NCBI C++ ToolKit
Functions | Variables
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 <algo/blast/core/blast_encoding.h>
#include <objtools/alnmgr/alnvec.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Score_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objtools/alnmgr/pairwise_aln.hpp>
#include <objtools/alnmgr/aln_converters.hpp>
#include <objtools/alnmgr/aln_generators.hpp>
#include <util/checksum.hpp>
#include <sstream>
+ Include dependency graph for score_builder.cpp:

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Functions

 USING_SCOPE (objects)
 
 USING_SCOPE (blast)
 
static void s_RecordMatch (size_t match, string &BTOP, string &flipped_BTOP)
 
static pair< string, strings_ComputeTraceback (CScope &scope, const CSeq_align &align)
 
void s_CleanSeqAlign (CSeq_align &align)
 

Variables

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

Function Documentation

◆ s_CleanSeqAlign()

void s_CleanSeqAlign ( CSeq_align align)

◆ s_ComputeTraceback()

static pair<string,string> s_ComputeTraceback ( CScope scope,
const CSeq_align align 
)
static

◆ s_RecordMatch()

static void s_RecordMatch ( size_t  match,
string BTOP,
string flipped_BTOP 
)
inlinestatic

Definition at line 679 of file score_builder.cpp.

References match(), and NStr::NumericToString().

Referenced by s_ComputeTraceback().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

Variable Documentation

◆ reverse_4na

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

Definition at line 206 of file score_builder.cpp.

Referenced by CScoreBuilder::GetBlastScoreDenseg().

Modified on Fri Jul 19 17:08:31 2024 by modify_doxy.py rev. 669887