named_collection_score_impl.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiobj.hpp>
#include <objects/seqalign/Score.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objtools/alnmgr/alnmap.hpp>
#include <util/range_coll.hpp>
#include <algo/align/util/named_collection_score_impl.hpp>
#include <cassert>
#include <sstream>
#include <iterator>

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Typedefs
typedef vector< CSeq_align const * >::const_iterator	TIterator
typedef pair< double, bool >(*	TCalculator) (CBioseq_Handle const &, TIterator, TIterator)

Functions
	USING_SCOPE (objects)
static vector< CScoreValue >	MakeSubjectScores (CScope &scope, CSeq_align_set const &coll, string name, TCalculator f)
static vector< CScoreValue >	MakeSubjectScores (CScope &scope, CSeq_align_set const &coll, vector< pair< string, TCalculator > > const &calculators)
static void	MakeSubjectScores (CScope &scope, CSeq_align_set &coll, vector< pair< string, TCalculator > > const &calculators)
static bool	Compare (CSeq_align const *lhs, CSeq_align const *rhs)
static CRange< TSeqPos > &	s_FixMinusStrandRange (CRange< TSeqPos > &rng)
static CRef< CSeq_align >	CreateDensegFromDendiag (CSeq_align const &aln)

Typedef Documentation

TCalculator

typedef pair<double, bool>(* TCalculator) (CBioseq_Handle const &, TIterator, TIterator)

Definition at line 60 of file named_collection_score_impl.cpp.

TIterator

typedef vector<CSeq_align const*>::const_iterator TIterator

Definition at line 59 of file named_collection_score_impl.cpp.

Function Documentation

Compare()

bool Compare ( CSeq_align const *  lhs, CSeq_align const *  rhs  )

static

Definition at line 265 of file named_collection_score_impl.cpp.

References CSeq_id::CompareOrdered(), CSeq_align::GetSeq_id(), and CSeq_align::GetSeqStart().

Referenced by MakeSubjectScores().

CreateDensegFromDendiag()

CRef< CSeq_align > CreateDensegFromDendiag ( CSeq_align const &  aln )

static

Definition at line 382 of file named_collection_score_impl.cpp.

References eUnknown, CSeq_align_Base::GetBounds(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::GetDim(), CSeq_align_Base::GetScore(), CSeq_align_Base::GetSegs(), CSeq_align_Base::GetType(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::IsSetBounds(), CSeq_align_Base::IsSetDim(), CSeq_align_Base::IsSetScore(), CSeq_align_Base::IsSetType(), ITERATE, NCBI_THROW, CSeq_align_Base::SetBounds(), CDense_seg_Base::SetDim(), CSeq_align_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetScore(), CDense_seg_Base::SetScores(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and CSeq_align_Base::SetType().

Referenced by CScoreUniqSeqCoverage::MakeScore(), CBlast_SAM_Formatter::Print(), and s_SeqAlignSetToXMLHsps().

MakeSubjectScores() [1/3]

void MakeSubjectScores ( CScope &  scope, CSeq_align_set &  coll, vector< pair< string, TCalculator > > const &  calculators  )

static

Definition at line 331 of file named_collection_score_impl.cpp.

References Compare(), CSeq_align_set_Base::Get(), CScope::GetBioseqHandle(), i, CSeq_id::Match(), CSeq_align_set_Base::Set(), CSeq_align::SetNamedScore(), ct::sort(), and value.

MakeSubjectScores() [2/3]

vector< CScoreValue > MakeSubjectScores ( CScope &  scope, CSeq_align_set const &  coll, string  name, TCalculator  f  )

static

Definition at line 282 of file named_collection_score_impl.cpp.

References f().

Referenced by CScoreSeqCoverage::Get(), CScoreUniqSeqCoverage::Get(), CSubjectsSequenceCoverage::Get(), CScoreSeqCoverage::Set(), CScoreUniqSeqCoverage::Set(), and CSubjectsSequenceCoverage::Set().

MakeSubjectScores() [3/3]

vector< CScoreValue > MakeSubjectScores ( CScope &  scope, CSeq_align_set const &  coll, vector< pair< string, TCalculator > > const &  calculators  )

static

Definition at line 289 of file named_collection_score_impl.cpp.

References Compare(), CSeq_align_set_Base::Get(), CScope::GetBioseqHandle(), CSeq_id_Handle::GetHandle(), i, CSeq_id::Match(), ct::sort(), and value.

s_FixMinusStrandRange()

CRange< TSeqPos > & s_FixMinusStrandRange ( CRange< TSeqPos > &  rng )

static

Definition at line 370 of file named_collection_score_impl.cpp.

References CRange_Base::GetFrom(), CRange_Base::GetTo(), and COpenRange< Position >::Set().

Referenced by CScoreSeqCoverage::MakeScore(), and CScoreUniqSeqCoverage::MakeScore().

USING_SCOPE()

USING_SCOPE

(

objects

)