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void GetProductToCDSMap (objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds) CRef< CCmdComposite > GetDeleteFeatureCommand (const objects::CSeq_feat_Handle &fh, bool remove_proteins=true) CRef< CCmdComposite > GetDeleteFeatureCommand (const objects::CSeq_feat_Handle &fh, bool remove_proteins, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds) CRef< CCmdComposite > GetDeleteSequenceCommand (objects::CBioseq_Handle bsh) CRef< CCmdComposite > GetDeleteAllFeaturesCommand (objects::CSeq_entry_Handle seh, size_t &count, bool remove_proteins=true) CRef< CCmdComposite > GetDeleteAllFeaturesCommand_Ex (objects::CSeq_entry_Handle seh, size_t &count, bool remove_proteins=true) CRef< CCmdComposite > TaxonomyLookupCommand (objects::CSeq_entry_Handle seh) CRef< CCmdComposite > CachedTaxonomyLookupCommand (objects::CSeq_entry_Handle seh, objects::taxupdate_func_t &updater) CRef< CCmdComposite > SpecificHostCleanupCommand (objects::CSeq_entry_Handle seh) CRef< CCmdComposite > CleanupCommand (objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax) CRef< CCmdComposite > CleanupHugeFileCommand (objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax, objects::taxupdate_func_t &updater, bool rmv_user_object) CRef< CCmdComposite > GetDisableStrainForwardingCommand (objects::CSeq_entry_Handle seh) CRef< CCmdComposite > GetEnableStrainForwardingCommand (objects::CSeq_entry_Handle seh) CRef< CCmdComposite > GetRmCultureNotesCommand (objects::CSeq_entry_Handle seh) CRef< CCmdComposite > GetSynchronizeProductMolInfoCommand (objects::CScope &scope, const objects::CSeq_feat &cds) CRef< CCmdComposite > GetSynchronizeProteinPartialsCommand (objects::CScope &scope, const objects::CSeq_feat &cds) CRef< CCmdComposite > GetRetranslateCDSCommand (objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only) CRef< CCmdComposite > GetRetranslateCDSCommand (objects::CScope &scope, const objects::CSeq_feat &cds, int &offset, bool create_general_only) CRef< CCmdComposite > GetRetranslateCDSCommand (objects::CScope &scope, objects::CSeq_feat &cds, bool &cds_change, bool create_general_only) CRef< CCmdComposite > GetRetranslateCDSCommand (objects::CScope &scope, objects::CSeq_feat &cds, bool &cds_change, int &offset, bool create_general_only) CRef< CCmdComposite > SetTranslExcept (objects::CSeq_entry_Handle seh, const string &comment, bool strict, bool extend, bool adjust_gene) CRef< CCmdComposite > GetReverseComplimentSequenceCommand (objects::CBioseq_Handle bsh) CRef< CCmdComposite > TrimStopsFromCompleteCDS (const objects::CSeq_feat &cds, objects::CScope &scope) void SetProteinFeature (objects::CSeq_feat &prot, objects::CBioseq_Handle product, const objects::CSeq_feat &cds) void AdjustProteinFeature (objects::CSeq_feat &prot, objects::CBioseq_Handle product, objects::CSeq_feat &cds, bool &cds_change) CRef< CCmdComposite > CreateOrAdjustProteinFeature (objects::CBioseq_Handle product, objects::CSeq_feat &cds, bool &cds_change) CRef< CCmdComposite > AutofixCommand (objects::CSeq_entry_Handle seh, const string &test_name, string *output, const string &suspect_rules=kEmptyStr) CRef< CCmdComposite > AutofixCommandHugeMode (objects::CSeq_entry_Handle seh, const string &test_name, map< string, size_t > &report, const string &suspect_rules=kEmptyStr) CRef< CCmdComposite > GetEditLocationCommand (const objects::edit::CLocationEditPolicy &policy, bool retranslate, bool adjust_gene, const objects::CSeq_feat &orig_feat, objects::CScope &scope, int &offset, bool create_general_only) CRef< CCmdChangeSeq_feat > AdjustGene (const objects::CSeq_feat &orig_feat, const objects::CSeq_feat &new_feat, objects::CScope &scope) CRef< CCmdComposite > GetNormalizeGeneQualsCommand (objects::CSeq_entry_Handle seh) CRef< CCmdComposite > GetRemoveDuplicateGOTermsCommand (objects::CSeq_entry_Handle seh) CRef< CCmdComposite > UpdatemRNAProduct (const objects::CSeq_feat &protein, objects::CScope &scope, string &message) CRef< CCmdComposite > UpdatemRNAProduct (const string &prot_product, CConstRef< CObject > object, objects::CScope &scope) ◆ AdjustGene() ◆ AdjustProteinFeature() ◆ AutofixCommand() ◆ AutofixCommandHugeMode() ◆ CachedTaxonomyLookupCommand() ◆ CleanupCommand() ◆ CleanupHugeFileCommand() ◆ CreateOrAdjustProteinFeature() ◆ GetDeleteAllFeaturesCommand() ◆ GetDeleteAllFeaturesCommand_Ex() ◆ GetDeleteFeatureCommand() [1/2] CRef<CCmdComposite> GetDeleteFeatureCommand ( const objects::CSeq_feat_Handle & fh, bool remove_proteins, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > & product_to_cds ) ◆ GetDeleteFeatureCommand() [2/2]Referenced by CReportTrim::AdjustAndTranslate(), CRmvCddFeatDbxref::apply_to(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CConvertProtToImp::Convert(), CConvertCDSToPseudoGene::Convert(), CCdsToMatPeptide::ConvertInner(), CRmDupFeaturesDlg::GetCommand(), CDesktopViewContext::OnCutSelection(), CSubPrep_panel::RemoveAllFeatures(), CRemoveFeaturesDlg::RemoveDuplicateFeatures(), CMacroBioData_FeatIterBase::RunDeleteCommand(), CMacroBioData_BioSourceIter::RunDeleteCommand(), CMacroBioData_PubdescIter::RunDeleteCommand(), CMacroFunction_RemoveAllFeatures::TheFunction(), CConvertFeatureBase::x_ConvertToCDS(), CBioseqEditor::x_DeleteObject(), CBioseqEditor::x_GetDeleteCommand(), and CConvertFeatureBase::x_SimpleConversion().
◆ GetDeleteSequenceCommand() ◆ GetDisableStrainForwardingCommand() ◆ GetEditLocationCommand() ◆ GetEnableStrainForwardingCommand() ◆ GetNormalizeGeneQualsCommand() ◆ GetProductToCDSMap() void GetProductToCDSMap ( objects::CScope & scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > & product_to_cds )Referenced by CTrimN::apply(), CRmvCddFeatDbxref::apply_to(), CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CCdsToMatPeptide::ConvertInner(), CRmDupFeaturesDlg::GetCommand(), CRemoveFeaturesDlg::GetCommand(), CSubPrep_panel::RemoveAllFeatures(), CRemoveFeaturesDlg::RemoveDuplicateFeatures(), CMacroBioData_FeatIterBase::SetToDelete(), CMacroFunction_TrimTerminalNs::TheFunction(), CMacroFunction_CreateProteinFeats::TheFunction(), and CMacroFunction_RemoveAllFeatures::TheFunction().
◆ GetRemoveDuplicateGOTermsCommand() ◆ GetRetranslateCDSCommand() [1/4] CRef<CCmdComposite> GetRetranslateCDSCommand ( objects::CScope & scope, const objects::CSeq_feat & cds, bool create_general_only )Referenced by CFixForTransSplicing::CombineFeatures(), CExtendPartialFeatDlg::ExtendCDS(), CExtendPartialFeatDlg::GetCommand(), CFuseFeaturesDlg::GetCommand(), CTruncateCDS::GetCommand(), CEditSequence::OnRetranslate(), CRetranslateCDS::RetranslateCDSCommand(), CMacroFunction_ApplyCDSFrame::TheFunction(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), and CMacroFunction_EditFeatLocation::x_RetranslateCDS().
◆ GetRetranslateCDSCommand() [2/4] ◆ GetRetranslateCDSCommand() [3/4] CRef<CCmdComposite> GetRetranslateCDSCommand ( objects::CScope & scope, objects::CSeq_feat & cds, bool & cds_change, bool create_general_only ) ◆ GetRetranslateCDSCommand() [4/4] CRef<CCmdComposite> GetRetranslateCDSCommand ( objects::CScope & scope, objects::CSeq_feat & cds, bool & cds_change, int & offset, bool create_general_only ) ◆ GetReverseComplimentSequenceCommand() ◆ GetRmCultureNotesCommand() ◆ GetSynchronizeProductMolInfoCommand() ◆ GetSynchronizeProteinPartialsCommand() ◆ SetProteinFeature() void SetProteinFeature ( objects::CSeq_feat & prot, objects::CBioseq_Handle product, const objects::CSeq_feat & cds ) ◆ SetTranslExcept() ◆ SpecificHostCleanupCommand() ◆ TaxonomyLookupCommand() ◆ TrimStopsFromCompleteCDS() ◆ UpdatemRNAProduct() [1/2] ◆ UpdatemRNAProduct() [2/2]RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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