genomic_compart.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <util/range.hpp>
#include <algo/align/util/genomic_compart.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seqalign/Dense_seg.hpp>

Include dependency graph for genomic_compart.cpp:

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Classes
struct	SRangesByStart
struct	SRangesBySize
struct	SRangesByScore
struct	SRangesByPctIdent
struct	SSeqAlignsBySize
struct	SSeqAlignsByScore
struct	SSeqAlignsByPctIdent
struct	SRangeIteratorsByAddress
struct	SCompartScore

Typedefs
typedef pair< TSeqRange, TSeqRange >	TRange
typedef pair< TRange, CRef< CSeq_align > >	TAlignRange
typedef multiset< TAlignRange, SRangesByStart >	TAlignRangeMultiSet

Functions
bool	IsIntersectingQuery (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)
bool	IsIntersectingSubject (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)
bool	IsConsistent (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)
TSeqPos	Difference (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)
void	FindCompartments (const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options, float diff_len_filter)
void	JoinCompartment (const CRef< CSeq_align_set > &compartment, float gap_ratio, list< CRef< CSeq_align > > &aligns)

Typedef Documentation

TAlignRange

typedef pair<TRange, CRef<CSeq_align> > TAlignRange

Definition at line 177 of file genomic_compart.cpp.

TAlignRangeMultiSet

typedef multiset<TAlignRange, SRangesByStart> TAlignRangeMultiSet

Definition at line 200 of file genomic_compart.cpp.

TRange

typedef pair<TSeqRange, TSeqRange> TRange

Definition at line 176 of file genomic_compart.cpp.

Function Documentation

Difference()

TSeqPos Difference	(	const pair< TSeqRange, TSeqRange > &	r1,
		const pair< TSeqRange, TSeqRange > &	r2,
		ENa_strand	s1,
		ENa_strand	s2
	)

Definition at line 120 of file genomic_compart.cpp.

References r1, and r2.

Referenced by FindCompartments().

FindCompartments()

void FindCompartments	(	const list< CRef< CSeq_align > > &	aligns,
		list< CRef< CSeq_align_set > > &	align_sets,
		TCompartOptions	options,
		float	diff_len_filter
	)

Definition at line 385 of file genomic_compart.cpp.

References set< Key, Compare >::begin(), count, Difference(), eNa_strand_minus, eNa_strand_plus, set< Key, Compare >::end(), fCompart_AllowInconsistentIntersection, fCompart_AllowIntersectionsBoth, fCompart_AllowIntersectionsQuery, fCompart_AllowIntersectionsSubject, fCompart_FilterByDiffLen, fCompart_SortByPctIdent, fCompart_SortByScore, CSeq_id_Handle::GetHandle(), hex(), i, set< Key, Compare >::insert(), int, IsConsistent(), IsIntersectingQuery(), IsIntersectingSubject(), ITERATE, kMax_Int, max(), min(), NON_CONST_ITERATE, r(), SCompartScore::Reset(), CRef< C, Locker >::Reset(), REVERSE_ITERATE, CSeq_align_set_Base::Set(), ct::sort(), swap(), SCompartScore::total_range, and SCompartScore::total_size.

Referenced by BOOST_AUTO_TEST_CASE(), CAdvancedAlignCleanup::GetGenomicCompartments(), CTestCompartApplication::Run(), CBLASTSeqToolJob::x_CreateProjectItems(), and CMergeAligner::x_MergeAlignments().

IsConsistent()

bool IsConsistent	(	const pair< TSeqRange, TSeqRange > &	r1,
		const pair< TSeqRange, TSeqRange > &	r2,
		ENa_strand	s1,
		ENa_strand	s2
	)

Definition at line 82 of file genomic_compart.cpp.

References eNa_strand_minus, r1, r2, and SameOrientation().

Referenced by FindCompartments().

IsIntersectingQuery()

bool IsIntersectingQuery	(	const pair< TSeqRange, TSeqRange > &	r1,
		const pair< TSeqRange, TSeqRange > &	r2
	)

Definition at line 46 of file genomic_compart.cpp.

References r1, and r2.

Referenced by FindCompartments().

IsIntersectingSubject()

bool IsIntersectingSubject	(	const pair< TSeqRange, TSeqRange > &	r1,
		const pair< TSeqRange, TSeqRange > &	r2
	)

Definition at line 64 of file genomic_compart.cpp.

References r1, and r2.

Referenced by FindCompartments().

JoinCompartment()

void JoinCompartment	(	const CRef< CSeq_align_set > &	compartment,
		float	gap_ratio,
		list< CRef< CSeq_align > > &	aligns
	)

Definition at line 876 of file genomic_compart.cpp.

References CSeq_align_Base::eType_disc, CSeq_align_set_Base::Get(), ITERATE, len, CRef< C, Locker >::Reset(), CSeq_align_set_Base::Set(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().