Search Toolkit Book for CUnorderedSplitter

#include <algo/align/ngalign/unordered_spliter.hpp>

Collaboration diagram for CUnorderedSplitter:

Public Types
typedef list< CRef< objects::CSeq_id > >	TSeqIdList

typedef list< CRef< objects::CSeq_align > >	TSeqAlignList

Public Member Functions
	CUnorderedSplitter (objects::CScope &Scope)

void	SplitId (const objects::CSeq_id &Id, TSeqIdList &SplitIds)

void	SplitLoc (const objects::CSeq_loc &Loc, TSeqIdList &SplitIds)

void	CombineAlignments (const TSeqAlignList &SourceAligns, TSeqAlignList &MergedAligns)

void	GetSplitIdList (TSeqIdList &SplitIdList)

Private Types
typedef map< string, CRef< objects::CSeq_interval > >	TSplitIntervalsMap

typedef list< CRef< objects::CSeq_interval > >	TIntervalList

typedef map< string, TIntervalList >	TSplitIntMap

Private Member Functions
void	x_SplitDeltaExt (const objects::CSeq_id &Id, objects::CBioseq_Handle OrigHandle, TSeqIdList &SplitIds, TSeqRange LimitRange=TSeqRange())

void	x_SplitSeqData (const objects::CSeq_id &Id, objects::CBioseq_Handle OrigHandle, TSeqIdList &SplitIds, TSeqRange LimitRange=TSeqRange())

CRef< objects::CSeq_align >	x_FixAlignment (const objects::CSeq_align &SourceAlignment)

void	x_SortAlignSet (TSeqAlignList &AlignSet)

void	x_MakeAlignmentsUnique (TSeqAlignList &Alignments)

void	x_MakeAlignmentPairUnique (CRef< objects::CSeq_align > First, CRef< objects::CSeq_align > Second)

void	x_TrimRows (const objects::CDense_seg &DomSeg, objects::CDense_seg &NonSeg, int Row)

bool	x_IsAllGap (const objects::CDense_seg &Denseg)

void	x_StripDistantAlignments (TSeqAlignList &Alignments)

Static Private Member Functions
static bool	s_SortByQueryStart (const CRef< objects::CSeq_align > &A, const CRef< objects::CSeq_align > &B)

Private Attributes
CRef< objects::CScope >	m_Scope

TSplitIntervalsMap	m_PartsMap

TSplitIntMap	m_SplitsMap

Detailed Description

Definition at line 70 of file unordered_spliter.hpp.

Member Typedef Documentation

◆ TIntervalList

typedef list< CRef<objects::CSeq_interval> > CUnorderedSplitter::TIntervalList

private

Definition at line 95 of file unordered_spliter.hpp.

◆ TSeqAlignList

typedef list<CRef<objects::CSeq_align> > CUnorderedSplitter::TSeqAlignList

Definition at line 80 of file unordered_spliter.hpp.

◆ TSeqIdList

typedef list<CRef<objects::CSeq_id> > CUnorderedSplitter::TSeqIdList

Definition at line 76 of file unordered_spliter.hpp.

◆ TSplitIntervalsMap

typedef map<string, CRef<objects::CSeq_interval> > CUnorderedSplitter::TSplitIntervalsMap

private

Definition at line 92 of file unordered_spliter.hpp.

◆ TSplitIntMap

typedef map<string, TIntervalList > CUnorderedSplitter::TSplitIntMap

private

Definition at line 96 of file unordered_spliter.hpp.

Constructor & Destructor Documentation

◆ CUnorderedSplitter()

CUnorderedSplitter::CUnorderedSplitter ( objects::CScope & Scope )

inline

Definition at line 74 of file unordered_spliter.hpp.

Member Function Documentation

◆ CombineAlignments()

void CUnorderedSplitter::CombineAlignments	(	const TSeqAlignList &	SourceAligns,
		TSeqAlignList &	MergedAligns
	)

Definition at line 150 of file unordered_spliter.cpp.

References ERR_POST, CSeq_align_Base::eType_disc, Info(), CRef< C, Locker >::IsNull(), ITERATE, NON_CONST_ITERATE, CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), x_FixAlignment(), x_IsAllGap(), x_MakeAlignmentsUnique(), x_SortAlignSet(), and x_StripDistantAlignments().

Referenced by CSplitSeqAlignMerger::GenerateAlignments().

◆ GetSplitIdList()

void CUnorderedSplitter::GetSplitIdList ( TSeqIdList & SplitIdList )

Definition at line 198 of file unordered_spliter.cpp.

References ITERATE, and m_PartsMap.

Referenced by CSplitSeqAlignMerger::GenerateAlignments().

◆ s_SortByQueryStart()

bool CUnorderedSplitter::s_SortByQueryStart	(	const CRef< objects::CSeq_align > &	A,
		const CRef< objects::CSeq_align > &	B
	)

staticprivate

Definition at line 502 of file unordered_spliter.cpp.

References A, and B.

Referenced by x_SortAlignSet().

◆ SplitId()

void CUnorderedSplitter::SplitId	(	const objects::CSeq_id &	Id,
		TSeqIdList &	SplitIds
	)

Definition at line 100 of file unordered_spliter.cpp.

References CSeq_id::AsFastaString(), CSeq_inst_Base::CanGetExt(), CBioseq_Handle::CanGetInst(), CSeq_inst_Base::CanGetSeq_data(), ERR_POST, Error(), CSeq_inst_Base::GetExt(), CBioseq_Handle::GetInst(), CSeq_ext_Base::IsDelta(), m_Scope, x_SplitDeltaExt(), and x_SplitSeqData().

Referenced by CSplitSeqIdListSet::AddSeqId().

◆ SplitLoc()

void CUnorderedSplitter::SplitLoc	(	const objects::CSeq_loc &	Loc,
		TSeqIdList &	SplitIds
	)

Definition at line 123 of file unordered_spliter.cpp.

References CSeq_inst_Base::CanGetExt(), CBioseq_Handle::CanGetInst(), CSeq_inst_Base::CanGetSeq_data(), ERR_POST, Error(), CSeq_inst_Base::GetExt(), CBioseq_Handle::GetInst(), CSeq_ext_Base::IsDelta(), Loc, m_Scope, x_SplitDeltaExt(), and x_SplitSeqData().

Referenced by CSplitSeqLocListSet::AddSeqLoc().

◆ x_FixAlignment()

CRef< CSeq_align > CUnorderedSplitter::x_FixAlignment ( const objects::CSeq_align & SourceAlignment )

private

Definition at line 471 of file unordered_spliter.cpp.

References CSeq_id::AsFastaString(), CSerialObject::Assign(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_align::GetSeq_id(), CRef< C, Locker >::IsNull(), ITERATE, m_PartsMap, CDense_seg::OffsetRow(), CDense_seg_Base::SetIds(), CSeq_align_Base::SetScore(), and CSeq_align_Base::SetSegs().

Referenced by CombineAlignments().

◆ x_IsAllGap()

bool CUnorderedSplitter::x_IsAllGap ( const objects::CDense_seg & Denseg )

private

Definition at line 637 of file unordered_spliter.cpp.

References CDense_seg_Base::GetDim(), CDense_seg_Base::GetNumseg(), and CDense_seg_Base::GetStarts().

Referenced by CombineAlignments(), x_MakeAlignmentPairUnique(), x_MakeAlignmentsUnique(), and x_TrimRows().

◆ x_MakeAlignmentPairUnique()

void CUnorderedSplitter::x_MakeAlignmentPairUnique	(	CRef< objects::CSeq_align >	First,
		CRef< objects::CSeq_align >	Second
	)

private

Definition at line 547 of file unordered_spliter.cpp.

References CDense_seg::Assign(), CDense_seg::Compact(), CDense_seg::FillUnaligned(), CSeq_align_Base::C_Segs::GetDenseg(), COpenRange< Position >::GetLength(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqRange(), CRef< C, Locker >::IsNull(), CDense_seg::RemovePureGapSegs(), CSeq_align_Base::SetSegs(), CDense_seg::TrimEndGaps(), x_IsAllGap(), and x_TrimRows().

Referenced by x_MakeAlignmentsUnique().

◆ x_MakeAlignmentsUnique()

void CUnorderedSplitter::x_MakeAlignmentsUnique ( TSeqAlignList & Alignments )

private

Definition at line 528 of file unordered_spliter.cpp.

References x_IsAllGap(), and x_MakeAlignmentPairUnique().

Referenced by CombineAlignments().

◆ x_SortAlignSet()

void CUnorderedSplitter::x_SortAlignSet ( TSeqAlignList & AlignSet )

private

Definition at line 515 of file unordered_spliter.cpp.

References copy(), s_SortByQueryStart(), and ct::sort().

Referenced by CombineAlignments().

◆ x_SplitDeltaExt()

void CUnorderedSplitter::x_SplitDeltaExt	(	const objects::CSeq_id &	Id,
		objects::CBioseq_Handle	OrigHandle,
		TSeqIdList &	SplitIds,
		TSeqRange	LimitRange = `TSeqRange()`
	)

private

Definition at line 208 of file unordered_spliter.cpp.

References CSeq_id::AsFastaString(), CSeq_literal_Base::CanGetSeq_data(), COpenRange< Position >::CombineWith(), eExtreme_Positional, COpenRange< Position >::Empty(), eNa_strand_plus, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CRange_Base::GetFrom(), CSeq_interval_Base::GetFrom(), CBioseq_Base::GetInst(), CBioseq_Handle::GetInst(), CSeq_literal_Base::GetLength(), COpenRange< Position >::GetLength(), CDelta_seq_Base::GetLiteral(), CDelta_seq_Base::GetLoc(), CSeq_inst_Base::GetMol(), CSeq_inst_Base::GetRepr(), CSeq_literal_Base::GetSeq_data(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CRange_Base::GetTo(), CSeq_interval_Base::GetTo(), COpenRange< Position >::IntersectionWith(), IsGap(), CSeq_data_Base::IsGap(), CDelta_seq_Base::IsLiteral(), CDelta_seq_Base::IsLoc(), ITERATE, m_PartsMap, m_Scope, COpenRange< Position >::NotEmpty(), NStr::ReplaceInPlace(), CRef< C, Locker >::Reset(), CRange_Base::SetFrom(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), COpenRange< Position >::SetLength(), CSeq_id_Base::SetLocal(), CObject_id_Base::SetStr(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), and NStr::UInt8ToString().

Referenced by SplitId(), and SplitLoc().

◆ x_SplitSeqData()

void CUnorderedSplitter::x_SplitSeqData	(	const objects::CSeq_id &	Id,
		objects::CBioseq_Handle	OrigHandle,
		TSeqIdList &	SplitIds,
		TSeqRange	LimitRange = `TSeqRange()`
	)

private

Definition at line 355 of file unordered_spliter.cpp.

References CSeq_id::AsFastaString(), CBioseq_Handle::eCoding_Iupac, COpenRange< Position >::Empty(), eNa_strand_plus, CRange_Base::GetFrom(), CSeq_interval_Base::GetFrom(), CBioseq_Handle::GetInst(), CSeq_interval::GetLength(), CSeq_inst_Base::GetMol(), CSeq_inst_Base::GetRepr(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CRange_Base::GetTo(), CSeq_interval_Base::GetTo(), COpenRange< Position >::IntersectionWith(), m_PartsMap, m_Scope, COpenRange< Position >::NotEmpty(), NStr::ReplaceInPlace(), CRange_Base::SetFrom(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_id_Base::SetLocal(), CObject_id_Base::SetStr(), CSeq_interval_Base::SetStrand(), CRange_Base::SetTo(), CSeq_interval_Base::SetTo(), CSeqVector::size(), and NStr::UInt8ToString().

Referenced by SplitId(), and SplitLoc().

◆ x_StripDistantAlignments()

void CUnorderedSplitter::x_StripDistantAlignments ( TSeqAlignList & Alignments )

private

Definition at line 649 of file unordered_spliter.cpp.

References CRange_Base::GetFrom(), CRange_Base::GetTo(), ITERATE, s_CalcDevs(), s_CalcMean(), and s_CalcStdDev().

Referenced by CombineAlignments().

◆ x_TrimRows()

void CUnorderedSplitter::x_TrimRows	(	const objects::CDense_seg &	DomSeg,
		objects::CDense_seg &	NonSeg,
		int	Row
	)

private

Definition at line 587 of file unordered_spliter.cpp.

References CDense_seg::Assign(), CDense_seg::ExtractSlice(), CRange_Base::GetFrom(), CDense_seg::GetSeqRange(), CRange_Base::GetTo(), COpenRange< Position >::IntersectionWith(), COpenRange< Position >::NotEmpty(), CRange_Base::SetFrom(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CRange_Base::SetTo(), and x_IsAllGap().

Referenced by x_MakeAlignmentPairUnique().

Member Data Documentation

◆ m_PartsMap

TSplitIntervalsMap CUnorderedSplitter::m_PartsMap

private

Definition at line 93 of file unordered_spliter.hpp.

Referenced by GetSplitIdList(), x_FixAlignment(), x_SplitDeltaExt(), and x_SplitSeqData().

◆ m_Scope

CRef<objects::CScope> CUnorderedSplitter::m_Scope

private

Definition at line 90 of file unordered_spliter.hpp.

Referenced by SplitId(), SplitLoc(), x_SplitDeltaExt(), and x_SplitSeqData().

◆ m_SplitsMap

TSplitIntMap CUnorderedSplitter::m_SplitsMap

private

Definition at line 97 of file unordered_spliter.hpp.

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

include/algo/align/ngalign/unordered_spliter.hpp
src/algo/align/ngalign/unordered_spliter.cpp

Public Types

Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ TIntervalList

◆ TSeqAlignList

◆ TSeqIdList

◆ TSplitIntervalsMap

◆ TSplitIntMap

Constructor & Destructor Documentation

◆ CUnorderedSplitter()

Member Function Documentation

◆ CombineAlignments()

◆ GetSplitIdList()

◆ s_SortByQueryStart()

◆ SplitId()

◆ SplitLoc()

◆ x_FixAlignment()

◆ x_IsAllGap()

◆ x_MakeAlignmentPairUnique()

◆ x_MakeAlignmentsUnique()

◆ x_SortAlignSet()

◆ x_SplitDeltaExt()

◆ x_SplitSeqData()

◆ x_StripDistantAlignments()

◆ x_TrimRows()

Member Data Documentation

◆ m_PartsMap

◆ m_Scope

◆ m_SplitsMap