src/algo/align/ngalign/banded_aligner.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbi_system.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:

Go to the source code of this file.

Classes
struct	SCallbackData
Functions
	USING_SCOPE (objects)
	USING_SCOPE (blast)
CRef< CSeq_loc >	s_CoverageSeqLoc (TAlignSetRef Alignments, int Row, CScope &Scope)
TSeqPos	s_CalcCoverageCount (TAlignSetRef Alignments, int Row, CScope &Scope)
bool	s_ProgressCallback (CNWAligner::SProgressInfo *ProgressInfo)

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Function Documentation

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

Definition at line 104 of file banded_aligner.cpp. References CSeq_loc_Base::e_Int, eNa_strand_plus, ITERATE, and s_CoverageSeqLoc(). Referenced by CSimpleBandedAligner::x_RunBanded().

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

Definition at line 72 of file banded_aligner.cpp. References ITERATE. Referenced by s_CalcCoverageCount().

bool s_ProgressCallback (  CNWAligner::SProgressInfo *  ProgressInfo  )

Definition at line 460 of file banded_aligner.cpp. References CTime::eCurrent, ERR_POST, CTimeSpan::GetAsDouble(), CTimeSpan::GetCompleteSeconds(), CNWAligner::SProgressInfo::m_data, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, SCallbackData::PreviousCount, SCallbackData::StartTime, SCallbackData::TimedOut, and SCallbackData::TimeOutSeconds.

USING_SCOPE (  blast   )

USING_SCOPE (  objects   )

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