#include <ncbi_pch.hpp>
#include <gui/framework/workbench_impl.hpp>
#include <gui/framework/view_manager_service.hpp>
#include <gui/core/project_tree_view.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/seqfeat_macros.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objects/seqloc/Seq_loc_mix.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/biblio/Cit_gen.hpp>
#include <objects/biblio/Cit_book.hpp>
#include <objects/biblio/Cit_proc.hpp>
#include <objects/biblio/Cit_art.hpp>
#include <objects/biblio/Cit_pat.hpp>
#include <objects/biblio/Cit_let.hpp>
#include <objects/biblio/Cit_jour.hpp>
#include <objects/biblio/Title.hpp>
#include <objects/biblio/Affil.hpp>
#include <objects/general/Name_std.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/valid/Comment_rule.hpp>
#include <objects/valid/Comment_set.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/seq_entry_ci.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <objtools/format/flat_file_config.hpp>
#include <objtools/format/flat_file_generator.hpp>
#include <objtools/format/flat_expt.hpp>
#include <objtools/edit/seqid_guesser.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/cmd_del_desc.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_del_seq_feat.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/objutils/cmd_change_bioseq_inst.hpp>
#include <gui/objutils/pub_fieldtype.hpp>
#include <gui/objutils/util_cmds.hpp>
#include <gui/widgets/edit/singleauthor_panel.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/widgets/edit/dblink_fieldtype.hpp>
#include <gui/widgets/edit/molinfo_fieldtype.hpp>
#include <gui/packages/pkg_sequence_edit/pub_field.hpp>
#include <gui/packages/pkg_sequence_edit/miscedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/molinfoedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/dblink_field.hpp>
#include <gui/packages/pkg_sequence_edit/seq_table_grid.hpp>

Include dependency graph for miscedit_util.cpp:

Go to the SVN repository for this file.

Typedefs
typedef SStaticPair< const char *, CGeneralIDField::EGeneralIDPart >	TGeneralIDPart

typedef CStaticArrayMap< string, CGeneralIDField::EGeneralIDPart >	TGenIdPartMap

Functions
	USING_SCOPE (ncbi::objects)

	USING_SCOPE (edit)

	DEFINE_STATIC_ARRAY_MAP (TGenIdPartMap, sm_GenIdMap, s_GenIDPartName)

static const string	kStructComment ("StructuredComment")

static const string	kStructCommentPrefix ("StructuredCommentPrefix")

static const string	kStructCommentSuffix ("StructuredCommentSuffix")

void	AddMiscColumnsToTable (CRef< CSeq_table > table, const vector< string > &fields, CSeq_entry_Handle entry)

static size_t	s_GetMaxRows (const vector< size_t > &rows)

CRef< CSeq_table >	GetMiscTableFromSeqEntry (const vector< string > &fields, CSeq_entry_Handle entry)

void	x_AdjustListPair (vector< CRef< CApplyObject > > prev_list, vector< CRef< CApplyObject > > this_list)

string	GetExistingTextInstruction (EExistingText existing)

string	MakeTableMetaInfoString (EExistingText rule, bool erase_blanks)

CRef< CUser_field >	MakeTableMetaInfoField (EExistingText rule, bool erase_blanks)

vector< CConstRef< CSeq_feat > >	s_GetProtFeatures (CBioseq_Handle p_bsh, CSeqFeatData::ESubtype constraint_type)

vector< CConstRef< CSeq_feat > >	GetRelatedFeatures (const CSeq_feat &obj_feat, CSeqFeatData::ESubtype constraint_type, CRef< CScope > scope)

vector< CRef< CApplyObject > >	s_GetProtApplyObjectsFeatures (CBioseq_Handle p_bsh, CSeqFeatData::ESubtype constraint_type)

vector< CRef< CApplyObject > >	GetRelatedFeatureApplyObjects (const CSeq_feat &obj_feat, CSeqFeatData::ESubtype constraint_type, CRef< CScope > scope)

CSeq_entry_Handle	s_GetNPParent (CSeq_entry_Handle seh)

bool	DoesObjectMatchFieldConstraint (const CObject &object, const string &field_name, CRef< CStringConstraint > string_constraint, CRef< CScope > scope)

bool	DoesApplyObjectMatchFieldConstraint (const CApplyObject &object, const string &field_name, CRef< CStringConstraint > string_constraint)

bool	IsSeqOrNP (CSeq_entry_Handle entry)

bool	PropagateDescriptor (CSeq_entry_Handle entry, const CSeqdesc &desc, CCmdComposite &cmd)

bool	PropagateDBLink (CSeq_entry_Handle entry, CCmdComposite &cmd)

CRef< CCmdComposite >	GetPropagateDBLinkCmd (CSeq_entry_Handle entry)

CRef< CCmdComposite >	GetCommandFromApplyObject (CApplyObject &obj)

void	GetViewObjects (IWorkbench *workbench, TConstScopedObjects &objects)

int	GetNumberOfViewedBioseqs (TConstScopedObjects &objects)

bool	FocusedOnNucleotides (TConstScopedObjects &objects, const CSeq_entry_Handle &tse)

bool	FocusedOnAll (TConstScopedObjects &objects, const objects::CSeq_entry_Handle &tse)

Variables
static const string	kGenomeProjectId = "ProjectID"

static const TGeneralIDPart	s_GenIDPartName []

Typedef Documentation

◆ TGeneralIDPart

typedef SStaticPair<const char*, CGeneralIDField::EGeneralIDPart> TGeneralIDPart

Definition at line 1107 of file miscedit_util.cpp.

◆ TGenIdPartMap

typedef CStaticArrayMap<string, CGeneralIDField::EGeneralIDPart> TGenIdPartMap

Definition at line 1115 of file miscedit_util.cpp.

Function Documentation

◆ AddMiscColumnsToTable()

void AddMiscColumnsToTable	(	CRef< CSeq_table >	table,
		const vector< string > &	fields,
		CSeq_entry_Handle	entry
	)

Definition at line 2917 of file miscedit_util.cpp.

References AddStringColumnToTable(), AddValueToColumn(), FillShortColumns(), CScope::GetBioseqHandle(), CSeq_entry_Handle::GetScope(), ITERATE, NON_CONST_ITERATE, table, and val.

◆ DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP	(	TGenIdPartMap	,
		sm_GenIdMap	,
		s_GenIDPartName
	)

◆ DoesApplyObjectMatchFieldConstraint()

bool DoesApplyObjectMatchFieldConstraint	(	const CApplyObject &	object,
		const string &	field_name,
		CRef< CStringConstraint >	string_constraint
	)

Definition at line 3613 of file miscedit_util.cpp.

References CStringConstraint::DoesListMatch(), CMiscSeqTableColumn::GetRelatedObjects(), CMiscSeqTableColumn::GetVals(), NStr::IsBlank(), and ITERATE.

◆ DoesObjectMatchFieldConstraint()

bool DoesObjectMatchFieldConstraint	(	const CObject &	object,
		const string &	field_name,
		CRef< CStringConstraint >	string_constraint,
		CRef< CScope >	scope
	)

Definition at line 3592 of file miscedit_util.cpp.

References CStringConstraint::DoesListMatch(), CMiscSeqTableColumn::GetRelatedObjects(), CMiscSeqTableColumn::GetVals(), NStr::IsBlank(), and ITERATE.

◆ FocusedOnAll()

bool FocusedOnAll	(	TConstScopedObjects &	objects,
		const objects::CSeq_entry_Handle &	tse
	)

Definition at line 3805 of file miscedit_util.cpp.

References CSeq_inst_Base::eMol_na, and GetNumberOfViewedBioseqs().

Referenced by s_Create5ColFeatTable().

◆ FocusedOnNucleotides()

bool FocusedOnNucleotides	(	TConstScopedObjects &	objects,
		const CSeq_entry_Handle &	tse
	)

Definition at line 3790 of file miscedit_util.cpp.

References CSeq_inst_Base::eMol_na, and GetNumberOfViewedBioseqs().

◆ GetCommandFromApplyObject()

CRef<CCmdComposite> GetCommandFromApplyObject ( CApplyObject & obj )

Definition at line 3701 of file miscedit_util.cpp.

References cmd, CApplyObject::GetOriginalObject(), CSeq_entry_Handle::GetScope(), CApplyObject::GetSEH(), CSeq_entry_Handle::GetSeq(), CScope::GetSeq_featHandle(), GetSeqEntryForSeqdesc(), NULL, CApplyObject::PreExists(), Ref(), and CApplyObject::SetObject().

◆ GetExistingTextInstruction()

string GetExistingTextInstruction ( EExistingText existing )

Definition at line 3022 of file miscedit_util.cpp.

References eExistingText_add_qual, eExistingText_append_colon, eExistingText_append_comma, eExistingText_append_none, eExistingText_append_semi, eExistingText_append_space, eExistingText_cancel, eExistingText_leave_old, eExistingText_prefix_colon, eExistingText_prefix_comma, eExistingText_prefix_none, eExistingText_prefix_semi, eExistingText_prefix_space, eExistingText_replace_old, and NStr::IsBlank().

Referenced by MakeTableMetaInfoString().

◆ GetMiscTableFromSeqEntry()

CRef<CSeq_table> GetMiscTableFromSeqEntry	(	const vector< string > &	fields,
		CSeq_entry_Handle	entry
	)

Definition at line 2956 of file miscedit_util.cpp.

References AddStringColumnToTable(), AddValueToColumn(), CSeqTable_column_info_Base::eField_id_location_id, eGetId_Best, FillShortColumns(), FindHighestFeatureId(), GetId(), CSeq_id_Handle::GetSeqId(), i, ITERATE, kSequenceIdColLabel, NON_CONST_ITERATE, s_GetMaxRows(), CSeqTable_column_Base::SetHeader(), table, and val.

◆ GetNumberOfViewedBioseqs()

int GetNumberOfViewedBioseqs ( TConstScopedObjects & objects )

Definition at line 3775 of file miscedit_util.cpp.

References ITERATE.

Referenced by FocusedOnAll(), and FocusedOnNucleotides().

◆ GetPropagateDBLinkCmd()

CRef<CCmdComposite> GetPropagateDBLinkCmd ( CSeq_entry_Handle entry )

Definition at line 3688 of file miscedit_util.cpp.

References cmd, NULL, and PropagateDBLink().

◆ GetRelatedFeatureApplyObjects()

vector<CRef<CApplyObject> > GetRelatedFeatureApplyObjects	(	const CSeq_feat &	obj_feat,
		CSeqFeatData::ESubtype	constraint_type,
		CRef< CScope >	scope
	)

Definition at line 3243 of file miscedit_util.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, eOverlap_Contained, eOverlap_Contains, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, f(), CSeq_loc::fMerge_SingleRange, GetBestCdsForMrna(), GetBestMrnaForCds(), CScope::GetBioseqHandle(), GetCDSForProduct(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), GetOverlappingFeatures(), GetOverlappingGene(), CRef< C, Locker >::GetPointer(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetSeq_entry_Handle(), CSeqFeatData::GetSubtype(), CSeqFeatData::GetTypeFromSubtype(), ITERATE, CSeq_loc::Merge(), NULL, s_GetProtApplyObjectsFeatures(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by CMiscSeqTableColumn::GetRelatedApplyObjects().

◆ GetRelatedFeatures()

vector<CConstRef<CSeq_feat> > GetRelatedFeatures	(	const CSeq_feat &	obj_feat,
		CSeqFeatData::ESubtype	constraint_type,
		CRef< CScope >	scope
	)

◆ GetViewObjects()

void GetViewObjects	(	IWorkbench *	workbench,
		TConstScopedObjects &	objects
	)

Definition at line 3744 of file miscedit_util.cpp.

References IProjectView::eType, ISelectionClient::GetActiveObjects(), IProjectView::GetLabel(), ISelectionClient::GetMainObject(), CProjectTreeView::GetSelection(), IServiceLocator::GetServiceByType(), CProjectTreeView::GetSingleObject(), IViewManagerService::GetViews(), and NON_CONST_ITERATE.

Referenced by CMRnaForCDS::apply(), CEditingBtnsPanel::EditSequence(), CSequenceEditingEventHandler::EditSequence(), CSelectFeatures::GetMainObject(), CSUCRefreshCntrl::GetRefreshedText(), CBulkCmdDlg::GetSelectedObjects(), CRemoveSet::GetSelectedObjects(), CBulkCmdDlg::GetTopLevelSeqEntryAndProcessor(), CFixForTransSplicing::Init(), CSUCRefreshCntrl::CSUCRefreshCntrlHelper::LoadData(), CClickableSortUniqueCount::LoadData(), CAddFeatureBetweenDlg::OnApplyButton(), CEditingBtnsPanel::OnDataChange(), CUnculTaxTool::OnRefreshBtn(), CEditingBtnsPanel::OnReverseAuthorNamesClick(), CSelectTargetDlg::OnSelTargetAcceptClick(), CEditingBtnsPanel::Save(), CGuiCoreHelper::Sync(), CValidatePanel::x_GetObjectsFromProjectItem(), CEditingBtnsPanel::x_GetSelectedLocations(), CCorrectGenesDialog::x_GetSelectedPair(), CEditingBtnsPanel::x_GetSelectedSeq(), CTableViewWithTextViewNav::x_GetViewObjects(), CSequinDesktopView::x_OnRefreshData(), CSequenceEditingEventHandler::x_OnSelectionEvent(), CFeatureTblFr::x_RefreshTable(), CSuspectProductRulesEditor::x_SetUpTSEandUnDoManager(), and CSequenceEditingEventHandler::x_SetUpTSEandUnDoManager().

◆ IsSeqOrNP()

bool IsSeqOrNP ( CSeq_entry_Handle entry )

Definition at line 3634 of file miscedit_util.cpp.

References CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSeq(), and CSeq_entry_Handle::IsSet().

Referenced by PropagateDBLink(), and PropagateDescriptor().

◆ kStructComment()

static const string kStructComment ( "StructuredComment" )

static

Referenced by CStructCommFieldValuePair::GetApplyObjects().

◆ kStructCommentPrefix()

static const string kStructCommentPrefix ( "StructuredCommentPrefix" )

static

Referenced by CStructCommDBName::ClearVal(), CStructCommFieldName::ClearVal(), CStructCommFieldName::GetVals(), and CStructCommFieldValuePair::x_InsertFieldAtCorrectPosition().

◆ kStructCommentSuffix()

static const string kStructCommentSuffix ( "StructuredCommentSuffix" )

static

Referenced by CStructCommDBName::ClearVal(), CStructCommFieldName::ClearVal(), CStructCommFieldName::GetVals(), and CStructCommFieldValuePair::x_InsertFieldAtCorrectPosition().

◆ MakeTableMetaInfoField()

CRef<CUser_field> MakeTableMetaInfoField	(	EExistingText	rule,
		bool	erase_blanks
	)

Definition at line 3106 of file miscedit_util.cpp.

References MakeTableMetaInfoString(), and CUser_field_Base::SetData().

◆ MakeTableMetaInfoString()

string MakeTableMetaInfoString	(	EExistingText	rule,
		bool	erase_blanks
	)

Definition at line 3092 of file miscedit_util.cpp.

References GetExistingTextInstruction(), and value.

Referenced by MakeTableMetaInfoField().

◆ PropagateDBLink()

bool PropagateDBLink	(	CSeq_entry_Handle	entry,
		CCmdComposite &	cmd
	)

Definition at line 3665 of file miscedit_util.cpp.

References cmd, CUser_object::eObjectType_DBLink, CSeq_descr_Base::Get(), CSeq_entry_Handle::GetDescr(), IsSeqOrNP(), CSeq_entry_Handle::IsSetDescr(), ITERATE, and PropagateDescriptor().

Referenced by GetPropagateDBLinkCmd().

◆ PropagateDescriptor()

bool PropagateDescriptor	(	CSeq_entry_Handle	entry,
		const CSeqdesc &	desc,
		CCmdComposite &	cmd
	)

Definition at line 3646 of file miscedit_util.cpp.

References CSerialObject::Assign(), cmd, CBioseq_set_Handle::GetCompleteBioseq_set(), CSeq_entry_Handle::GetScope(), CScope::GetSeq_entryHandle(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Handle::GetSet(), IsSeqOrNP(), CSeq_entry_Handle::IsSet(), and ITERATE.

Referenced by PropagateDBLink().

◆ s_GetMaxRows()

static size_t s_GetMaxRows ( const vector< size_t > & rows )

static

Definition at line 2947 of file miscedit_util.cpp.

References i.

Referenced by GetMiscTableFromSeqEntry().

◆ s_GetNPParent()

CSeq_entry_Handle s_GetNPParent ( CSeq_entry_Handle seh )

Definition at line 3503 of file miscedit_util.cpp.

References CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), and CBioseq_set_Handle::IsSetClass().

Referenced by CMiscSeqTableColumn::GetRelatedApplyObjects().

◆ s_GetProtApplyObjectsFeatures()

vector<CRef<CApplyObject> > s_GetProtApplyObjectsFeatures	(	CBioseq_Handle	p_bsh,
		CSeqFeatData::ESubtype	constraint_type
	)

Definition at line 3211 of file miscedit_util.cpp.

References AdjustProteinFeaturePartialsToMatchCDS(), CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_prot, f(), GetCDSForProduct(), CBioseq_Handle::GetId(), CBioseq_Handle::GetInst_Length(), CRef< C, Locker >::GetPointer(), CBioseq_Handle::GetSeq_entry_Handle(), NULL, CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by GetRelatedFeatureApplyObjects().

◆ s_GetProtFeatures()

vector<CConstRef<CSeq_feat> > s_GetProtFeatures	(	CBioseq_Handle	p_bsh,
		CSeqFeatData::ESubtype	constraint_type
	)

Definition at line 3114 of file miscedit_util.cpp.

References f().

Referenced by GetRelatedFeatures().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( edit )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( ncbi::objects )

◆ x_AdjustListPair()

void x_AdjustListPair	(	vector< CRef< CApplyObject > >	prev_list,
		vector< CRef< CApplyObject > >	this_list
	)

Definition at line 3010 of file miscedit_util.cpp.

References NON_CONST_ITERATE, and t.

Variable Documentation

◆ kGenomeProjectId

const string kGenomeProjectId = "ProjectID"

static

Definition at line 662 of file miscedit_util.cpp.

Referenced by CGenomeProjectField::IsGenomeProjectID(), and CGenomeProjectField::SetVal().

◆ s_GenIDPartName

const TGeneralIDPart s_GenIDPartName[]

static

Initial value:

= {
        { "", CGeneralIDField::eUnknown },
        { "Entire General ID", CGeneralIDField::eGenId },
        { "General ID DB", CGeneralIDField::eGenIdDb },
        { "General ID Tag", CGeneralIDField::eGenIdTag },
}

Definition at line 1108 of file miscedit_util.cpp.

Typedefs

Functions

Variables

Typedef Documentation

◆ TGeneralIDPart

◆ TGenIdPartMap

Function Documentation

◆ AddMiscColumnsToTable()

◆ DEFINE_STATIC_ARRAY_MAP()

◆ DoesApplyObjectMatchFieldConstraint()

◆ DoesObjectMatchFieldConstraint()

◆ FocusedOnAll()

◆ FocusedOnNucleotides()

◆ GetCommandFromApplyObject()

◆ GetExistingTextInstruction()

◆ GetMiscTableFromSeqEntry()

◆ GetNumberOfViewedBioseqs()

◆ GetPropagateDBLinkCmd()

◆ GetRelatedFeatureApplyObjects()

◆ GetRelatedFeatures()

◆ GetViewObjects()

◆ IsSeqOrNP()

◆ kStructComment()

◆ kStructCommentPrefix()

◆ kStructCommentSuffix()

◆ MakeTableMetaInfoField()

◆ MakeTableMetaInfoString()

◆ PropagateDBLink()

◆ PropagateDescriptor()

◆ s_GetMaxRows()

◆ s_GetNPParent()

◆ s_GetProtApplyObjectsFeatures()

◆ s_GetProtFeatures()

◆ USING_SCOPE() [1/2]

◆ USING_SCOPE() [2/2]

◆ x_AdjustListPair()

Variable Documentation

◆ kGenomeProjectId

◆ s_GenIDPartName