CEditingActionFeatGbQual Class Reference

Search Toolkit Book for CEditingActionFeatGbQual

#include <gui/packages/pkg_sequence_edit/editing_action_features.hpp>

Inheritance diagram for CEditingActionFeatGbQual:

Collaboration diagram for CEditingActionFeatGbQual:

Public Member Functions
	CEditingActionFeatGbQual (CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual, const string &name="CEditingActionFeatGbQual")
Public Member Functions inherited from IEditingActionFeat
	IEditingActionFeat (CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &name)
virtual void	SetFeat (CSeq_feat_Handle fh)
CSeq_feat_Handle	GetFeatHandle (void)
CSeqFeatData::ESubtype	GetActionFeatSubtype ()
CSeq_feat_Handle	x_FindGeneForFeature (const CSeq_loc &loc, CScope &scope, CSeqFeatData::ESubtype subtype)
Public Member Functions inherited from IEditingAction
	IEditingAction (CSeq_entry_Handle seh, const string &name, CConstRef< objects::CSeq_submit > submit=CConstRef< objects::CSeq_submit >(NULL))
virtual	~IEditingAction ()
const string	GetName (void) const
const map< CSeq_feat_Handle, CRef< CSeq_feat > > &	GetChangedFeatures (void)
const map< CSeq_feat_Handle, CSeq_entry_Handle > &	GetCreatedFeatures (void)
const map< const CSeqdesc *, CRef< CSeqdesc > > &	GetChangedDescriptors (void)
const map< const CSeqdesc *, CSeq_entry_Handle > &	GetContextForDescriptors (void)
const map< const CSeqdesc *, CSeq_entry_Handle > &	GetCreatedDescriptors (void)
const map< const CSeqdesc *, CSeq_entry_Handle > &	GetDeletedDescriptors (void)
const map< CBioseq_Handle, CRef< CSeq_inst > > &	GetChangedInstances (void)
CRef< CSubmit_block >	GetChangedSubmitBlock (void)
const vector< string > &	GetChangedValues (void)
bool	GetChangedIds (void)
void	ResetChangedFeatures (void)
void	ResetChangedDescriptors (void)
void	ResetChangedInstances (void)
void	ResetChangedIds (void)
void	ResetChangedValues (void)
void	SetExistingText (edit::EExistingText existing_text)
void	SetConstraint (CRef< CEditingActionConstraint > constraint)
void	SetTopSeqEntry (CSeq_entry_Handle seh)
void	SetCurrentSeqEntry (CSeq_entry_Handle seh)
CRef< CCmdComposite >	GetActionCommand (void)
CConstRef< objects::CSeq_submit >	GetSeqSubmit (void)
bool	CheckValue (void)
bool	CheckValues (void)
const vector< string > &	GetValues (void)
void	Apply (const string &value)
void	Edit (const string &find, const string &replace, macro::CMacroFunction_EditStringQual::ESearchLoc edit_loc, bool case_insensitive, bool is_regex)
void	Remove (void)
void	RemoveOutside (CRef< macro::CRemoveTextOptions > options)
void	ConvertFrom (ECapChange cap_change, bool leave_on_original, const string &strip_name, IEditingAction *destination)
void	ConvertTo (const string &value, IEditingAction *source)
void	CopyFrom (IEditingAction *destination)
void	CopyTo (const string &value, IEditingAction *source)
void	SwapFrom (IEditingAction *destination)
void	SwapTo (const string &value, IEditingAction *source)
void	ParseFrom (edit::CParseTextOptions parse_options, IEditingAction *destination)
void	ParseTo (const string &value, IEditingAction *source)
void	NOOP (void)
int	CheckForExistingText (CIRef< IEditingAction > action2, EActionType action_type, edit::CParseTextOptions parse_options=edit::CParseTextOptions())
void	SetUpdateMRNAProduct (bool value)
void	SetRetranslateCds (bool value)
bool	IsModified ()
void	SetMaxRecords (size_t max)
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Protected Member Functions
virtual void	Modify (EActionType action)
virtual bool	IsSetValue (void)
virtual void	SetValue (const string &value)
virtual string	GetValue (void)
virtual void	ResetValue (void)
Protected Member Functions inherited from IEditingActionFeat
virtual void	Find (EActionType action)
virtual void	FindRelated (EActionType action)
virtual void	SwapContext (IEditingAction *source)
virtual bool	SameObject ()
bool	OtherFeatIs (const CSeqFeatData::ESubtype subtype)
void	FindFeatForAnotherFeat (EActionType action, SAnnotSelector other_selector)
void	FindRelatedFeatForAnotherFeat (EActionType action, SAnnotSelector other_selector)
void	FindOrCreateProtFeat (EActionType action)
void	FindRelatedOrCreateProtFeat (EActionType action)
void	GoToProtFeature (void)
void	GoToOrigFeature (void)
bool	x_TestGeneForFeature (const CSeq_loc &gene_loc, const CSeq_loc &feat_loc, CScope &scope, bool &exact, TSeqPos &diff)
CRef< CSeq_loc >	x_GetSublocOnBioseq (CBioseq_Handle bsh, const CSeq_loc &loc)
CRef< CSeq_loc >	x_MergeFeatureLocation (const CSeq_loc &loc, CScope &scope)
void	RemoveGeneXref (void)
void	SetFeatForAnotherFeat (CSeq_feat_Handle fh, const CSeqFeatData::ESubtype subtype)
CSeq_entry_Handle	GetCurrentSeqEntryHandleFromFeatHandle (CSeq_feat_Handle fh)
bool	MatchBioseqConstraintForFeatHandle (CSeq_feat_Handle fh)
virtual void	ResetScope ()
Protected Member Functions inherited from IEditingAction
bool	IsNOOP (EActionType action)
bool	IsFrom (EActionType action)
bool	IsTo (EActionType action)
bool	IsCreateNew (EActionType action)
CIRef< IEditCommand >	GetUpdateMRNAProductNameCmd (const CSeq_feat_Handle fh, const CRef< CSeq_feat > feat)
CRef< CCmdComposite >	GetRetranslateCdsCmd (const CSeq_feat_Handle fh, const CRef< CSeq_feat > feat, int &offset, bool create_general_only)
void	Action (EActionType action)
void	DoApply (void)
void	DoEdit (void)
void	DoRemove (void)
void	DoRemoveOutside (void)
void	DoConvertFrom (void)
void	DoConvertTo (void)
void	DoCopyFrom (void)
void	DoCopyTo (void)
void	DoSwapFrom (void)
void	DoSwapTo (void)
void	DoParseFrom (void)
void	DoParseTo (void)
void	DoNOOP (void)
void	HandleValue (const string &value)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
string	m_qual
CRef< CGb_qual >	m_GBqual
bool	m_erase
Protected Attributes inherited from IEditingActionFeat
CRef< CScope >	m_scope
SAnnotSelector	m_selector
string	m_ncRNAclass
CSeq_feat_Handle	m_Feat
CRef< CSeq_feat >	m_EditedFeat
CSeq_feat_Handle	m_SavedFeat
CRef< CSeq_feat >	m_SavedEditedFeat
bool	m_saved_feat_enabled
Protected Attributes inherited from IEditingAction
map< CSeq_feat_Handle, CRef< CSeq_feat > >	m_ChangedFeatures
map< CSeq_feat_Handle, CSeq_entry_Handle >	m_CreatedFeatures
map< const CSeqdesc *, CRef< CSeqdesc > >	m_ChangedDescriptors
map< const CSeqdesc *, CSeq_entry_Handle >	m_ContextForDescriptors
map< const CSeqdesc *, CSeq_entry_Handle >	m_CreatedDescriptors
map< const CSeqdesc *, CSeq_entry_Handle >	m_DeletedDescriptors
map< CBioseq_Handle, CRef< CSeq_inst > >	m_ChangedInstances
CRef< CSubmit_block >	m_ChangedSubmitBlock
vector< string >	m_ChangedValues
bool	m_ChangedIds
string	m_Name
CSeq_entry_Handle	m_TopSeqEntry
CConstRef< objects::CSeq_submit >	m_SeqSubmit
CSeq_entry_Handle	m_CurrentSeqEntry
bool	m_modified
IEditingAction *	m_Other
string	m_value
string	m_find
string	m_replace
string	m_strip_name
macro::CMacroFunction_EditStringQual::ESearchLoc	m_edit_loc
bool	m_case_insensitive
bool	m_is_regex
CRef< macro::CRemoveTextOptions >	m_remove_options
ECapChange	m_cap_change
bool	m_leave_on_original
edit::CParseTextOptions	m_parse_options
edit::EExistingText	m_existing_text
CRef< CEditingActionConstraint >	m_constraint
bool	m_update_mrna
bool	m_retranslate_cds
size_t	m_max_records

Additional Inherited Members
Public Types inherited from IEditingAction
enum	EActionType {   eActionType_NOOP = 0 , eActionType_Apply , eActionType_Edit , eActionType_Remove ,   eActionType_RemoveOutside , eActionType_ConvertFrom , eActionType_CopyFrom , eActionType_ParseFrom ,   eActionType_SwapFrom , eActionType_ConvertTo , eActionType_CopyTo , eActionType_ParseTo ,   eActionType_SwapTo }
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...
typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...
typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...
Static Public Member Functions inherited from IEditingActionFeat
static bool	s_IsSetncRNAClass (const objects::CRNA_ref &rna_ref)
static const string &	s_GetncRNAClass (const objects::CRNA_ref &rna_ref)
Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)
static EAllocFillMode	GetAllocFillMode (void)
static void	SetAllocFillMode (EAllocFillMode mode)
static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...
Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Definition at line 130 of file editing_action_features.hpp.

Constructor & Destructor Documentation

CEditingActionFeatGbQual()

CEditingActionFeatGbQual::CEditingActionFeatGbQual	(	CSeq_entry_Handle	seh,
		const CSeqFeatData::ESubtype	subtype,
		const CSeqFeatData::E_Choice	feat_type,
		const string &	ncRNA_class,
		const string &	qual,
		const string &	name = "CEditingActionFeatGbQual"
	)

Definition at line 1272 of file editing_action_features.cpp.

Member Function Documentation

GetValue()

string CEditingActionFeatGbQual::GetValue ( void  )

protectedvirtual

Implements IEditingAction.

Reimplemented in CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatTranslation, CEditingActionFeatAllele, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatDualVal2, and CEditingActionFeatDualVal1.

Definition at line 1332 of file editing_action_features.cpp.

References CSeq_feat::GetNamedQual(), CGb_qual_Base::GetVal(), IEditingActionFeat::m_EditedFeat, m_GBqual, and m_qual.

IsSetValue()

bool CEditingActionFeatGbQual::IsSetValue ( void  )

protectedvirtual

Implements IEditingAction.

Reimplemented in CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatTranslation, CEditingActionFeatAllele, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatDualVal2, and CEditingActionFeatDualVal1.

Definition at line 1315 of file editing_action_features.cpp.

References CSeq_feat::GetNamedQual(), CGb_qual_Base::IsSetVal(), IEditingActionFeat::m_EditedFeat, m_GBqual, and m_qual.

Modify()

void CEditingActionFeatGbQual::Modify ( EActionType  action )

protectedvirtual

Reimplemented from IEditingActionFeat.

Reimplemented in CEditingActionFeatTranslExcept, and CEditingActionFeatGbQualTwoNames.

Definition at line 1279 of file editing_action_features.cpp.

References EDIT_EACH_GBQUAL_ON_SEQFEAT, ERASE_GBQUAL_ON_SEQFEAT, CSeq_feat_Base::GetQual(), IEditingAction::IsCreateNew(), IEditingAction::IsFrom(), CSeq_feat_Base::IsSetQual(), IEditingActionFeat::m_EditedFeat, m_erase, m_GBqual, m_qual, IEditingActionFeat::Modify(), CRef< C, Locker >::Reset(), CSeq_feat_Base::ResetQual(), and CSeq_feat_Base::SetQual().

Referenced by CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), CEditingActionFeatGeneLocus::FindRelated(), and CEditingActionFeatTranslExcept::Modify().

ResetValue()

void CEditingActionFeatGbQual::ResetValue ( void  )

protectedvirtual

Implements IEditingAction.

Reimplemented in CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatTranslation, CEditingActionFeatAllele, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatDualVal2, and CEditingActionFeatDualVal1.

Definition at line 1342 of file editing_action_features.cpp.

References m_erase.

SetValue()

void CEditingActionFeatGbQual::SetValue ( const string &  value )

protectedvirtual

Implements IEditingAction.

Reimplemented in CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatTranslation, CEditingActionFeatAllele, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatDualVal2, and CEditingActionFeatDualVal1.

Definition at line 1323 of file editing_action_features.cpp.

References CSeq_feat::AddQualifier(), eExistingText_add_qual, IEditingActionFeat::m_EditedFeat, IEditingAction::m_existing_text, m_GBqual, m_qual, CGb_qual_Base::SetVal(), and rapidjson::value.

Member Data Documentation

m_erase

bool CEditingActionFeatGbQual::m_erase

protected

Definition at line 147 of file editing_action_features.hpp.

Referenced by Modify(), CEditingActionFeatGbQualTwoNames::Modify(), CEditingActionFeatTranslExcept::Modify(), ResetValue(), CEditingActionFeatDualVal1::ResetValue(), CEditingActionFeatDualVal2::ResetValue(), CEditingActionFeatCodonsRecognized::ResetValue(), CEditingActionFeatAnticodon::ResetValue(), CEditingActionFeatTranslExcept::ResetValue(), CEditingActionFeatRegion::ResetValue(), CEditingActionFeatCodonStart::ResetValue(), CEditingActionFeatTranslTable::ResetValue(), CEditingActionFeatDesc::ResetValue(), CEditingActionFeatLocus_tag::ResetValue(), CEditingActionFeatMaploc::ResetValue(), CEditingActionFeatAllele::ResetValue(), CEditingActionFeatTranslation::ResetValue(), CEditingActionFeatGeneLocus::ResetValue(), and CEditingActionFeatTranscriptId::ResetValue().

m_GBqual

CRef< CGb_qual > CEditingActionFeatGbQual::m_GBqual

protected

Definition at line 146 of file editing_action_features.hpp.

Referenced by GetValue(), CEditingActionFeatDualVal1::GetValue(), CEditingActionFeatDualVal2::GetValue(), CEditingActionFeatCodonsRecognized::GetValue(), CEditingActionFeatAnticodon::GetValue(), CEditingActionFeatTranslExcept::GetValue(), CEditingActionFeatRegion::GetValue(), CEditingActionFeatCodonStart::GetValue(), CEditingActionFeatTranslTable::GetValue(), CEditingActionFeatDesc::GetValue(), CEditingActionFeatLocus_tag::GetValue(), CEditingActionFeatMaploc::GetValue(), CEditingActionFeatAllele::GetValue(), CEditingActionFeatTranslation::GetValue(), CEditingActionFeatGeneLocus::GetValue(), CEditingActionFeatTranscriptId::GetValue(), IsSetValue(), CEditingActionFeatDualVal1::IsSetValue(), CEditingActionFeatDualVal2::IsSetValue(), CEditingActionFeatCodonsRecognized::IsSetValue(), CEditingActionFeatAnticodon::IsSetValue(), CEditingActionFeatTranslExcept::IsSetValue(), CEditingActionFeatRegion::IsSetValue(), CEditingActionFeatCodonStart::IsSetValue(), CEditingActionFeatTranslTable::IsSetValue(), CEditingActionFeatDesc::IsSetValue(), CEditingActionFeatLocus_tag::IsSetValue(), CEditingActionFeatMaploc::IsSetValue(), CEditingActionFeatAllele::IsSetValue(), CEditingActionFeatTranslation::IsSetValue(), CEditingActionFeatGeneLocus::IsSetValue(), CEditingActionFeatTranscriptId::IsSetValue(), Modify(), CEditingActionFeatGbQualTwoNames::Modify(), CEditingActionFeatDualVal1::ResetValue(), CEditingActionFeatDualVal2::ResetValue(), CEditingActionFeatCodonsRecognized::ResetValue(), CEditingActionFeatAnticodon::ResetValue(), CEditingActionFeatTranslExcept::ResetValue(), CEditingActionFeatRegion::ResetValue(), CEditingActionFeatCodonStart::ResetValue(), CEditingActionFeatTranslTable::ResetValue(), CEditingActionFeatDesc::ResetValue(), CEditingActionFeatLocus_tag::ResetValue(), CEditingActionFeatMaploc::ResetValue(), CEditingActionFeatAllele::ResetValue(), CEditingActionFeatTranslation::ResetValue(), CEditingActionFeatGeneLocus::ResetValue(), CEditingActionFeatTranscriptId::ResetValue(), SetValue(), CEditingActionFeatDualVal1::SetValue(), CEditingActionFeatDualVal2::SetValue(), CEditingActionFeatCodonsRecognized::SetValue(), CEditingActionFeatAnticodon::SetValue(), CEditingActionFeatTranslExcept::SetValue(), CEditingActionFeatRegion::SetValue(), CEditingActionFeatCodonStart::SetValue(), CEditingActionFeatTranslTable::SetValue(), CEditingActionFeatDesc::SetValue(), CEditingActionFeatLocus_tag::SetValue(), CEditingActionFeatMaploc::SetValue(), CEditingActionFeatAllele::SetValue(), CEditingActionFeatTranslation::SetValue(), CEditingActionFeatGeneLocus::SetValue(), and CEditingActionFeatTranscriptId::SetValue().

m_qual

string CEditingActionFeatGbQual::m_qual

protected

Definition at line 145 of file editing_action_features.hpp.

Referenced by GetValue(), IsSetValue(), Modify(), CEditingActionFeatGbQualTwoNames::Modify(), SetValue(), CEditingActionFeatDualVal1::SetValue(), CEditingActionFeatDualVal2::SetValue(), CEditingActionFeatCodonsRecognized::SetValue(), CEditingActionFeatAnticodon::SetValue(), CEditingActionFeatTranslExcept::SetValue(), CEditingActionFeatRegion::SetValue(), CEditingActionFeatCodonStart::SetValue(), CEditingActionFeatTranslTable::SetValue(), CEditingActionFeatDesc::SetValue(), CEditingActionFeatLocus_tag::SetValue(), CEditingActionFeatMaploc::SetValue(), CEditingActionFeatAllele::SetValue(), CEditingActionFeatTranslation::SetValue(), CEditingActionFeatGeneLocus::SetValue(), and CEditingActionFeatTranscriptId::SetValue().

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The documentation for this class was generated from the following files:

• include/gui/packages/pkg_sequence_edit/editing_action_features.hpp
• src/gui/packages/pkg_sequence_edit/editing_action_features.cpp