Searched refs:CCDSInfo (Results 1 – 9 of 9) sorted by relevance
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | gnomon_model.cpp | 269 bool CCDSInfo::operator== (const CCDSInfo& a) const in operator ==()
285 CCDSInfo CCDSInfo::MapFromEditedToOrig(const CAlignMap& amap) const in MapFromEditedToOrig()
287 CCDSInfo empty_cds; in MapFromEditedToOrig()
288 CCDSInfo new_cds(true); in MapFromEditedToOrig()
335 CCDSInfo CCDSInfo::MapFromOrigToEdited(const CAlignMap& amap) const in MapFromOrigToEdited()
337 CCDSInfo new_cds(false); in MapFromOrigToEdited()
486 void CCDSInfo::CombineWith(const CCDSInfo& another_cds_info) in CombineWith()
491 CCDSInfo new_cds_info; in CombineWith()
642 void CCDSInfo::Clear() in Clear()
1977 CCDSInfo::EStatus status = CCDSInfo::eUnknown; in ParseAttributes()
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| H A D | gnomon_objmgr.cpp | 431 CCDSInfo cds_info_t; in CAlignModel()
439 CCDSInfo cds_info_g = cds_info_t.MapFromEditedToOrig(m_alignmap); in CAlignModel()
480 CCDSInfo cds_info = GetCdsInfo(); in GetCdsDnaSequence()
506 CCDSInfo cds_info = GetCdsInfo(); in GetProtein()
511 ITERATE(CCDSInfo::TPStops, stp, cds_info.PStops()) { in GetProtein()
512 if(stp->m_status == CCDSInfo::eSelenocysteine) in GetProtein()
534 CCDSInfo cds_info = GetCdsInfo(); in GetProtein()
539 ITERATE(CCDSInfo::TPStops, stp, cds_info.PStops()) { in GetProtein()
540 if(stp->m_status == CCDSInfo::eSelenocysteine) in GetProtein()
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| H A D | annot.cpp | 574 CCDSInfo cds = nested.back().GetCdsInfo(); in Predict()
677 CCDSInfo cds_info = it->GetCdsInfo(); in Predict()
691 CCDSInfo::TPStops pstops = cds_info.PStops(); in Predict()
693 ITERATE(CCDSInfo::TPStops, ps, pstops) { in Predict()
708 ITERATE(CCDSInfo::TPStops, stp, it->GetCdsInfo().PStops()) { in Predict()
709 if(stp->m_status != CCDSInfo::eSelenocysteine) in Predict()
718 CCDSInfo cds_info = it->GetCdsInfo(); in Predict()
758 CCDSInfo cds_info = m.GetCdsInfo(); in transform_model()
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| H A D | chainer.cpp | 246 const CCDSInfo* m_cds_info;
1877 list<CCDSInfo> m_extra_cds;
2155 CCDSInfo cds; in ReplicatePStops()
2236 CCDSInfo& acdsinfo = const_cast<CCDSInfo&>(*mbr.m_cds_info); in Duplicate5pendsAndShortCDSes()
4142 algn.SetCdsInfo(CCDSInfo()); in RemovePoorCds()
4585 CCDSInfo cds = GetCdsInfo(); in CalculateSupportAndWeightFromMembers()
4593 CCDSInfo cds_info = cds; in CalculateSupportAndWeightFromMembers()
4791 CCDSInfo cds = GetCdsInfo(); in RestoreReasonableConfirmedStart()
6407 CCDSInfo edited_cds; in FindSelenoproteinsClipProteinsToStartStop()
6689 CCDSInfo cdsinfo; in transform_align()
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| H A D | asn1.cpp | 85 CCDSInfo cds = model.GetCdsInfo(); in SModelData()
282 const CCDSInfo& cds = model.GetCdsInfo(); in create_cdregion_feature()
292 ITERATE(CCDSInfo::TPStops,s,cds.PStops()) { in create_cdregion_feature()
307 if(s->m_status == CCDSInfo::eSelenocysteine) in create_cdregion_feature()
670 const CCDSInfo& cds_info = model.GetCdsInfo(); in create_internal_feature()
1065 CCDSInfo cds_info = model.GetCdsInfo(); in RestoreModelAttributes()
1071 CCDSInfo cds_info_t = model.GetCdsInfo(); in RestoreModelAttributes()
1072 CCDSInfo cds_info_g = cds_info_t.MapFromEditedToOrig(model.GetAlignMap()); in RestoreModelAttributes()
1116 … CCDSInfo cds_info(false); // mrna coordinates; will be projected to genome at the end if possible in RestoreModelReadingFrame()
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| H A D | score.cpp | 240 CCDSInfo cds_info = align.GetCdsInfo(); in CSeqScores()
248 cds_info.AddPStop(pstop, CCDSInfo::eUnknown); in CSeqScores()
1303 CCDSInfo cds_info = model.GetCdsInfo(); in SelectBestReadingFrame()
1402 CCDSInfo cds_info = model.GetCdsInfo(); in GetScore()
1407 CCDSInfo::TPStops pstops = cds_info.PStops(); in GetScore()
1411 CCDSInfo::TPStops::iterator it = find(pstops.begin(), pstops.end(), pstop); in GetScore()
1451 CCDSInfo ci; in GetScore()
1488 CCDSInfo ci; in GetScore()
1560 CCDSInfo::EStatus status = CCDSInfo::eUnknown; in GetScore()
1561 CCDSInfo::TPStops::iterator it = find(pstops.begin(), pstops.end(), pstop); in GetScore()
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| H A D | select_alignments_alt.cpp | 181 CCDSInfo cds_info = model.GetCdsInfo(); in FilterGenes()
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| H A D | parse.cpp | 687 CCDSInfo cds_info; in GetGenes()
696 ITERATE(CCDSInfo::TPStops,s,gene.GetCdsInfo().PStops()) in GetGenes()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
| H A D | gnomon_model.hpp | 223 class CCDSInfo { class
227 bool operator== (const CCDSInfo& another) const;
232 CCDSInfo MapFromOrigToEdited(const CAlignMap& amap) const;
257 void CombineWith(const CCDSInfo& another_cds_info);
411 m_cds_info = CCDSInfo(); in ClearExons()
443 const CCDSInfo& GetCdsInfo() const { return m_cds_info; } in GetCdsInfo()
444 void SetCdsInfo(const CCDSInfo& cds_info);
447 void CombineCdsInfo(const CCDSInfo& cds_info, bool ensure_cds_invariant = true);
576 vector<CCDSInfo>* SetEdgeReadingFrames() { return &m_edge_reading_frames; } in SetEdgeReadingFrames()
602 CCDSInfo m_cds_info;
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