#include <ncbi_pch.hpp>#include <objmgr/util/seq_loc_util.hpp>#include <objmgr/util/feature.hpp>#include <objmgr/util/sequence.hpp>#include <objmgr/seq_annot_ci.hpp>#include <objmgr/bioseq_ci.hpp>#include <objmgr/object_manager.hpp>#include <gui/widgets/edit/bioseq_editor.hpp>#include <objtools/edit/string_constraint.hpp>#include <objtools/cleanup/cleanup.hpp>#include <gui/objutils/cmd_create_feat.hpp>#include <gui/objutils/cmd_change_seq_feat.hpp>#include <gui/objutils/cmd_create_desc.hpp>#include <gui/objutils/cmd_del_desc.hpp>#include <gui/objutils/descriptor_change.hpp>#include <gui/objutils/cmd_change_bioseq_inst.hpp>#include <objects/seqfeat/seqfeat_macros.hpp>#include <objects/seqfeat/Gb_qual.hpp>#include <objects/general/Dbtag.hpp>#include <objects/general/Object_id.hpp>#include <objtools/edit/cds_fix.hpp>#include <objtools/edit/apply_object.hpp>#include <objects/seq/Seq_data.hpp>#include <objmgr/seq_vector.hpp>#include <objtools/edit/source_edit.hpp>#include <gui/widgets/edit/source_field_name_panel.hpp>#include <gui/widgets/edit/rna_field_name_panel.hpp>#include <gui/widgets/edit/cds_gene_prot_field_name_panel.hpp>#include <gui/packages/pkg_sequence_edit/misc_field_panel.hpp>#include <gui/widgets/edit/struct_fieldvalue_panel.hpp>#include <gui/widgets/edit/feature_field_name_panel.hpp>#include <gui/packages/pkg_sequence_edit/retranslate_cds.hpp>#include <gui/packages/pkg_sequence_edit/editing_actions.hpp>#include <gui/packages/pkg_sequence_edit/editing_action_features.hpp>#include <gui/packages/pkg_sequence_edit/editing_action_biosource.hpp>#include <gui/packages/pkg_sequence_edit/editing_action_desc.hpp>#include <gui/packages/pkg_sequence_edit/editing_action_seqid.hpp>#include <gui/packages/pkg_sequence_edit/editing_action_misc.hpp>#include <gui/packages/pkg_sequence_edit/editing_action_constraint.hpp>
Include dependency graph for editing_actions.cpp:
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Functions | |
| USING_SCOPE (objects) | |
| CIRef< IEditingAction > | CreateAction (CSeq_entry_Handle seh, const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class, CConstRef< objects::CSeq_submit > submit) |
| int | GetSubtype (CFieldNamePanel *field_name_panel, string &ncRNA_class) |
| int | CorrectForncRNASubtypes (CSeqFeatData::ESubtype subtype, string &ncRNA_class) |
| CRef< CObject > | GetNewObject (CConstRef< CObject > object) |
| CRef< CCmdComposite > | GetReplacementCommand (CConstRef< CObject > oldobj, CRef< CObject > newobj, CScope &scope, const string &cmd_name) |
| vector< CConstRef< CObject > > | GetObjects (CSeq_entry_Handle seh, const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class, CConstRef< CSeq_submit > submit, CRef< CEditingActionConstraint > constraint, vector< CSeq_entry_Handle > *descr_context) |
Function Documentation
◆ CorrectForncRNASubtypes()
| int CorrectForncRNASubtypes | ( | CSeqFeatData::ESubtype | subtype, |
| string & | ncRNA_class | ||
| ) |
Definition at line 975 of file editing_actions.cpp.
References CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_scRNA, CSeqFeatData::eSubtype_snoRNA, and CSeqFeatData::eSubtype_snRNA.
Referenced by CBulkEditFeatDlg::GetCommand(), CAddFeatureBetweenDlg::GetFeatureLocations(), and GetSubtype().
◆ CreateAction()
| CIRef<IEditingAction> CreateAction | ( | CSeq_entry_Handle | seh, |
| const string & | field, | ||
| CFieldNamePanel::EFieldType | field_type, | ||
| int | subtype, | ||
| const string & | ncRNA_class, | ||
| CConstRef< objects::CSeq_submit > | submit | ||
| ) |
Definition at line 843 of file editing_actions.cpp.
References CreateActionBiosource(), CreateActionCdsGeneProt(), CreateActionDesc(), CreateActionFeat(), CreateActionMisc(), CreateActionRna(), CreateActionSeqid(), CFieldNamePanel::eFieldType_BankITComment, CFieldNamePanel::eFieldType_CDSGeneProt, CFieldNamePanel::eFieldType_Comment, CFieldNamePanel::eFieldType_DBLink, CFieldNamePanel::eFieldType_Dbxref, CFieldNamePanel::eFieldType_DefLine, CFieldNamePanel::eFieldType_Feature, CFieldNamePanel::eFieldType_FileId, CFieldNamePanel::eFieldType_FlatFile, CFieldNamePanel::eFieldType_GeneralId, CFieldNamePanel::eFieldType_LocalId, CFieldNamePanel::eFieldType_Misc, CFieldNamePanel::eFieldType_MolInfo, CFieldNamePanel::eFieldType_Pub, CFieldNamePanel::eFieldType_RNA, CFieldNamePanel::eFieldType_SeqId, CFieldNamePanel::eFieldType_Source, CFieldNamePanel::eFieldType_StructuredComment, CFieldNamePanel::eFieldType_Taxname, CFieldNamePanel::eFieldType_TaxnameAfterBinomial, CSeqFeatData::eSubtype_any, CSeqFeatData::GetTypeFromSubtype(), and NULL.
Referenced by CExportTableDlg::AddCdsGeneMrnaTable(), CExportTableDlg::AddDblinkToTable(), CExportTableDlg::AddPubsToTable(), CExportTableDlg::AddRnaToTable(), CExportTableDlg::AddSourceToTable(), CEditingActionSummaryConstraint::CEditingActionSummaryConstraint(), IActionPanel::CreateAction1(), IActionPanel::CreateAction2_imp(), CQualChoicePanel::CreateEditingAction(), CSameConstraintMatcher::CSameConstraintMatcher(), IActionPanel::GetAutopopulateValue(), CReplaceSingleFieldPanel::GetCommand(), CEditCdsFrame::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), GetObjects(), CBulkCDS::GetValuesTableFromSeqEntry(), CMiscSeqTable::s_GetValueToSehMap(), and CMiscSeqTable::x_CreateEditingActions().
◆ GetNewObject()
Definition at line 995 of file editing_actions.cpp.
References CSerialObject::Assign(), and NULL.
Referenced by CEvidencePanel::AddCommand(), CStrandPanel::AddCommand(), and CRevIntPanel::AddCommand().
◆ GetObjects()
| vector<CConstRef<CObject> > GetObjects | ( | CSeq_entry_Handle | seh, |
| const string & | field, | ||
| CFieldNamePanel::EFieldType | field_type, | ||
| int | subtype, | ||
| const string & | ncRNA_class, | ||
| CConstRef< CSeq_submit > | submit, | ||
| CRef< CEditingActionConstraint > | constraint, | ||
| vector< CSeq_entry_Handle > * | descr_context | ||
| ) |
Definition at line 1045 of file editing_actions.cpp.
References CreateAction(), map_checker< Container >::empty(), and CSeq_submit_Base::GetSub().
◆ GetReplacementCommand()
| CRef<CCmdComposite> GetReplacementCommand | ( | CConstRef< CObject > | oldobj, |
| CRef< CObject > | newobj, | ||
| CScope & | scope, | ||
| const string & | cmd_name | ||
| ) |
Definition at line 1016 of file editing_actions.cpp.
References cmd, CConstRef< C, Locker >::GetPointer(), CRef< C, Locker >::GetPointer(), CScope::GetSeq_featHandle(), GetSeqEntryForSeqdesc(), NULL, and Ref().
Referenced by CEvidencePanel::AddCommand(), CStrandPanel::AddCommand(), and CRevIntPanel::AddCommand().
◆ GetSubtype()
| int GetSubtype | ( | CFieldNamePanel * | field_name_panel, |
| string & | ncRNA_class | ||
| ) |
Definition at line 890 of file editing_actions.cpp.
References CorrectForncRNASubtypes(), CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mat_peptide_aa, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_otherRNA, CSeqFeatData::eSubtype_preRNA, CSeqFeatData::eSubtype_prot, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_tmRNA, CSeqFeatData::eSubtype_tRNA, CFeatureFieldNamePanel::GetFeatureType(), CCDSGeneProtFieldNamePanel::GetFieldName(), CRNAFieldNamePanel::GetNcrnaType(), CDualRNAFieldNamePanel::GetNcrnaType(), CRNAFieldNamePanel::GetRnaTypeOnly(), CDualRNAFieldNamePanel::GetRnaTypeOnly(), and CSeqFeatData::SubtypeNameToValue().
Referenced by IActionPanel::CreateAction1(), IActionPanel::CreateAction2_imp(), CQualChoicePanel::CreateEditingAction(), IActionPanel::GetAutopopulateValue(), CAECRFrame::GetCommand(), CParseTextDlg::GetCommand(), CConstraintPanel::GetConstraint(), CAddFeatureBetweenDlg::GetFeatureLocations(), CFeatGlyph::GetHTMLActiveAreas(), CPresentMatcherPanel< T >::GetMatcher(), CSameMatcherPanel< T >::GetMatcher(), and CAdvStringConstraintPanel< T >::GetMatcher().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
