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USING_SCOPE (objects) static void s_AppendProtRefInfo (CProt_ref ¤t_ref, const CProt_ref &other_ref) static void s_SetProtRef (const CSeq_feat &cds, CConstRef< CSeq_feat > pMrna, CProt_ref &prot_ref) static bool s_TranslateCds (const CSeq_feat &cds, CScope &scope) static bool s_HasUnprocessedCdregions (const CSeq_entry &nuc_prot) static void s_ReportDuplicateMods (const set< string > &duplicateMods, const string &idString, TSeqPos lineNumber, objects::ILineErrorListener &logger) static CBioseq_Handle s_MatchProteinById (const CBioseq &protein, CSeq_entry_Handle seh) static CBioseq_Handle s_GetSingleNucSeq (CSeq_entry_Handle seh) static CRef< CSeq_loc > s_GetCDSLoc (CScope &scope, const CSeq_id &proteinId, const CSeq_loc &genomicLoc, TSeqPos bioseqLength, const CTable2AsnContext::SPrtAlnOptions &prtAlnOptions) static CRef< CSeq_feat > s_MakeCDSFeat (CSeq_loc &loc, bool isPartial, CSeq_id &productId) static bool s_UnknownEstimatedLength (const CSeq_feat &feat) static const CSeq_id * s_GetIdFromLocation (const CSeq_loc &loc) static void s_GatherRegionIterators (list< CRef< CSeq_annot >> &annots, list< SRegionIterators > &its) static bool s_MoveProteinSpecificFeats (CSeq_entry &entry) ◆ s_AppendProtRefInfo()Definition at line 451 of file feature_table_reader.cpp.
References CProt_ref_Base::eProcessed_not_set, CProt_ref_Base::GetActivity(), CProt_ref_Base::GetDb(), CProt_ref_Base::GetDesc(), CProt_ref_Base::GetEc(), CProt_ref_Base::GetName(), CProt_ref_Base::GetProcessed(), CProt_ref_Base::IsSetActivity(), CProt_ref_Base::IsSetDb(), CProt_ref_Base::IsSetDesc(), CProt_ref_Base::IsSetEc(), CProt_ref_Base::IsSetName(), CProt_ref_Base::SetActivity(), CProt_ref_Base::SetDb(), CProt_ref_Base::SetDesc(), CProt_ref_Base::SetEc(), CProt_ref_Base::SetName(), and CProt_ref_Base::SetProcessed().
Referenced by s_SetProtRef().
◆ s_GatherRegionIterators() ◆ s_GetCDSLoc()Definition at line 1440 of file feature_table_reader.cpp.
References CSeq_id::Assign(), eExtreme_Biological, eNa_strand_minus, CProSplignOutputOptions::ePassThrough, CProSplignOutputOptions::eWithHoles, CTable2AsnContext::SPrtAlnOptions::filterQueryString, CProSplign::FindAlignment(), CTable2AsnContext::SPrtAlnOptions::intronless, NStr::IsBlank(), CAlignFilter::Match(), Ref(), CTable2AsnContext::SPrtAlnOptions::refineAlignment, s_ExtendIntervalToEnd(), and CProSplignOptions_Base::SetAltStarts().
Referenced by CFeatureTableReader::xAddProteinToSeqEntry().
◆ s_GetIdFromLocation() ◆ s_GetSingleNucSeq() ◆ s_HasUnprocessedCdregions()Definition at line 732 of file feature_table_reader.cpp.
References _ASSERT, CScope::AddTopLevelSeqEntry(), CBioseq_set_Base::eClass_nuc_prot, set< Key, Compare >::end(), set< Key, Compare >::find(), CBioseq_Base::GetAnnot(), CBioseq_set_Base::GetClass(), CBioseq_Base::GetId(), CObjectManager::GetInstance(), CSeq_entry_Base::GetSet(), CBioseq::IsNa(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetAnnot(), CBioseq_set_Base::IsSetClass(), CBioseq_Base::IsSetId(), Ref(), s_TranslateCds(), and transform().
Referenced by CFeatureTableReader::xMergeCDSFeatures_impl().
◆ s_MakeCDSFeat() ◆ s_MatchProteinById() ◆ s_MoveProteinSpecificFeats() ◆ s_ReportDuplicateMods() ◆ s_SetProtRef()Definition at line 502 of file feature_table_reader.cpp.
References CConstRef< C, Locker >::Empty(), NStr::EqualNocase(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CRNA_ref_Base::C_Ext::GetName(), CSeq_feat::GetNamedQual(), CSeq_feat::GetProtXref(), CSeqFeatData_Base::GetRna(), NStr::IsBlank(), CRNA_ref_Base::C_Ext::IsName(), CRNA_ref_Base::IsSetExt(), CProt_ref_Base::IsSetName(), s_AppendProtRefInfo(), and CProt_ref_Base::SetName().
Referenced by CFeatureTableReader::xTranslateProtein().
◆ s_TranslateCds() ◆ s_UnknownEstimatedLength() ◆ USING_SCOPE()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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