src/algo/align/util/score_builder.cpp File Reference

#include <ncbi_pch.hpp>
#include <algo/align/util/score_builder.hpp>
#include <algo/blast/api/blast_aux.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/core/blast_setup.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_options.h>
#include <objmgr/util/sequence.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Prot_pos.hpp>

Include dependency graph for score_builder.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
	USING_SCOPE (blast)
static size_t	s_GetAlignmentLength (const CSeq_align &align, bool ungapped)
	calculate the length of our alignment
static void	s_GetCountIdentityMismatch (CScope &scope, const CSeq_align &align, int *identities, int *mismatches)
	calculate mismatches and identities in a seq-align
static void	s_GetPercentIdentity (CScope &scope, const CSeq_align &align, int *identities, int *mismatches, double *pct_identity)
	calculate the percent identity we also return the count of identities and mismatches
static size_t	s_GetCoveredBases (const CSeq_align &align, int row)
	calculate the length of our alignment
static void	s_GetPercentCoverage (CScope &scope, const CSeq_align &align, double *pct_coverage)
	calculate the percent coverage
Variables
static const unsigned char	reverse_4na [16] = {0, 8, 4, 0, 2, 0, 0, 0, 1}

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Function Documentation

static size_t s_GetAlignmentLength (  const CSeq_align &  align, bool  ungapped )  [static]

calculate the length of our alignment we have at least one row of sequence pass 1: find total ranges skip pass 2: determine shortest length genomic-ins is not handled explicitly Definition at line 163 of file score_builder.cpp. References align, and len. Referenced by CScoreBuilder::GetAlignLength(), s_GetCountIdentityMismatch(), and s_GetPercentIdentity().

static void s_GetCountIdentityMismatch (  CScope &  scope, const CSeq_align &  align, int *  identities, int *  mismatches )  [static]

calculate mismatches and identities in a seq-align shortcut: if 'num_ident' is present, we trust it we compute ungapped identities gap on at least one row, so we skip this segment shortcut: if 'num_ident' is present, we trust it Definition at line 306 of file score_builder.cpp. References _ASSERT, align, len, and s_GetAlignmentLength(). Referenced by CScoreBuilder::AddScore(), CScoreBuilder::GetIdentityCount(), CScoreBuilder::GetMismatchCount(), and s_GetPercentIdentity().

static size_t s_GetCoveredBases (  const CSeq_align &  align, int  row )  [static]

calculate the length of our alignment skip Definition at line 453 of file score_builder.cpp. References align, CDense_seg_Base::GetDim(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetStarts(), and len. Referenced by s_GetPercentCoverage().

static void s_GetPercentCoverage (  CScope &  scope, const CSeq_align &  align, double *  pct_coverage )  [static]

calculate the percent coverage Definition at line 545 of file score_builder.cpp. References align, eNa_strand_minus, and s_GetCoveredBases(). Referenced by CScoreBuilder::AddScore(), and CScoreBuilder::GetPercentCoverage().

static void s_GetPercentIdentity (  CScope &  scope, const CSeq_align &  align, int *  identities, int *  mismatches, double *  pct_identity )  [static]

calculate the percent identity we also return the count of identities and mismatches Definition at line 433 of file score_builder.cpp. References align, s_GetAlignmentLength(), and s_GetCountIdentityMismatch(). Referenced by CScoreBuilder::AddScore(), and CScoreBuilder::GetPercentIdentity().

USING_SCOPE (  blast   )

USING_SCOPE (  objects   )

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Variable Documentation

const unsigned char reverse_4na[16] = {0, 8, 4, 0, 2, 0, 0, 0, 1} [static]

Definition at line 638 of file score_builder.cpp.

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