::AbstractMatch * > &  ancestral_matches )

Definition at line 1945 of file ProgressiveAligner.cpp. References mems::UngappedLocalAlignment< AbstractMatchImpl >::Copy(), mems::EliminateOverlaps_v2(), mems::Match, mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), and uint.

bool mems::ProgressiveAligner::getUseLcbWeightScaling (  void   )  [inline]

Definition at line 105 of file ProgressiveAligner.h. References use_weight_scaling.

bool mems::ProgressiveAligner::getUseSeedFamilies (  void   )  [inline]

Definition at line 102 of file ProgressiveAligner.h. References use_seed_families.

void mems::ProgressiveAligner::linkSuperIntervals (  node_id_t  node1, uint  seqI, node_id_t  ancestor )

Definition at line 272 of file ProgressiveAligner.cpp. References alignment_tree, node_id_t, and uint. Referenced by recursiveApplyAncestralBreakpoints().

ProgressiveAligner& mems::ProgressiveAligner::operator= (  const ProgressiveAligner &  al  )

void mems::ProgressiveAligner::pairwiseAnchorSearch (  mems::MatchList &  r_list, mems::Match *  r_begin, mems::Match *  r_end, const mems::AbstractMatch *  iv, uint  oseqI, uint  oseqJ )

Definition at line 588 of file ProgressiveAligner.cpp. References mems::EliminateOverlaps_v2(), getDefaultSeedWeight(), mems::getInterveningCoordinates(), getSeed(), mems::GenericMatchList< MatchPtrType >::LengthFilter(), mems::Match, mems::MatchList, MIN_DNA_SEED_WEIGHT, mems::GenericMatchList< MatchPtrType >::seq_table, mems::GenericMatchList< MatchPtrType >::sml_table, uint, mems::uint64, and use_seed_families. Referenced by recurseOnPairs().

void mems::ProgressiveAligner::pairwiseScoreTrackingMatches (  std::vector< mems::TrackingMatch > &  tracking_matches, std::vector< node_id_t > &  node1_descendants, std::vector< node_id_t > &  node2_descendants, boost::multi_array< double, 3 > &  tm_score_array )

Definition at line 1756 of file ProgressiveAligner.cpp. References alignment_tree, computeAvgAncestralMatchScores(), mems::GetPairwiseAnchorScore(), mems::AbstractMatch::LeftEnd(), node_id_t, mems::LcbTrackingMatch< MatchType >::node_match, node_sequence_map, PhyloTree< AlignmentTreeNode >::resize(), sol_list, subst_scoring, and mems::TrackingMatch.

template<class MatchType> void mems::ProgressiveAligner::propagateDescendantBreakpoints (  node_id_t  node1, uint  seqI, std::vector< MatchType * > &  iv_list )

Definition at line 235 of file ProgressiveAligner.cpp. References alignment_tree, mems::applyBreakpoints(), node_id_t, and uint. Referenced by constructLcbTrackingMatches().

template<class GappedAlignmentType> void mems::ProgressiveAligner::recurseOnPairs (  const std::vector< node_id_t > &  node1_seqs, const std::vector< node_id_t > &  node2_seqs, const GappedAlignmentType &  iv, Matrix< mems::MatchList > &  matches, Matrix< std::vector< mems::search_cache_t > > &  search_cache_db, Matrix< std::vector< mems::search_cache_t > > &  new_cache_db, boost::multi_array< std::vector< std::vector< int64 > >, 2 > &  iv_regions )

Definition at line 680 of file ProgressiveAligner.cpp. References alignment_tree, mems::cache_comparator, mems::UngappedLocalAlignment< AbstractMatchImpl >::Copy(), mems::Match, mems::MatchList, node_sequence_map, pairwiseAnchorSearch(), mems::search_cache_t, mems::GenericMatchList< MatchPtrType >::seq_table, mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), uint, and using_cache_db.

void mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints (  node_id_t  ancestor  )

Definition at line 527 of file ProgressiveAligner.cpp. References alignment_tree, mems::applyAncestralBreakpoints(), TreeNode::children, mems::debug_aligner, linkSuperIntervals(), node_id_t, mems::AlignmentTreeNode::ordering, mems::progress_msgs, PhyloTree< AlignmentTreeNode >::size(), and validateSuperIntervals().

void mems::ProgressiveAligner::refineAlignment (  mems::GappedAlignment &  gal, node_id_t  ancestor, bool  profile_aln, AlnProgressTracker &  apt )

Definition at line 1081 of file ProgressiveAligner.cpp. References alignment_tree, mems::AlnProgressTracker::cur_leftend, getAlignedChildren(), mems::GetAlignment(), mems::IsDenseEnough(), mems::SparseAbstractMatch<>::LeftEnd(), mems::max_window_size, mems::SparseAbstractMatch<>::Multiplicity(), node_id_t, node_sequence_map, mems::AlnProgressTracker::prev_progress, mems::printProgress(), mems::MuscleInterface::ProfileAlignFast(), mems::MuscleInterface::RefineFast(), mems::removeLargeGapsPP(), mems::SparseAbstractMatch<>::SeqCount(), mems::GappedAlignment::SetAlignment(), mems::splitGappedAlignment(), mems::AlnProgressTracker::total_len, and uint. Referenced by doGappedAlignment().

void mems::ProgressiveAligner::setBpDistEstimateMinScore (  double  min_score  )  [inline]

Definition at line 113 of file ProgressiveAligner.h. References bp_dist_estimate_score.

void mems::ProgressiveAligner::setBreakpointDistanceScale (  double  bp_dist_scale  )  [inline]

Definition at line 107 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::setBreakpointPenalty (  double  bp_penalty  )  [inline]

sets the breakpoint penalty Definition at line 66 of file ProgressiveAligner.h. References breakpoint_penalty.

void mems::ProgressiveAligner::setCollinear (  boolean  collinear  )  [inline]

assume all genomes are collinear when set to true Definition at line 70 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::setConservationDistanceScale (  double  conservation_dist_scale  )  [inline]

Definition at line 110 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::setGappedAlignment (  bool  do_gapped_alignment  )  [inline]

Set whether iterative refinement using MUSCLE should be performed (true/false). Definition at line 86 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::setInputGuideTreeFileName (  std::string &  fname  )  [inline]

use a precomputed guide tree stored in the given file Definition at line 74 of file ProgressiveAligner.h. References input_guide_tree_fname.

void mems::ProgressiveAligner::setLcbScoringScheme (  LcbScoringScheme  scheme  )  [inline]

set LCB the scoring scheme Definition at line 98 of file ProgressiveAligner.h. References scoring_scheme.

void mems::ProgressiveAligner::SetMaxGappedAlignmentLength (  size_t  len  )

set the max length (in columns) of alignments passed to MUSCLE Definition at line 153 of file ProgressiveAligner.cpp. References max_gapped_alignment_length, and mems::max_window_size.

void mems::ProgressiveAligner::setMinimumBreakpointPenalty (  double  min_bp_penalty  )  [inline]

sets the the minimum breakpoint penalty after scaling Definition at line 68 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::setOutputGuideTreeFileName (  std::string &  fname  )  [inline]

write the guide tree stored to the given file Definition at line 76 of file ProgressiveAligner.h. References output_guide_tree_fname.

void mems::ProgressiveAligner::setPairwiseMatches (  mems::MatchList &  pair_ml  )

use a list of precomputed matches instead of computing them Definition at line 3141 of file ProgressiveAligner.cpp.

void mems::ProgressiveAligner::setPairwiseScoringScheme (  const mems::PairwiseScoringScheme &  pss  )  [inline]

Definition at line 88 of file ProgressiveAligner.h. References subst_scoring.

void mems::ProgressiveAligner::setRefinement (  bool  refine  )  [inline]

Set whether iterative refinement using MUSCLE should be performed (true/false). Definition at line 84 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::SetUseCacheDb (  bool  cbd  )  [inline]

set whether a cache database should be used to speed up recursive anchor search Definition at line 81 of file ProgressiveAligner.h. References using_cache_db.

void mems::ProgressiveAligner::setUseLcbWeightScaling (  bool  use_weight_scaling  )  [inline]

Definition at line 104 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::setUseSeedFamilies (  bool  use_seed_families  )  [inline]

Definition at line 101 of file ProgressiveAligner.h.

void mems::ProgressiveAligner::translateGappedCoordinates (  std::vector< mems::AbstractMatch * > &  ml, uint  seqI, node_id_t  extant, node_id_t  ancestor )

Definition at line 324 of file ProgressiveAligner.cpp. References mems::AbstractMatchSeqManipulator, alignment_tree, mems::applyAncestralBreakpoints(), mems::CompactGappedAlignment< BaseType >::Copy(), mems::debug_aligner, mems::CompactGappedAlignment< BaseType >::Free(), getPath(), node_id_t, mems::CompactGappedAlignment< BaseType >::translate(), and uint. Referenced by extractAlignment(), and getAncestralMatches().

bool mems::ProgressiveAligner::validatePairwiseIntervals (  node_id_t  node1, node_id_t  node2, std::vector< mems::Interval * > &  pair_iv )

Definition at line 2806 of file ProgressiveAligner.cpp. References alignment_tree, and uint.

bool mems::ProgressiveAligner::validateSuperIntervals (  node_id_t  node1, node_id_t  node2, node_id_t  ancestor )

Definition at line 2734 of file ProgressiveAligner.cpp. Referenced by doGappedAlignment(), and recursiveApplyAncestralBreakpoints().

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Member Data Documentation

PhyloTree< AlignmentTreeNode > mems::ProgressiveAligner::alignment_tree [protected]

Definition at line 197 of file ProgressiveAligner.h. Referenced by alignNodes(), constructLcbTrackingMatches(), ConstructSuperIntervalFromMSA(), doGappedAlignment(), extractAlignment(), FixLeftEnds(), getAlignedChildren(), getAlignment(), getPath(), linkSuperIntervals(), pairwiseScoreTrackingMatches(), propagateDescendantBreakpoints(), recurseOnPairs(), recursiveApplyAncestralBreakpoints(), refineAlignment(), translateGappedCoordinates(), and validatePairwiseIntervals().

double mems::ProgressiveAligner::bp_dist_estimate_score [protected]

the minimum LCB score to use when estimating BP distance should be conservative (high) Definition at line 218 of file ProgressiveAligner.h. Referenced by getBpDistEstimateMinScore(), and setBpDistEstimateMinScore().

double mems::ProgressiveAligner::bp_dist_scale [protected]

Definition at line 215 of file ProgressiveAligner.h. Referenced by getBreakpointDistanceScale().

boost::multi_array<double, 2> mems::ProgressiveAligner::bp_distance [protected]

pairwise breakpoint distances dims will be [seq_count][seq_count] Definition at line 208 of file ProgressiveAligner.h. Referenced by computeInternalNodeDistances().

double mems::ProgressiveAligner::breakpoint_penalty [protected]

Definition at line 199 of file ProgressiveAligner.h. Referenced by setBreakpointPenalty().

double mems::ProgressiveAligner::conservation_dist_scale [protected]

Definition at line 216 of file ProgressiveAligner.h. Referenced by getConservationDistanceScale().

boost::multi_array<double, 2> mems::ProgressiveAligner::conservation_distance [protected]

pairwise genome conservation distances dims will be [seq_count][seq_count] Definition at line 209 of file ProgressiveAligner.h. Referenced by computeInternalNodeDistances().

boolean mems::ProgressiveAligner::debug [protected]

Flag for debugging output. Reimplemented from mems::Aligner. Definition at line 203 of file ProgressiveAligner.h.

std::string mems::ProgressiveAligner::input_guide_tree_fname [protected]

Definition at line 201 of file ProgressiveAligner.h. Referenced by setInputGuideTreeFileName().

size_t mems::ProgressiveAligner::max_gapped_alignment_length [protected]

Definition at line 220 of file ProgressiveAligner.h. Referenced by ProgressiveAligner(), and SetMaxGappedAlignmentLength().

double mems::ProgressiveAligner::min_breakpoint_penalty [protected]

Definition at line 200 of file ProgressiveAligner.h.

std::vector< uint > mems::ProgressiveAligner::node_sequence_map [protected]

Definition at line 198 of file ProgressiveAligner.h. Referenced by computeInternalNodeDistances(), constructLcbTrackingMatches(), ConstructSuperIntervalFromMSA(), extractAlignment(), getAncestralMatches(), getPairwiseMatches(), pairwiseScoreTrackingMatches(), recurseOnPairs(), and refineAlignment().

mems::MatchList mems::ProgressiveAligner::original_ml [protected]

The list of matches calculated among all sequences. Also contains the full sequences and sorted mer lists Definition at line 196 of file ProgressiveAligner.h. Referenced by getAncestralMatches(), getPairwiseMatches(), and ~ProgressiveAligner().

std::string mems::ProgressiveAligner::output_guide_tree_fname [protected]

Definition at line 202 of file ProgressiveAligner.h. Referenced by setOutputGuideTreeFileName().

boolean mems::ProgressiveAligner::refine [protected]

Definition at line 204 of file ProgressiveAligner.h. Referenced by getAlignment().

LcbScoringScheme mems::ProgressiveAligner::scoring_scheme [protected]

Definition at line 211 of file ProgressiveAligner.h. Referenced by getLcbScoringScheme(), and setLcbScoringScheme().

std::vector< SeedOccurrenceList > mems::ProgressiveAligner::sol_list [protected]

Definition at line 207 of file ProgressiveAligner.h. Referenced by pairwiseScoreTrackingMatches().

mems::PairwiseScoringScheme mems::ProgressiveAligner::subst_scoring [protected]

Definition at line 222 of file ProgressiveAligner.h. Referenced by pairwiseScoreTrackingMatches(), and setPairwiseScoringScheme().

bool mems::ProgressiveAligner::use_seed_families [protected]

Definition at line 213 of file ProgressiveAligner.h. Referenced by getUseSeedFamilies(), and pairwiseAnchorSearch().

bool mems::ProgressiveAligner::use_weight_scaling [protected]

Definition at line 212 of file ProgressiveAligner.h. Referenced by getUseLcbWeightScaling().

bool mems::ProgressiveAligner::using_cache_db [protected]

Definition at line 205 of file ProgressiveAligner.h. Referenced by recurseOnPairs(), and SetUseCacheDb().

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

• libMems/ProgressiveAligner.h
• libMems/ProgressiveAligner.cpp

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