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Searched refs:CInDelInfo (Results 1 – 11 of 11) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_objmgr.cpp209 CInDelInfo::SSource fill_src; in CAlignModel()
233 CInDelInfo::EStatus indelstatus = CInDelInfo::eUnknown; in CAlignModel()
250 …CInDelInfo fs(Strand()==ePlus?nuc_cur_start+pos:nuc_cur_end-pos+1, product_ins, CInDelInfo::eDel, … in CAlignModel()
259 indels.push_back(CInDelInfo(nuc_cur_start+pos, genomic_ins, CInDelInfo::eIns)); in CAlignModel()
261 …indels.insert(indels.begin(), CInDelInfo(nuc_cur_end-pos-genomic_ins+1, genomic_ins, CInDelInfo::e… in CAlignModel()
275 … indels.push_back(CInDelInfo(nuc_cur_start+pos, mismatch_len, CInDelInfo::eMism, v)); in CAlignModel()
278 …indels.insert(indels.begin(), CInDelInfo(nuc_cur_end-pos-mismatch_len+1, mismatch_len, CInDelInfo:… in CAlignModel()
286 if(indelstatus != CInDelInfo::eUnknown) { in CAlignModel()
343 *indl = CInDelInfo(indl->Loc(), indl->Len(), CInDelInfo::eMism, new_seq); in CAlignModel()
346 … *indl = CInDelInfo(indl->Loc(), indl->Len(), CInDelInfo::eMism, new_seq.substr(0,indl->Len())); in CAlignModel()
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H A Dglb_align.cpp101 … CInDelInfo indl(spos-len+sstart, len, CInDelInfo::eMism, string(query+qpos-len, len)); in GetInDels()
111 … CInDelInfo indl(spos-len+sstart, len, CInDelInfo::eMism, string(query+qpos-len, len)); in GetInDels()
115 CInDelInfo indl(spos+sstart, i->m_len, CInDelInfo::eIns); in GetInDels()
119 CInDelInfo indl(spos+sstart, i->m_len, CInDelInfo::eDel, string(query+qpos, i->m_len)); in GetInDels()
H A Dgnomon_model.cpp678 FrameShifts().push_back(CInDelInfo(loc, len, CInDelInfo::eIns)); in RemoveShortHolesAndRescore()
892 …indels.push_back(CInDelInfo(e->GetFrom(),indl->Len()-extra,CInDelInfo::eMism,indl->GetInDelV().sub… in RemoveExtraFShifts()
1588 if(indel.GetStatus() == CInDelInfo::eGenomeCorrect) in BuildGFF3Gap()
1613 const CInDelInfo& indel = *indelp; in BuildGFF3Gap()
1639 CInDelInfo::EStatus status = CInDelInfo::eUnknown; in readGFF3Gap()
1641 status = CInDelInfo::eGenomeCorrect; in readGFF3Gap()
1644 status = CInDelInfo::eGenomeNotCorrect; in readGFF3Gap()
1651 indels.push_back(CInDelInfo(loc,len,CInDelInfo::eIns)); in readGFF3Gap()
1658 indels.push_back(CInDelInfo(loc,len,CInDelInfo::eDel,seq)); in readGFF3Gap()
1665 indels.push_back(CInDelInfo(loc,len,CInDelInfo::eMism,seq)); in readGFF3Gap()
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H A Daligncollapser.cpp1404 if(indl->GetStatus() != CInDelInfo::eGenomeNotCorrect) in FilterAlignments()
1825 CInDelInfo p(i->GetFrom(), 1, CInDelInfo::eDel); in CheckAndInsert()
2140 CInDelInfo::SSource left_src; in FillGapsInAlignmentAndAddToGenomicGaps()
2141 CInDelInfo::SSource right_src; in FillGapsInAlignmentAndAddToGenomicGaps()
2175 …tion_data.m_correction_indels.push_back(CInDelInfo(max(0,ig->first+2*ig->second/3), left_seq.lengt… in FillGapsInAlignmentAndAddToGenomicGaps()
2193 CInDelInfo::SSource src; in FillGapsInAlignmentAndAddToGenomicGaps()
2203 …_correction_data.m_correction_indels.push_back(CInDelInfo(ig->first+ig->second/2, seq.length(), CI… in FillGapsInAlignmentAndAddToGenomicGaps()
2223 …rrection_data.m_correction_indels.push_back(CInDelInfo(ig->first+ig->second/3, right_seq.length(),… in FillGapsInAlignmentAndAddToGenomicGaps()
2261 … m_correction_data.m_correction_indels.back().SetStatus(CInDelInfo::eGenomeNotCorrect); in AddAlignment()
H A Dchainer.cpp7071 fshifts.push_back(CInDelInfo(fs->Loc(), l, CInDelInfo::eIns)); in DropAlignmentInfo()
7456 combined_indels.push_back(CInDelInfo(pos,len,CInDelInfo::eIns)); in CombineCorrectionsAndIndels()
7461 combined_indels.push_back(CInDelInfo(pb, s.size(), CInDelInfo::eDel, s)); in CombineCorrectionsAndIndels()
7479 CInDelInfo::SSource src; in MapOneModelToOrigContig()
7543 erepl.push_back(CInDelInfo(loc, 1, CInDelInfo::eMism, string(1,c))); in MapOneModelToOrigContig()
7545 erepl.push_back(CInDelInfo(loc, 1, CInDelInfo::eMism, string(1,c))); in MapOneModelToOrigContig()
7549 erepl.back() = CInDelInfo(loc, s.size(), CInDelInfo::eMism, s); in MapOneModelToOrigContig()
7679 list<CInDelInfo> exon_indels; in MapOneModelToEditedContig()
8082 CInDelInfo Ns(l, BLOCK_OF_Ns, CInDelInfo::eDel, string(BLOCK_OF_Ns,'N')); in SetGenomic()
8122 … m_reversed_corrections.push_back(CInDelInfo(loc, ig->Len(), CInDelInfo::eDel, NStr::ToUpper(s))); in SetGenomic()
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H A Dasn1.cpp805 const CInDelInfo& indel = *indel_i; in AlignModelToSeqalign()
900 case CInDelInfo::eGenomeNotCorrect: in AlignModelToSeqalign()
902 case CInDelInfo::eGenomeCorrect: in AlignModelToSeqalign()
H A Dgnomon_seq.cpp315 void PushInDel(TInDels& indels, bool fs_only, TSignedSeqPos p, int len, CInDelInfo::EType type, con… in PushInDel()
317 indels.push_back(CInDelInfo(p, len, type, seq)); in PushInDel()
H A Dscore.cpp252 align.FrameShifts().push_back(CInDelInfo(p, hole_len%3, CInDelInfo::eIns)); in CSeqScores()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp100 class NCBI_XALGOGNOMON_EXPORT CInDelInfo { class
113 …CInDelInfo(TSignedSeqPos l, int len, EType type, const string& v = kEmptyStr, const SSource& s = S… in CInDelInfo() function in CInDelInfo
126 bool operator<(const CInDelInfo& fsi) const // source is ignored!!!!!!!!!!! in operator <()
137 bool operator!=(const CInDelInfo& fsi) const { return (*this < fsi || fsi < *this); } in operator !=()
138 bool operator==(const CInDelInfo& fsi) const { return !(*this != fsi); } in operator ==()
169 typedef vector<CInDelInfo> TInDels;
185 …sig = "", double ident = 0, const string& seq = "", const CInDelInfo::SSource& src = CInDelInfo::S… in CModelExon()
214 CInDelInfo::SSource m_source;
400 … ss = "", double ident = 0, const string& seq = "", const CInDelInfo::SSource& src = CInDelInfo::S…
402 void AddGgapExon(double ident, const string& seq, const CInDelInfo::SSource& src, bool infront);
H A Daligncollapser.hpp156 bool operator()(const CInDelInfo& a, const CInDelInfo& b) const in operator ()()
H A Dvariations.hpp14 …CLiteIndel(const CInDelInfo& indl) : m_loc(indl.Loc()), m_len(indl.Len()), m_indelv(indl.IsDeletio… in CLiteIndel()