NCBI C++ ToolKit
Public Member Functions | Protected Member Functions | List of all members
CEditingActionFeatAllele Class Reference

Search Toolkit Book for CEditingActionFeatAllele

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

+ Inheritance diagram for CEditingActionFeatAllele:
+ Collaboration diagram for CEditingActionFeatAllele:

Public Member Functions

 CEditingActionFeatAllele (CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
 
- Public Member Functions inherited from 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")
 
- 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_blockGetChangedSubmitBlock (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< CCmdCompositeGetActionCommand (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...
 
CObjectoperator= (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 bool IsSetValue (void)
 
virtual void SetValue (const string &value)
 
virtual string GetValue (void)
 
virtual void ResetValue (void)
 
- Protected Member Functions inherited from CEditingActionFeatGbQual
virtual void Modify (EActionType action)
 
- 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_locx_GetSublocOnBioseq (CBioseq_Handle bsh, const CSeq_loc &loc)
 
CRef< CSeq_locx_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< IEditCommandGetUpdateMRNAProductNameCmd (const CSeq_feat_Handle fh, const CRef< CSeq_feat > feat)
 
CRef< CCmdCompositeGetRetranslateCdsCmd (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...
 

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< Uint8TCounter
 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 strings_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...
 
- Protected Attributes inherited from CEditingActionFeatGbQual
string m_qual
 
CRef< CGb_qualm_GBqual
 
bool m_erase
 
- Protected Attributes inherited from IEditingActionFeat
CRef< CScopem_scope
 
SAnnotSelector m_selector
 
string m_ncRNAclass
 
CSeq_feat_Handle m_Feat
 
CRef< CSeq_featm_EditedFeat
 
CSeq_feat_Handle m_SavedFeat
 
CRef< CSeq_featm_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_Handlem_CreatedFeatures
 
map< const CSeqdesc *, CRef< CSeqdesc > > m_ChangedDescriptors
 
map< const CSeqdesc *, CSeq_entry_Handlem_ContextForDescriptors
 
map< const CSeqdesc *, CSeq_entry_Handlem_CreatedDescriptors
 
map< const CSeqdesc *, CSeq_entry_Handlem_DeletedDescriptors
 
map< CBioseq_Handle, CRef< CSeq_inst > > m_ChangedInstances
 
CRef< CSubmit_blockm_ChangedSubmitBlock
 
vector< stringm_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
 
IEditingActionm_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< CEditingActionConstraintm_constraint
 
bool m_update_mrna
 
bool m_retranslate_cds
 
size_t m_max_records
 

Detailed Description

Definition at line 428 of file editing_action_features.hpp.

Constructor & Destructor Documentation

◆ CEditingActionFeatAllele()

CEditingActionFeatAllele::CEditingActionFeatAllele ( CSeq_entry_Handle  seh,
const CSeqFeatData::ESubtype  subtype,
const CSeqFeatData::E_Choice  feat_type,
const string ncRNA_class 
)

Definition at line 2630 of file editing_action_features.cpp.

Member Function Documentation

◆ GetValue()

string CEditingActionFeatAllele::GetValue ( void  )
protectedvirtual

◆ IsSetValue()

bool CEditingActionFeatAllele::IsSetValue ( void  )
protectedvirtual

◆ ResetValue()

void CEditingActionFeatAllele::ResetValue ( void  )
protectedvirtual

◆ SetValue()

void CEditingActionFeatAllele::SetValue ( const string value)
protectedvirtual

The documentation for this class was generated from the following files:
Modified on Wed Dec 06 07:12:54 2023 by modify_doxy.py rev. 669887