NCBI C++ ToolKit
Functions
single_aln_tests.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/seqqa/single_aln_tests.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/IUPACna.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <algo/sequence/consensus_splice.hpp>
+ Include dependency graph for single_aln_tests.cpp:

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Functions

 USING_SCOPE (objects)
 
static ENa_strand s_GetSeqStrand (const CSeq_align &aln, CSeq_align::TDim row)
 
static CRef< CSeq_aligns_SplicedToDisc (const CSeq_align &spliced_seg_aln)
 
static size_t s_GetPolyA_genomic_priming (const CSeq_align &aln, CScope &scope, int neighborhood)
 
static vector< TSignedSeqPoss_CalculateStarts (const vector< TSeqPos > &lens, ENa_strand strand, TSeqPos start, TSeqPos end)
 
static CRef< CDense_segs_ExonToDenseg (const CSpliced_exon &exon, ENa_strand product_strand, ENa_strand genomic_strand, const CSeq_id &product_id, const CSeq_id &genomic_id)
 

Function Documentation

◆ s_CalculateStarts()

static vector<TSignedSeqPos> s_CalculateStarts ( const vector< TSeqPos > &  lens,
ENa_strand  strand,
TSeqPos  start,
TSeqPos  end 
)
static

Definition at line 768 of file single_aln_tests.cpp.

References IsReverse(), ITERATE, len, and offset.

Referenced by s_ExonToDenseg().

◆ s_ExonToDenseg()

static CRef<CDense_seg> s_ExonToDenseg ( const CSpliced_exon exon,
ENa_strand  product_strand,
ENa_strand  genomic_strand,
const CSeq_id product_id,
const CSeq_id genomic_id 
)
static

◆ s_GetPolyA_genomic_priming()

static size_t s_GetPolyA_genomic_priming ( const CSeq_align aln,
CScope scope,
int  neighborhood 
)
static

◆ s_GetSeqStrand()

static ENa_strand s_GetSeqStrand ( const CSeq_align aln,
CSeq_align::TDim  row 
)
static

◆ s_SplicedToDisc()

static CRef< CSeq_align > s_SplicedToDisc ( const CSeq_align spliced_seg_aln)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Mon Jul 15 05:33:19 2024 by modify_doxy.py rev. 669887