#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.
Go to the SVN repository for this file.
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 | ||
| ) |
Definition at line 578 of file tabular_fmt.cpp.
References CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CSeq_align_Base::C_Segs::GetDisc(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CDense_seg_Base::GetStarts(), i, ITERATE, NCBI_THROW, compile_time_bits::range(), row, and CSeq_align_Base::C_Segs::Which().
Referenced by CTabularFormatter_MismatchPositions::Print().
◆ s_CodonVariation()
|
static |
Definition at line 2596 of file tabular_fmt.cpp.
References CSeq_id::Assign(), CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, eNa_strand_minus, eNa_strand_plus, CSeq_align::GetSeq_id(), CSeqVector::GetSeqData(), CSeq_loc::GetStart(), CSeq_loc::GetStrand(), CSeq_loc_Mapper_Base::Map(), NStr::NumericToString(), query, row, CSeqVector::size(), and subject.
Referenced by CTabularFormatter_StartCodonChanges::Print(), and CTabularFormatter_StopCodonChanges::Print().
◆ s_FindGaps()
| TSeqPos s_FindGaps | ( | const CGC_Assembly & | Assembly, |
| const CSeq_id & | Id, | ||
| const TSeqPos | Offset, | ||
| list< TSeqRange > & | Gaps | ||
| ) |
Definition at line 2365 of file tabular_fmt.cpp.
References CGC_Assembly::eChooseAny, CGC_Assembly::Find(), CSeq_id_Handle::GetHandle(), COpenRange< Position >::GetLength(), ITERATE, Offset(), CRange_Base::SetFrom(), and COpenRange< Position >::SetLength().
Referenced by CTabularFormatter_NearestGap::Print().
◆ s_Split()
|
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 | ) |
