#include <ncbi_pch.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbi_system.hpp>
#include <math.h>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/annot_ci.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/disc_nucl_options.hpp>
#include <algo/align/util/score_builder.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objmgr/seq_vector.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/seq/Seq_hist.hpp>
#include <objmgr/util/sequence.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/blastinput/blastn_args.hpp>
#include <algo/align/ngalign/alignment_scorer.hpp>

Include dependency graph for alignment_scorer.cpp:

Go to the SVN repository for this file.

Functions
	USING_SCOPE (objects)

	USING_SCOPE (blast)

static void	s_ScoreAlignments (const CSeq_align_set &alignments, CScope &Scope, CScoreBuilder &Scorer, bool skip_unsupported)

Variables
static const Int8	kEffectiveSearchSpace = NCBI_CONST_INT8(1050668186940)

Function Documentation

◆ s_ScoreAlignments()

static void s_ScoreAlignments	(	const CSeq_align_set &	alignments,
		CScope &	Scope,
		CScoreBuilder &	Scorer,
		bool	skip_unsupported
	)

static

Definition at line 78 of file alignment_scorer.cpp.

References CSeq_align_Base::C_Segs::e_Disc, CSeq_align::eScore_BitScore, CSeq_align::eScore_Blast, CSeq_align::eScore_EValue, CSeq_align::eScore_IdentityCount, CSeq_align_Base::C_Segs::GetDisc(), CSeq_align::GetNamedScore(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::IsDenseg(), ITERATE, and CSeq_align_Base::C_Segs::Which().

Referenced by CBlastScorer::ScoreAlignments().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects )

Variable Documentation

◆ kEffectiveSearchSpace

const Int8 kEffectiveSearchSpace = NCBI_CONST_INT8(1050668186940)

static

Definition at line 76 of file alignment_scorer.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastScorer::ScoreAlignments().