NCBI C++ ToolKit
Functions
tabular_fmt.cpp File Reference
#include <ncbi_pch.hpp>
#include <util/xregexp/regexp.hpp>
#include <util/range_coll.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Prot_pos.hpp>
#include <objects/taxon1/taxon1.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objtools/alnmgr/alnmix.hpp>
#include <algo/sequence/gene_model.hpp>
#include <algo/align/util/algo_align_util_exceptions.hpp>
#include <algo/align/util/tabular_fmt.hpp>
#include <util/value_convert.hpp>
#include <limits>
+ Include dependency graph for tabular_fmt.cpp:

Go to the source code of this file.

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Functions

 USING_SCOPE (objects)
 
void s_AlignToSeqRanges (const CSeq_align &align, int row, list< TSeqRange > &ranges)
 
TSeqPos s_FindGaps (const CGC_Assembly &Assembly, const CSeq_id &Id, const TSeqPos Offset, list< TSeqRange > &Gaps)
 
static string s_CodonVariation (const CSeq_align &align, TSeqPos pos, CScope &scope, int row)
 
static void s_Split (const string &format, const string &separators, vector< string > &toks)
 Split a string, but ignore separators within parentheses. More...
 

Function Documentation

◆ s_AlignToSeqRanges()

void s_AlignToSeqRanges ( const CSeq_align align,
int  row,
list< TSeqRange > &  ranges 
)

◆ s_CodonVariation()

static string s_CodonVariation ( const CSeq_align align,
TSeqPos  pos,
CScope scope,
int  row 
)
static

◆ s_FindGaps()

TSeqPos s_FindGaps ( const CGC_Assembly Assembly,
const CSeq_id Id,
const TSeqPos  Offset,
list< TSeqRange > &  Gaps 
)

◆ s_Split()

static void s_Split ( const string format,
const string separators,
vector< string > &  toks 
)
static

Split a string, but ignore separators within parentheses.

Definition at line 3079 of file tabular_fmt.cpp.

References eUnknown, format, ITERATE, and NCBI_THROW.

Referenced by CTabularFormatter::SetFormat().

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Wed Jul 17 13:22:54 2024 by modify_doxy.py rev. 669887