aln_converters.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seq/seq_loc_mapper_base.hpp>
#include <objtools/alnmgr/alnexception.hpp>
#include <objtools/alnmgr/pairwise_aln.hpp>
#include <objtools/alnmgr/aln_user_options.hpp>
#include <objtools/alnmgr/aln_stats.hpp>

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Typedefs
typedef vector< TAlnSeqIdIRef >	TAlnSeqIdVec
typedef list< CRef< CPairwiseAln > >	TPairwiseAlnList

Functions
void	ConvertSeqAlignToPairwiseAln (CPairwiseAln &pairwise_aln, const objects::CSeq_align &sa, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)
	Build pairwise alignment from the selected rows of a seq-align. More...
void	ConvertDensegToPairwiseAln (CPairwiseAln &pairwise_aln, const objects::CDense_seg &ds, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)
	Build pairwise alignment from the selected rows of a dense-seg. More...
void	ConvertPackedsegToPairwiseAln (CPairwiseAln &pairwise_aln, const objects::CPacked_seg &ps, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)
	Build pairwise alignment from the selected rows of a packed-seg. More...
void	ConvertStdsegToPairwiseAln (CPairwiseAln &pairwise_aln, const objects::CSeq_align::TSegs::TStd &stds, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)
	Build pairwise alignment from the selected rows of an std-seg. More...
void	ConvertDendiagToPairwiseAln (CPairwiseAln &pairwise_aln, const objects::CSeq_align::TSegs::TDendiag &dendiags, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)
	Build pairwise alignment from the selected rows of a dendiag. More...
void	ConvertSparseToPairwiseAln (CPairwiseAln &pairwise_aln, const objects::CSparse_seg &sparse_seg, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)
	Build pairwise alignment from the selected rows of a sparse-seg. More...
void	ConvertSplicedToPairwiseAln (CPairwiseAln &pairwise_aln, const objects::CSpliced_seg &spliced_seg, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)
	Build pairwise alignment from the selected rows of a spliced-seg. More...
void	ConvertSeqLocsToPairwiseAln (CPairwiseAln &aln, const objects::CSeq_loc &loc_1, const objects::CSeq_loc &loc_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections)
	Build pairwise alignment from a pair of seq-locs. More...
void	SeqLocMapperToPairwiseAligns (const objects::CSeq_loc_Mapper_Base &mapper, TPairwiseAlnList &aligns)
	Build a list of pairwise alignments from a seq-loc mapper's mappings. More...
template<class _TAlnStats >
CRef< CAnchoredAln >	CreateAnchoredAlnFromAln (const _TAlnStats &aln_stats, size_t aln_idx, const CAlnUserOptions &options, objects::CSeq_align::TDim explicit_anchor_row=-1)
	Create an anchored alignment from Seq-align using hints. More...
template<class _TAlnStats >
void	CreateAnchoredAlnVec (_TAlnStats &aln_stats, TAnchoredAlnVec &out_vec, const CAlnUserOptions &options)
	Create anchored alignment from each seq-align in the stats. More...
CRef< CPairwiseAln >	CreatePairwiseAlnFromSeqAlign (const objects::CSeq_align &seq_align)
	A simple API that assumes that the seq_align has exactly two rows and you want to create a pairwise with the default policy. More...

Typedef Documentation

TAlnSeqIdVec

typedef vector<TAlnSeqIdIRef> TAlnSeqIdVec

Definition at line 52 of file aln_converters.hpp.

TPairwiseAlnList

typedef list< CRef<CPairwiseAln> > TPairwiseAlnList

Definition at line 181 of file aln_converters.hpp.

Function Documentation

ConvertDendiagToPairwiseAln()

void ConvertDendiagToPairwiseAln	(	CPairwiseAln &	pairwise_aln,
		const objects::CSeq_align::TSegs::TDendiag &	dendiags,
		objects::CSeq_align::TDim	row_1,
		objects::CSeq_align::TDim	row_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections,
		const TAlnSeqIdVec *	ids = 0
	)

Build pairwise alignment from the selected rows of a dendiag.

See also

ConvertSeqAlignToPairwiseAln

ConvertDensegToPairwiseAln()

void ConvertDensegToPairwiseAln	(	CPairwiseAln &	pairwise_aln,
		const objects::CDense_seg &	ds,
		objects::CSeq_align::TDim	row_1,
		objects::CSeq_align::TDim	row_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections,
		const TAlnSeqIdVec *	ids = 0
	)

Build pairwise alignment from the selected rows of a dense-seg.

See also

ConvertSeqAlignToPairwiseAln

ConvertPackedsegToPairwiseAln()

void ConvertPackedsegToPairwiseAln	(	CPairwiseAln &	pairwise_aln,
		const objects::CPacked_seg &	ps,
		objects::CSeq_align::TDim	row_1,
		objects::CSeq_align::TDim	row_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections,
		const TAlnSeqIdVec *	ids = 0
	)

Build pairwise alignment from the selected rows of a packed-seg.

See also

ConvertSeqAlignToPairwiseAln

ConvertSeqAlignToPairwiseAln()

void ConvertSeqAlignToPairwiseAln	(	CPairwiseAln &	pairwise_aln,
		const objects::CSeq_align &	sa,
		objects::CSeq_align::TDim	row_1,
		objects::CSeq_align::TDim	row_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections,
		const TAlnSeqIdVec *	ids = 0
	)

Build pairwise alignment from the selected rows of a seq-align.

Parameters

pairwise_aln	Output pairwise alignment. Should be initialized with the correct ids (the functions does not check if the ids in the pairwise alignment correspond to the ids of the selected rows).
sa	Input seq-align object.
row_1	First row index.
row_2	Second row index.
direction	Flag indicating if the output pairwise alignment should include direct, reverse, or any segments. NOTE: segment direction in pariwise alignments is relative (second vs first row).
ids	Optional vector of alignment seq-ids used only to check if the source alignment contains mixed sequence types. All ids from the vector are compared, not just the two selected rows.

Referenced by BOOST_AUTO_TEST_CASE(), CreateAnchoredAlnFromAln(), CAlnTestApp::Run(), s_GetAlignmentSpans_Interval(), s_GetSplicedSegIdentityMismatch(), and CHitMatrixDataSource::x_CreateHits_Diagonal().

ConvertSeqLocsToPairwiseAln()

void ConvertSeqLocsToPairwiseAln	(	CPairwiseAln &	aln,
		const objects::CSeq_loc &	loc_1,
		const objects::CSeq_loc &	loc_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections
	)

Build pairwise alignment from a pair of seq-locs.

Each seq-loc must reference a single sequence.

Parameters

aln	Output pairwise alignment. Should be initialized with the correct ids (the functions does not check if the ids in the pairwise alignment correspond to the ids of the seq-locs).
loc_1	First seq-loc.
loc_2	Second seq-loc.
direction	Flag indicating if the output pairwise alignment should include direct, reverse, or any segments. NOTE: segment direction in pariwise alignments is relative (second vs first row).

Definition at line 793 of file aln_converters.cpp.

References _ASSERT, CAlnUserOptions::eBothDirections, CAlnUserOptions::eDirect, CAlnUserOptions::eReverse, CPairwiseAln::GetFirstBaseWidth(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CSeq_loc_CI::GetRange(), CPairwiseAln::GetSecondBaseWidth(), CSeq_loc_CI::GetStrand(), CAlignRangeCollectionList< TAlnRange >::insert(), CSeq_loc_CI::IsEmpty(), IsReverse(), len, and CPairwiseAln::SetUsingGenomic().

Referenced by CFeatGlyph::x_DrawProjectedRuler(), and CFeatGlyph::x_DrawRuler().

ConvertSparseToPairwiseAln()

void ConvertSparseToPairwiseAln	(	CPairwiseAln &	pairwise_aln,
		const objects::CSparse_seg &	sparse_seg,
		objects::CSeq_align::TDim	row_1,
		objects::CSeq_align::TDim	row_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections,
		const TAlnSeqIdVec *	ids = 0
	)

Build pairwise alignment from the selected rows of a sparse-seg.

See also

ConvertSeqAlignToPairwiseAln

ConvertSplicedToPairwiseAln()

void ConvertSplicedToPairwiseAln	(	CPairwiseAln &	pairwise_aln,
		const objects::CSpliced_seg &	spliced_seg,
		objects::CSeq_align::TDim	row_1,
		objects::CSeq_align::TDim	row_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections,
		const TAlnSeqIdVec *	ids = 0
	)

Build pairwise alignment from the selected rows of a spliced-seg.

See also

ConvertSeqAlignToPairwiseAln

ConvertStdsegToPairwiseAln()

void ConvertStdsegToPairwiseAln	(	CPairwiseAln &	pairwise_aln,
		const objects::CSeq_align::TSegs::TStd &	stds,
		objects::CSeq_align::TDim	row_1,
		objects::CSeq_align::TDim	row_2,
		CAlnUserOptions::EDirection	direction = CAlnUserOptions::eBothDirections,
		const TAlnSeqIdVec *	ids = 0
	)

Build pairwise alignment from the selected rows of an std-seg.

See also

ConvertSeqAlignToPairwiseAln

CreateAnchoredAlnFromAln()

template<class _TAlnStats >

CRef<CAnchoredAln> CreateAnchoredAlnFromAln	(	const _TAlnStats &	aln_stats,
		size_t	aln_idx,
		const CAlnUserOptions &	options,
		objects::CSeq_align::TDim	explicit_anchor_row = -1
	)

Create an anchored alignment from Seq-align using hints.

Optionally, choose the anchor row explicitly (this overrides options.GetAnchorId()). NOTE: Potentially, this "shrinks" the alignment vertically in case some row was not aligned to the anchor.

Parameters

aln_stats	Input alignment stats (see CAlnStats template).
aln_idx	Index of the input alignment in the stats.
options	Options for building the anchored alignment.
explicit_anchor_row	Explicit anchor row index (this overrides anchor id set in the options). By default the anchor row is selected automatically.

See also

CAlnStats

Definition at line 205 of file aln_converters.hpp.

References _ALNMGR_ASSERT, ConvertSeqAlignToPairwiseAln(), CAlnUserOptions::eDirect, ctll::empty(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fAllowMixedDir, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fAllowOverlap, CAlnUserOptions::fAnchorRowFirst, CAlnUserOptions::fIgnoreInsertions, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fIgnoreInsertions, map_checker< Container >::find(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fKeepNormalized, flags, CAlnUserOptions::GetAnchorId(), CSeq_align_Base::GetSegs(), i, CSeq_align_Base::C_Segs::IsStd(), CAlnUserOptions::m_Direction, CAlnUserOptions::m_MergeFlags, NCBI_THROW, CRef< C, Locker >::Reset(), row, CAnchoredAln::SetAnchorRow(), CAnchoredAln::SetDim(), CAnchoredAln::SetPairwiseAlns(), and ncbi::grid::netcache::search::fields::size.

Referenced by BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), ConvertSeq_align(), CreateAnchoredAlnVec(), CAlnBuildApp::Run(), and CAlnTestApp::Run().

CreateAnchoredAlnVec()

template<class _TAlnStats >

void CreateAnchoredAlnVec	(	_TAlnStats &	aln_stats,
		TAnchoredAlnVec &	out_vec,
		const CAlnUserOptions &	options
	)

Create anchored alignment from each seq-align in the stats.

See also

CreateAnchoredAlnFromAln

Definition at line 363 of file aln_converters.hpp.

References _ASSERT, CAlignRangeCollectionList< TAlnRange >::begin(), CreateAnchoredAlnFromAln(), CAlignRangeCollectionList< TAlnRange >::end(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fMixedDir, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fOverlap, CAnchoredAln::GetAnchorRow(), CAnchoredAln::GetDim(), CPairwiseAln::GetFirstId(), CAnchoredAln::GetPairwiseAlns(), CAlignRangeCollectionList< TAlnRange >::GetPolicyFlags(), CPairwiseAln::GetSecondId(), CSeq_align_Base::GetSegs(), CAlignRangeCollectionList< TAlnRange >::IsSet(), CSeq_align_Base::C_Segs::IsStd(), ITERATE, row, CAnchoredAln::SetAnchorRow(), CAnchoredAln::SetDim(), CAnchoredAln::SetPairwiseAlns(), and CAnchoredAln::SetScore().

Referenced by BOOST_AUTO_TEST_CASE(), CAlnSpanVertModel::CAlnSpanVertModel(), CAlignCleanup::CreatePairwiseFromMultiple(), CAlnBuildApp::Run(), CAlnTestApp::Run(), CAlignCleanup::x_Cleanup_AnchoredAln(), CMergeAlignmentsJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CAlnMultiDSBuilder::x_PreCreateSparseDataSource(), and CValidError_align::x_ValidateAlignPercentIdentity().

CreatePairwiseAlnFromSeqAlign()

CRef<CPairwiseAln> CreatePairwiseAlnFromSeqAlign

(

const objects::CSeq_align &

seq_align

)

A simple API that assumes that the seq_align has exactly two rows and you want to create a pairwise with the default policy.

See also

ConvertSeqAlignToPairwiseAln

Referenced by CScoreBuilder::GetBlastScoreSpliced(), and CScoreBuilder::GetBlastScoreStd().

SeqLocMapperToPairwiseAligns()

void SeqLocMapperToPairwiseAligns	(	const objects::CSeq_loc_Mapper_Base &	mapper,
		TPairwiseAlnList &	aligns
	)

Build a list of pairwise alignments from a seq-loc mapper's mappings.

Definition at line 925 of file aln_converters.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CMappingRange::GetDst_from(), CMappingRange::GetDstIdHandle(), CMappingRanges::GetIdMap(), CMappingRange::GetLength(), CMappingRange::GetReverse(), CSeq_id_Handle::GetSeqId(), CMappingRange::GetSrc_from(), ITERATE, Ref(), and s_GetBestSynonym().