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NCBI C++ ToolKit: include/objtools/edit/cds_fix.hpp File Reference

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AdjustProteinFeaturePartialsToMatchCDS A function to change an existing MolInfo to match a coding region.

Parameters

new_prot The protein feature to be adjusted (if necessary) cds The CDS to match

Returns

Boolean to indicate whether the protein feature was changed

Definition at line 398 of file cds_fix.cpp.

References AdjustFeaturePartialFlagForLocation(), eExtreme_Biological, CSeq_feat_Base::GetLocation(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), and CSeq_feat_Base::SetLocation().

Referenced by AdjustForCDSPartials(), CFeatGapInfo::AdjustProteinSeq(), AdjustSingleFeature(), BOOST_AUTO_TEST_CASE(), CProductColumn::GetApplyObjects(), GetRetranslateCDSCommand(), GetSynchronizeProteinPartialsCommand(), CRetranslateCDS::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), s_GetProtApplyObjectsFeatures(), CAdjustFeaturesForGaps::x_DoOne(), and CEditObjectSeq_feat::x_HandleCdsProduct().

ExtendCDSToStopCodon A function to extend a CDS location to the first in-frame stop codon in the protein translation.

Note that adjustments are not made to the protein sequence in this function, only the location and partialness of the coding region.

Parameters

cds The feature to adjust scope The scope in which adjustments are to be made (if necessary)

Returns

true if stop codon was found, false otherwise

Definition at line 835 of file cds_fix.cpp.

References CSeq_loc::Add(), CSeq_loc::Assign(), CSeqVector::begin(), CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, eExtreme_Positional, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eNa_strand_minus, CScope::GetBioseqHandle(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CTrans_table::GetCodonResidue(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_loc::GetId(), CBioseq_Handle::GetInst_Length(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CGen_code_table::GetTransTable(), i, CSeqFeatData_Base::IsCdregion(), CCdregion_Base::IsSetCode(), CSeq_feat_Base::IsSetData(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::IsSetLocation(), CSeq_loc::IsSetStrand(), len, mod(), CTrans_table::NextCodonState(), CRef< C, Locker >::Reset(), SeqLocExtend(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetPartialStop(), CSeq_loc::SetStrand(), and CSeqVector::size().

Referenced by BOOST_AUTO_TEST_CASE().

Definition at line 197 of file cds_fix.cpp.

References CSeq_loc::Assign(), eExtreme_Biological, eNa_strand_minus, CSeq_loc::fMerge_All, CSeq_loc::fSort, CSeq_loc::GetId(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), len, Seq_loc_Add(), and CSeq_loc::SetInt().

Referenced by ExtendLocationForTranslExcept(), and SetTranslExcept().

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when constructing a coding region for a given Bioseq (if the default code should not be used).

Parameters

bh The Bioseq_Handle of the nucleotide sequence on which the coding region is to be created.

Returns

CRef<CGenetic_code> for new CGenetic_code (will be NULL if default should be used)

Definition at line 707 of file cds_fix.cpp.

References CSeqdesc_Base::e_Source, CBioSource::GetGenCode(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), CBioSource_Base::IsSetOrg(), and COrg_ref_Base::IsSetOrgname().

Referenced by CBulkCDSAddPanel::AddOneCmd(), CAlignCDSAddPanel::AddOneCommand(), BOOST_AUTO_TEST_CASE(), CEditObjectSeq_feat::CreateWindowImpl(), CMacroFunction_ApplyCDS::TheFunction(), and CImportFeatTable::x_DoImportCDS().

Definition at line 138 of file cds_fix.cpp.

References CSeq_id::Assign(), eExtreme_Biological, eNa_strand_minus, CSeq_loc::GetId(), GetLastPartialCodonLength(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), and CSeq_loc::SetInt().

Referenced by AddTerminalCodeBreak(), IsOverhangOkForTerminalCodeBreak(), and CCdregionValidator::x_ValidateFeatComment().

Referenced by AddProteinToSeqEntry(), CFeatGapInfo::AdjustForRelevantGapIntervals(), CSplitCDSwithTooManyXs::AdjustSingleCDS(), AdjustSingleFeature(), BOOST_AUTO_TEST_CASE(), CreateTranslatedProteinSequence(), CRemoveSeqId::CRemoveSeqId(), CCmdAddCDS::Execute(), g_InstantiateMissingProteins(), GetProtRefSeqId(), CCdsToMatPeptide::MergeConvert(), PropagateToTarget(), CRetranslateCDS::RetranslateCDSCommand(), TranslateCDSCommand(), CCleanup::WGSCleanup(), CEditObjectSeq_feat::x_HandleCdsProduct(), CSequenceUpdater::x_ImportCDSProduct(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), and CCDSTranslationPanel::x_SetProtein().

Referenced by CBlkEdtFeatLocationPanel::AddCommand(), CAddSequences::apply(), CGroupExplode::apply(), CSplitCDSwithTooManyXs::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CCombineAdjacentGaps::apply_impl(), CRawSeqToDeltaSeqByLoc::apply_impl(), BOOST_AUTO_TEST_CASE(), CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures_impl(), ConvertRawToDeltaByNsCommand_impl(), ConvertRawToDeltaByNsHugeFileCmd_impl(), CExtendPartialFeatDlg::ExtendCDS(), IEditingAction::GetActionCommand(), CApplyRNAITSDlg::GetCommand(), CBulkCDSAddPanel::GetCommand(), CCdsFromGeneMrnaExon::GetCommand(), CConvertFeatDlg::GetCommand(), CExtendPartialFeatDlg::GetCommand(), CFixForTransSplicing::GetCommand(), CFuseFeaturesDlg::GetCommand(), CTruncateCDS::GetCommand(), CAlignCDSAddPanel::GetCommand(), CRetranslateCDS::GetCommand(), CEditCdsFrame::GetCommand(), CAdjustFeaturesForGaps::GetCommand_impl(), CEditObjectFeaturePropagate::GetEditCommand(), CCdsToMatPeptide::MergeConvert(), CSubPrep_panel::OnAddSequenceBtnClick(), CEditSequence::OnRetranslate(), CUpdateMultiSeq_Dlg::OnUpdateAllSequenceClick(), CUpdateMultiSeq_Dlg::OnUpdateThisSequenceClick(), CMacroBioData_FeatIterBase::SetCreateGeneralIdFlag(), CMacroFunction_ApplyCDS::TheFunction(), CCleanup::WGSCleanup(), CEditObjectSeq_feat::x_HandleCdsProduct(), CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), and CCDSTranslationPanel::x_SetProtein().

MakemRNAforCDS A function to create a CSeq_feat that represents the appropriate mRNA for a given CDS.

Note that this feature is not added to the Seq-annot in the record; this step is left for the caller.

Parameters

cds The feature for which the mRNA to be made, if one is not already present scope The scope in which adjustments are to be made (if necessary)

Returns

CRef<CSeq_feat> for new mRNA (will be NULL if one was already present)

Definition at line 525 of file cds_fix.cpp.

References CSeq_loc::Assign(), eExtreme_Positional, eOverlap_CheckIntervals, NStr::Equal(), CSeqFeatData::eSubtype_3UTR, CSeqFeatData::eSubtype_5UTR, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_mRNA, CRNA_ref_Base::eType_mRNA, CSeq_loc::fMerge_All, CSeq_loc::fSort, CSeq_feat_Handle::GetAnnot(), GetBestGeneForCds(), CScope::GetBioseqHandle(), CSeq_loc::GetId(), GetLength(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), GetOverlappingmRNA(), CScope::GetSeq_featHandle(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::IsReverseStrand(), IsSameBioseq(), CSeq_feat_Base::IsSetLocation(), len, CRef< C, Locker >::Reset(), s_GetmRNAName(), s_GetProductName(), Seq_loc_Add(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), and TestForOverlap64().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), and CMRnaForCDS::x_ChkAndMakeMRna().

TruncateCDSAtStop A function to truncate a CDS location after the first stop codon in the protein translation.

Note that adjustments are not made to the protein sequence in this function, only the location and partialness of the coding region.

Parameters

cds The feature to adjust scope The scope in which adjustments are to be made (if necessary)

Returns

true if stop codon was found, false otherwise

Definition at line 786 of file cds_fix.cpp.

References eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, NStr::Find(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_feat_Base::GetLocation(), CSeq_loc::IsPartialStart(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::ResetPartial(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeqTranslator::Translate(), CSeqTranslator::TranslateToProtein(), and TruncateSeqLoc().

Referenced by BOOST_AUTO_TEST_CASE(), CTruncateCDS::GetCommand(), and CRetranslateCDS::GetCommand().

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