NCBI C++ ToolKit
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#include <corelib/ncbiobj.hpp>
#include <gui/gui_export.h>
#include <objects/taxon3/itaxon3.hpp>
#include <objtools/edit/loc_edit.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
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Functions | |
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) |
CRef<CCmdChangeSeq_feat> AdjustGene | ( | const objects::CSeq_feat & | orig_feat, |
const objects::CSeq_feat & | new_feat, | ||
objects::CScope & | scope | ||
) |
void AdjustProteinFeature | ( | objects::CSeq_feat & | prot, |
objects::CBioseq_Handle | product, | ||
objects::CSeq_feat & | cds, | ||
bool & | cds_change | ||
) |
Referenced by CMacroFunction_CreateProteinFeats::TheFunction().
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> CachedTaxonomyLookupCommand | ( | objects::CSeq_entry_Handle | seh, |
objects::taxupdate_func_t & | updater | ||
) |
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> CreateOrAdjustProteinFeature | ( | objects::CBioseq_Handle | product, |
objects::CSeq_feat & | cds, | ||
bool & | cds_change | ||
) |
Referenced by CEditObjectSeq_feat::x_HandleCdsProduct().
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 |
||
) |
Referenced by CRemoveFeaturesDlg::RemoveAllFeatures_Ex().
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> GetDeleteFeatureCommand | ( | const objects::CSeq_feat_Handle & | fh, |
bool | remove_proteins = true |
||
) |
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().
CRef<CCmdComposite> GetDeleteSequenceCommand | ( | objects::CBioseq_Handle | bsh | ) |
Referenced by CTrimN::apply(), CRemoveSequencesDlg::GetCommand(), and CDesktopViewContext::OnCutSelection().
CRef<CCmdComposite> GetDisableStrainForwardingCommand | ( | objects::CSeq_entry_Handle | seh | ) |
Referenced by CSequenceEditingEventHandler::DisableStrainForwarding().
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 | ||
) |
Referenced by CBlkEdtFeatLocationPanel::AddCommand().
CRef<CCmdComposite> GetEnableStrainForwardingCommand | ( | objects::CSeq_entry_Handle | seh | ) |
Referenced by CSequenceEditingEventHandler::EnableStrainForwarding().
CRef<CCmdComposite> GetNormalizeGeneQualsCommand | ( | objects::CSeq_entry_Handle | seh | ) |
Referenced by CSequenceEditingEventHandler::NormalizeGeneQuals().
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().
CRef<CCmdComposite> GetRemoveDuplicateGOTermsCommand | ( | objects::CSeq_entry_Handle | seh | ) |
Referenced by CSequenceEditingEventHandler::RemoveDuplicateGoTerms().
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().
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> GetReverseComplimentSequenceCommand | ( | objects::CBioseq_Handle | bsh | ) |
Referenced by CLabelRna::AddNewMrnaCommand().
CRef<CCmdComposite> GetRmCultureNotesCommand | ( | objects::CSeq_entry_Handle | seh | ) |
Referenced by CEditingBtnsPanel::RmCultureNotes(), and CSequenceEditingEventHandler::RmCultureNotes().
CRef<CCmdComposite> GetSynchronizeProductMolInfoCommand | ( | objects::CScope & | scope, |
const objects::CSeq_feat & | cds | ||
) |
CRef<CCmdComposite> GetSynchronizeProteinPartialsCommand | ( | objects::CScope & | scope, |
const objects::CSeq_feat & | cds | ||
) |
void SetProteinFeature | ( | objects::CSeq_feat & | prot, |
objects::CBioseq_Handle | product, | ||
const objects::CSeq_feat & | cds | ||
) |
CRef<CCmdComposite> SetTranslExcept | ( | objects::CSeq_entry_Handle | seh, |
const string & | comment, | ||
bool | strict, | ||
bool | extend, | ||
bool | adjust_gene | ||
) |
Referenced by CheckTerminalExceptionResults(), and CAddTranslExceptDlg::GetCommand().
CRef<CCmdComposite> SpecificHostCleanupCommand | ( | objects::CSeq_entry_Handle | seh | ) |
Referenced by CSequenceEditingEventHandler::SpecificHostCleanup().
CRef<CCmdComposite> TaxonomyLookupCommand | ( | objects::CSeq_entry_Handle | seh | ) |
CRef<CCmdComposite> TrimStopsFromCompleteCDS | ( | const objects::CSeq_feat & | cds, |
objects::CScope & | scope | ||
) |
CRef<CCmdComposite> UpdatemRNAProduct | ( | const objects::CSeq_feat & | protein, |
objects::CScope & | scope, | ||
string & | message | ||
) |
Referenced by CMiscSeqTableColumn::ClearValCmd(), CMiscSeqTableColumn::SetValCmd(), CMacroFunction_SwapRelFeatQual::TheFunction(), CMacroFunction_SetRelFeatQual::TheFunction(), CMacroFunction_ConvertFeatQual::TheFunction(), CMacroFunction_ParseFeatQual::TheFunction(), CMacroFunction_AddParsedToFeatQual::TheFunction(), CMacroFunction_CopyFeatQual::TheFunction(), CMacroFunction_RemoveOutside::TheFunction(), and CMacroFunction_RmvOutsideRelFeatQual::TheFunction().