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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...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, row, CRange_Base::SetFrom(), COpenRange< Position >::SetLength(), and CSeq_align_Base::C_Segs::Which().
Referenced by CTabularFormatter_MismatchPositions::Print().
◆ s_CodonVariation()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() ◆ s_Split() ◆ USING_SCOPE()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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