Lines Matching refs:pFeature
393 CRef< CSeq_feat > pFeature(new CSeq_feat); in xUpdateAnnotFeature() local
397 return xUpdateAnnotExon(gffRecord, pFeature, annot, pEC); in xUpdateAnnotFeature()
400 return xUpdateAnnotCds(gffRecord, pFeature, annot, pEC); in xUpdateAnnotFeature()
403 return xUpdateAnnotGene(gffRecord, pFeature, annot, pEC); in xUpdateAnnotFeature()
406 return xUpdateAnnotMrna(gffRecord, pFeature, annot, pEC); in xUpdateAnnotFeature()
409 return xUpdateAnnotRegion(gffRecord, pFeature, annot, pEC); in xUpdateAnnotFeature()
411 if (!xUpdateAnnotGeneric(gffRecord, pFeature, annot, pEC)) { in xUpdateAnnotFeature()
454 CRef<CSeq_feat> pFeature, in xUpdateAnnotExon() argument
473 if (!xInitializeFeature(record, pFeature)) { in xUpdateAnnotExon()
476 return xAddFeatureToAnnot(pFeature, annot); in xUpdateAnnotExon()
532 CRef<CSeq_feat> pFeature, in xUpdateAnnotCds() argument
550 m_MapIdToFeature[cdsId] = pFeature; in xUpdateAnnotCds()
551 xInitializeFeature(record, pFeature); in xUpdateAnnotCds()
552 xAddFeatureToAnnot(pFeature, annot); in xUpdateAnnotCds()
557 xFeatureSetQualifier("Parent", parentId, pFeature); in xUpdateAnnotCds()
558 xFeatureSetXrefParent(parentId, pFeature); in xUpdateAnnotCds()
560 xFeatureSetXrefGrandParent(parentId, pFeature); in xUpdateAnnotCds()
570 CRef<CSeq_feat> pFeature) in xFeatureSetXrefGrandParent() argument
594 pFeature->SetXref().push_back(pGrandParentXref); in xFeatureSetXrefGrandParent()
598 pGrandChildId->Assign(pFeature->GetId()); in xFeatureSetXrefGrandParent()
667 CRef<CSeq_feat> pFeature, in xUpdateAnnotGeneric() argument
713 if (!xInitializeFeature(record, pFeature)) { in xUpdateAnnotGeneric()
716 if (! xAddFeatureToAnnot(pFeature, annot)) { in xUpdateAnnotGeneric()
721 m_MapIdToFeature[strId] = pFeature; in xUpdateAnnotGeneric()
723 if (pFeature->GetData().IsRna() || in xUpdateAnnotGeneric()
724 pFeature->GetData().GetSubtype() == CSeqFeatData::eSubtype_misc_RNA) { in xUpdateAnnotGeneric()
726 rnaLoc->Assign(pFeature->GetLocation().GetInt()); in xUpdateAnnotGeneric()
735 CRef<CSeq_feat> pFeature, in xUpdateAnnotMrna() argument
745 if (!xInitializeFeature(record, pFeature)) { in xUpdateAnnotMrna()
755 if (!xFeatureSetXrefParent(*cit, pFeature)) { in xUpdateAnnotMrna()
767 m_MapIdToFeature[strId] = pFeature; in xUpdateAnnotMrna()
770 CSeq_loc::E_Choice choice = pFeature->GetLocation().Which(); in xUpdateAnnotMrna()
778 mrnaLoc->Assign(pFeature->GetLocation().GetInt()); in xUpdateAnnotMrna()
784 CRef< CSeq_feat > pFeature(new CSeq_feat); in xUpdateAnnotMrna() local
785 xUpdateAnnotExon(exonRecord, pFeature, annot, pEC); in xUpdateAnnotMrna()
787 if (! xAddFeatureToAnnot(pFeature, annot)) { in xUpdateAnnotMrna()
796 CRef<CSeq_feat> pFeature, in xUpdateAnnotGene() argument
806 if (!xInitializeFeature(record, pFeature)) { in xUpdateAnnotGene()
809 if (! xAddFeatureToAnnot(pFeature, annot)) { in xUpdateAnnotGene()
814 m_MapIdToFeature[strId] = pFeature; in xUpdateAnnotGene()
829 CRef<CSeq_feat> pFeature, in xUpdateAnnotRegion() argument
834 if (!record.InitializeFeature(m_iFlags, pFeature)) { in xUpdateAnnotRegion()
838 if (! xAddFeatureToAnnot(pFeature, annot)) { in xUpdateAnnotRegion()
844 m_MapIdToFeature[strId] = pFeature; in xUpdateAnnotRegion()
851 CRef< CSeq_feat > pFeature, in xAddFeatureToAnnot()
855 annot.SetData().SetFtable().push_back( pFeature ) ; in xAddFeatureToAnnot()
996 CRef<CSeq_feat> pFeature) in xInitializeFeature() argument
999 if (!record.InitializeFeature(m_iFlags, pFeature)) { in xInitializeFeature()
1070 CRef<CSeq_feat> pFeature = itFeature->second; in xPostProcessAnnot() local
1071 pFeature->SetLocation(*pNewLoc); in xPostProcessAnnot()
1072 if (pFeature->GetData().IsCdregion()) { in xPostProcessAnnot()
1073 auto& cdrData = pFeature->SetData().SetCdregion(); in xPostProcessAnnot()