NCBI C++ ToolKit
Classes | Functions
banded_aligner.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/ncbi_signal.hpp>
#include <math.h>
#include <algo/align/ngalign/banded_aligner.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/scope.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 <objmgr/seq_vector.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/blastinput/blastn_args.hpp>
#include <algo/align/contig_assembly/contig_assembly.hpp>
#include <algo/align/nw/nw_band_aligner.hpp>
#include <algo/align/nw/mm_aligner.hpp>
#include <algo/align/util/blast_tabular.hpp>
#include <algo/align/util/compartment_finder.hpp>
#include <algo/sequence/align_cleanup.hpp>
+ Include dependency graph for banded_aligner.cpp:

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Classes

struct  SCallbackData
 

Functions

 USING_SCOPE (objects)
 
 USING_SCOPE (blast)
 
CRef< CSeq_locs_CoverageSeqLoc (TAlignSetRef Alignments, int Row, CScope &Scope)
 
TSeqPos s_CalcCoverageCount (TAlignSetRef Alignments, int Row, CScope &Scope)
 
bool s_ProgressCallback (CNWAligner::SProgressInfo *ProgressInfo)
 

Function Documentation

◆ s_CalcCoverageCount()

TSeqPos s_CalcCoverageCount ( TAlignSetRef  Alignments,
int  Row,
CScope Scope 
)

◆ s_CoverageSeqLoc()

CRef<CSeq_loc> s_CoverageSeqLoc ( TAlignSetRef  Alignments,
int  Row,
CScope Scope 
)

◆ s_ProgressCallback()

bool s_ProgressCallback ( CNWAligner::SProgressInfo ProgressInfo)

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )
Modified on Sat May 25 14:18:41 2024 by modify_doxy.py rev. 669887