NCBI C++ ToolKit
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IEditingAction Class Referenceabstract

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

+ Inheritance diagram for IEditingAction:
+ Collaboration diagram for IEditingAction:

Public Types

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...
 

Public Member Functions

 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

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)
 
virtual void Find (EActionType action)=0
 
virtual void FindRelated (EActionType action)=0
 
virtual void Modify (EActionType action)=0
 
virtual void SwapContext (IEditingAction *source)
 
virtual bool SameObject ()=0
 
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)
 
virtual bool IsSetValue (void)=0
 
virtual void SetValue (const string &value)=0
 
virtual string GetValue (void)=0
 
virtual void ResetValue (void)=0
 
virtual void ResetScope ()
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

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
 

Additional Inherited Members

- 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 49 of file editing_actions.hpp.

Member Enumeration Documentation

◆ EActionType

Enumerator
eActionType_NOOP 
eActionType_Apply 
eActionType_Edit 
eActionType_Remove 
eActionType_RemoveOutside 
eActionType_ConvertFrom 
eActionType_CopyFrom 
eActionType_ParseFrom 
eActionType_SwapFrom 
eActionType_ConvertTo 
eActionType_CopyTo 
eActionType_ParseTo 
eActionType_SwapTo 

Definition at line 97 of file editing_actions.hpp.

Constructor & Destructor Documentation

◆ IEditingAction()

IEditingAction::IEditingAction ( CSeq_entry_Handle  seh,
const string name,
CConstRef< objects::CSeq_submit >  submit = CConstRef<objects::CSeq_submit>(NULL) 
)

Definition at line 76 of file editing_actions.cpp.

◆ ~IEditingAction()

virtual IEditingAction::~IEditingAction ( )
inlinevirtual

Definition at line 53 of file editing_actions.hpp.

Member Function Documentation

◆ Action()

void IEditingAction::Action ( EActionType  action)
protected

◆ Apply()

void IEditingAction::Apply ( const string value)

Definition at line 422 of file editing_actions.cpp.

References eActionType_Apply, Find(), m_value, and rapidjson::value.

◆ CheckForExistingText()

int IEditingAction::CheckForExistingText ( CIRef< IEditingAction action2,
EActionType  action_type,
edit::CParseTextOptions  parse_options = edit::CParseTextOptions() 
)

◆ CheckValue()

bool IEditingAction::CheckValue ( void  )

◆ CheckValues()

bool IEditingAction::CheckValues ( void  )

◆ ConvertFrom()

void IEditingAction::ConvertFrom ( ECapChange  cap_change,
bool  leave_on_original,
const string strip_name,
IEditingAction destination 
)

◆ ConvertTo()

void IEditingAction::ConvertTo ( const string value,
IEditingAction source 
)

◆ CopyFrom()

void IEditingAction::CopyFrom ( IEditingAction destination)

Definition at line 476 of file editing_actions.cpp.

References eActionType_CopyFrom, Find(), and m_Other.

Referenced by CheckForExistingText().

◆ CopyTo()

void IEditingAction::CopyTo ( const string value,
IEditingAction source 
)

◆ DoApply()

void IEditingAction::DoApply ( void  )
protected

Definition at line 554 of file editing_actions.cpp.

References CheckValue(), HandleValue(), m_constraint, m_value, and CEditingActionConstraint::Match().

Referenced by Action().

◆ DoConvertFrom()

void IEditingAction::DoConvertFrom ( void  )
protected

◆ DoConvertTo()

void IEditingAction::DoConvertTo ( void  )
protected

Definition at line 619 of file editing_actions.cpp.

References CheckValue(), GetValue(), HandleValue(), m_ChangedValues, and m_value.

Referenced by Action().

◆ DoCopyFrom()

void IEditingAction::DoCopyFrom ( void  )
protected

Definition at line 629 of file editing_actions.cpp.

References CheckValue(), CopyTo(), GetValue(), m_CurrentSeqEntry, m_Other, SetTopSeqEntry(), and val.

Referenced by Action().

◆ DoCopyTo()

void IEditingAction::DoCopyTo ( void  )
protected

Definition at line 639 of file editing_actions.cpp.

References CheckValue(), GetValue(), HandleValue(), m_ChangedValues, and m_value.

Referenced by Action().

◆ DoEdit()

void IEditingAction::DoEdit ( void  )
protected

◆ DoNOOP()

void IEditingAction::DoNOOP ( void  )
protected

Definition at line 719 of file editing_actions.cpp.

References CheckValue(), GetValue(), m_ChangedValues, and m_modified.

Referenced by Action().

◆ DoParseFrom()

void IEditingAction::DoParseFrom ( void  )
protected

◆ DoParseTo()

void IEditingAction::DoParseTo ( void  )
protected

Definition at line 709 of file editing_actions.cpp.

References CheckValue(), GetValue(), HandleValue(), m_ChangedValues, and m_value.

Referenced by Action().

◆ DoRemove()

void IEditingAction::DoRemove ( void  )
protected

Definition at line 577 of file editing_actions.cpp.

References CheckValue(), m_modified, and ResetValue().

Referenced by Action().

◆ DoRemoveOutside()

void IEditingAction::DoRemoveOutside ( void  )
protected

Definition at line 586 of file editing_actions.cpp.

References CheckValue(), GetValue(), m_modified, m_remove_options, SetValue(), and str().

Referenced by Action().

◆ DoSwapFrom()

void IEditingAction::DoSwapFrom ( void  )
protected

◆ DoSwapTo()

void IEditingAction::DoSwapTo ( void  )
protected

Definition at line 666 of file editing_actions.cpp.

References GetValue(), IsSetValue(), m_modified, m_Other, m_value, and SetValue().

Referenced by Action().

◆ Edit()

void IEditingAction::Edit ( const string find,
const string replace,
macro::CMacroFunction_EditStringQual::ESearchLoc  edit_loc,
bool  case_insensitive,
bool  is_regex 
)

◆ Find()

virtual void IEditingAction::Find ( EActionType  action)
protectedpure virtual

◆ FindRelated()

virtual void IEditingAction::FindRelated ( EActionType  action)
protectedpure virtual

◆ GetActionCommand()

CRef< CCmdComposite > IEditingAction::GetActionCommand ( void  )

◆ GetChangedDescriptors()

const map< const CSeqdesc *, CRef< CSeqdesc > > & IEditingAction::GetChangedDescriptors ( void  )

Definition at line 97 of file editing_actions.cpp.

References m_ChangedDescriptors.

Referenced by GetActionCommand().

◆ GetChangedFeatures()

const map< CSeq_feat_Handle, CRef< CSeq_feat > > & IEditingAction::GetChangedFeatures ( void  )

Definition at line 87 of file editing_actions.cpp.

References m_ChangedFeatures.

Referenced by GetActionCommand().

◆ GetChangedIds()

bool IEditingAction::GetChangedIds ( void  )

Definition at line 127 of file editing_actions.cpp.

References m_ChangedIds.

◆ GetChangedInstances()

const map< CBioseq_Handle, CRef< CSeq_inst > > & IEditingAction::GetChangedInstances ( void  )

Definition at line 117 of file editing_actions.cpp.

References m_ChangedInstances.

Referenced by GetActionCommand().

◆ GetChangedSubmitBlock()

CRef< CSubmit_block > IEditingAction::GetChangedSubmitBlock ( void  )

Definition at line 122 of file editing_actions.cpp.

References m_ChangedSubmitBlock.

Referenced by GetActionCommand().

◆ GetChangedValues()

const vector< string > & IEditingAction::GetChangedValues ( void  )

Definition at line 132 of file editing_actions.cpp.

References m_ChangedValues.

Referenced by CheckForExistingText(), CheckValues(), and GetValues().

◆ GetContextForDescriptors()

const map< const CSeqdesc *, CSeq_entry_Handle > & IEditingAction::GetContextForDescriptors ( void  )

Definition at line 102 of file editing_actions.cpp.

References m_ContextForDescriptors.

Referenced by GetActionCommand().

◆ GetCreatedDescriptors()

const map< const CSeqdesc *, CSeq_entry_Handle > & IEditingAction::GetCreatedDescriptors ( void  )

Definition at line 107 of file editing_actions.cpp.

References m_CreatedDescriptors.

Referenced by GetActionCommand().

◆ GetCreatedFeatures()

const map< CSeq_feat_Handle, CSeq_entry_Handle > & IEditingAction::GetCreatedFeatures ( void  )

Definition at line 92 of file editing_actions.cpp.

References m_CreatedFeatures.

Referenced by GetActionCommand().

◆ GetDeletedDescriptors()

const map< const CSeqdesc *, CSeq_entry_Handle > & IEditingAction::GetDeletedDescriptors ( void  )

Definition at line 112 of file editing_actions.cpp.

References m_DeletedDescriptors.

Referenced by GetActionCommand().

◆ GetName()

const string IEditingAction::GetName ( void  ) const

Definition at line 82 of file editing_actions.cpp.

References m_Name.

◆ GetRetranslateCdsCmd()

CRef< CCmdComposite > IEditingAction::GetRetranslateCdsCmd ( const CSeq_feat_Handle  fh,
const CRef< CSeq_feat feat,
int offset,
bool  create_general_only 
)
protected

◆ GetSeqSubmit()

CConstRef< objects::CSeq_submit > IEditingAction::GetSeqSubmit ( void  )

Definition at line 352 of file editing_actions.cpp.

References m_SeqSubmit.

Referenced by IEditingActionDesc::FindRelated().

◆ GetUpdateMRNAProductNameCmd()

CIRef< IEditCommand > IEditingAction::GetUpdateMRNAProductNameCmd ( const CSeq_feat_Handle  fh,
const CRef< CSeq_feat feat 
)
protected

◆ GetValue()

virtual string IEditingAction::GetValue ( void  )
protectedpure virtual

Implemented in CEditingActionGeneralIdTag, CEditingActionGeneralIdDb, CEditingActionEntireGeneralId, CEditingActionFileId, CEditingActionSeqid, CEditingActionFlatFile, CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatProduct, CEditingActionFeatFunction, CEditingActionFeatEcNumber, CEditingActionFeatTranslation, CEditingActionFeatPartial, CEditingActionFeatActivity, CEditingActionFeatAllele, CEditingActionFeatSynonym, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatNcRnaClass, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatRnaQual, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatPseudo, CEditingActionFeatEvidence, CEditingActionFeatDbxref, CEditingActionFeatDualVal2, CEditingActionFeatDualVal1, CEditingActionFeatGbQual, CEditingActionFeatException, CEditingActionFeatComment, CEditingActionDescComment, CEditingActionDescLocalId, CEditingActionDescAuthorNameList, CEditingActionDescStatus, CEditingActionDescPages, CEditingActionDescIssue, CEditingActionDescVolume, CEditingActionDescJournal, CEditingActionDescAuthorInitials, CEditingActionDescAuthorConsortium, CEditingActionDescAuthorSuffix, CEditingActionDescAuthorLastName, CEditingActionDescAuthorFirstName, CEditingActionDescEmail, CEditingActionDescCountry, CEditingActionDescState, CEditingActionDescCity, CEditingActionDescStreet, CEditingActionDescDepartment, CEditingActionDescAffil, CEditingActionDescPubPmid, CEditingActionDescPubTitle, CEditingActionMolInfoStrand, CEditingActionMolInfoTopology, CEditingActionMolInfoClass, CEditingActionMolInfoCompletedness, CEditingActionMolInfoTechnique, CEditingActionMolInfoMolecule, CEditingActionDescStructCommFieldName, CEditingActionDescStructCommDbName, CEditingActionDescUserObject, CEditingActionDescGenomeProjectId, CEditingActionDescKeyword, CEditingActionDescDefline, CEditingActionDescCommentDescriptor, CEditingActionBiosourceDbxref, CEditingActionBiosourceStructuredVoucher, CEditingActionBiosourceAllNotes, CEditingActionBiosourceSubSource, CEditingActionBiosourceOrgMod, CEditingActionBiosourcePrimers, CEditingActionBiosourceOrigin, CEditingActionBiosourceLocation, CEditingActionBiosourceLineage, CEditingActionBiosourceDivision, CEditingActionBiosourceCommonName, CEditingActionBiosourceTaxnameAfterBinomial, and CEditingActionBiosourceTaxname.

Referenced by CheckValue(), DoConvertFrom(), DoConvertTo(), DoCopyFrom(), DoCopyTo(), DoEdit(), DoNOOP(), DoParseFrom(), DoParseTo(), DoRemoveOutside(), DoSwapFrom(), DoSwapTo(), and HandleValue().

◆ GetValues()

const vector< string > & IEditingAction::GetValues ( void  )

◆ HandleValue()

void IEditingAction::HandleValue ( const string value)
protected

◆ IsCreateNew()

bool IEditingAction::IsCreateNew ( EActionType  action)
protected

◆ IsFrom()

bool IEditingAction::IsFrom ( EActionType  action)
protected

◆ IsModified()

bool IEditingAction::IsModified ( )
inline

Definition at line 116 of file editing_actions.hpp.

References m_modified.

Referenced by DoConvertFrom(), DoParseFrom(), and DoSwapFrom().

◆ IsNOOP()

bool IEditingAction::IsNOOP ( EActionType  action)
protected

◆ IsSetValue()

virtual bool IEditingAction::IsSetValue ( void  )
protectedpure virtual

Implemented in CEditingActionGeneralIdTag, CEditingActionGeneralIdDb, CEditingActionEntireGeneralId, CEditingActionFileId, CEditingActionSeqid, CEditingActionFlatFile, CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatProduct, CEditingActionFeatFunction, CEditingActionFeatEcNumber, CEditingActionFeatTranslation, CEditingActionFeatPartial, CEditingActionFeatActivity, CEditingActionFeatAllele, CEditingActionFeatSynonym, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatNcRnaClass, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatRnaQual, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatPseudo, CEditingActionFeatEvidence, CEditingActionFeatDbxref, CEditingActionFeatDualVal2, CEditingActionFeatDualVal1, CEditingActionFeatGbQual, CEditingActionFeatException, CEditingActionFeatComment, CEditingActionDescComment, CEditingActionDescLocalId, CEditingActionDescAuthorNameList, CEditingActionDescStatus, CEditingActionDescPages, CEditingActionDescIssue, CEditingActionDescVolume, CEditingActionDescJournal, CEditingActionDescAuthorInitials, CEditingActionDescAuthorConsortium, CEditingActionDescAuthorSuffix, CEditingActionDescAuthorLastName, CEditingActionDescAuthorFirstName, CEditingActionDescEmail, CEditingActionDescCountry, CEditingActionDescState, CEditingActionDescCity, CEditingActionDescStreet, CEditingActionDescDepartment, CEditingActionDescAffil, CEditingActionDescPubPmid, CEditingActionDescPubTitle, CEditingActionMolInfoStrand, CEditingActionMolInfoTopology, CEditingActionMolInfoClass, CEditingActionMolInfoCompletedness, CEditingActionMolInfoTechnique, CEditingActionMolInfoMolecule, CEditingActionDescStructCommFieldName, CEditingActionDescStructCommDbName, CEditingActionDescUserObject, CEditingActionDescGenomeProjectId, CEditingActionDescKeyword, CEditingActionDescDefline, CEditingActionDescCommentDescriptor, CEditingActionBiosourceDbxref, CEditingActionBiosourceStructuredVoucher, CEditingActionBiosourceAllNotes, CEditingActionBiosourceSubSource, CEditingActionBiosourceOrgMod, CEditingActionBiosourcePrimers, CEditingActionBiosourceOrigin, CEditingActionBiosourceLocation, CEditingActionBiosourceLineage, CEditingActionBiosourceDivision, CEditingActionBiosourceCommonName, CEditingActionBiosourceTaxnameAfterBinomial, and CEditingActionBiosourceTaxname.

Referenced by CheckValue(), DoSwapTo(), and HandleValue().

◆ IsTo()

bool IEditingAction::IsTo ( EActionType  action)
protected

◆ Modify()

virtual void IEditingAction::Modify ( EActionType  action)
protectedpure virtual

◆ NOOP()

void IEditingAction::NOOP ( void  )

Definition at line 549 of file editing_actions.cpp.

References eActionType_NOOP, and Find().

Referenced by CheckForExistingText().

◆ ParseFrom()

void IEditingAction::ParseFrom ( edit::CParseTextOptions  parse_options,
IEditingAction destination 
)

Definition at line 524 of file editing_actions.cpp.

References eActionType_ParseFrom, Find(), m_Other, and m_parse_options.

Referenced by CheckForExistingText().

◆ ParseTo()

void IEditingAction::ParseTo ( const string value,
IEditingAction source 
)

◆ Remove()

void IEditingAction::Remove ( void  )

Definition at line 438 of file editing_actions.cpp.

References eActionType_Remove, and Find().

◆ RemoveOutside()

void IEditingAction::RemoveOutside ( CRef< macro::CRemoveTextOptions >  options)

Definition at line 443 of file editing_actions.cpp.

References eActionType_RemoveOutside, Find(), and m_remove_options.

◆ ResetChangedDescriptors()

void IEditingAction::ResetChangedDescriptors ( void  )

◆ ResetChangedFeatures()

void IEditingAction::ResetChangedFeatures ( void  )

◆ ResetChangedIds()

void IEditingAction::ResetChangedIds ( void  )

Definition at line 158 of file editing_actions.cpp.

References m_ChangedIds.

Referenced by CheckForExistingText().

◆ ResetChangedInstances()

void IEditingAction::ResetChangedInstances ( void  )

Definition at line 153 of file editing_actions.cpp.

References map_checker< Container >::clear(), and m_ChangedInstances.

Referenced by CheckForExistingText().

◆ ResetChangedValues()

void IEditingAction::ResetChangedValues ( void  )

Definition at line 163 of file editing_actions.cpp.

References m_ChangedValues.

Referenced by CheckForExistingText(), CheckValues(), and GetValues().

◆ ResetScope()

virtual void IEditingAction::ResetScope ( )
inlineprotectedvirtual

Reimplemented in IEditingActionFeat.

Definition at line 154 of file editing_actions.hpp.

Referenced by ResetChangedFeatures().

◆ ResetValue()

virtual void IEditingAction::ResetValue ( void  )
protectedpure virtual

Implemented in CEditingActionSeqid, CEditingActionFlatFile, CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatProduct, CEditingActionFeatFunction, CEditingActionFeatEcNumber, CEditingActionFeatTranslation, CEditingActionFeatPartial, CEditingActionFeatActivity, CEditingActionFeatAllele, CEditingActionFeatSynonym, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatNcRnaClass, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatRnaQual, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatPseudo, CEditingActionFeatEvidence, CEditingActionFeatDbxref, CEditingActionFeatDualVal2, CEditingActionFeatDualVal1, CEditingActionFeatGbQual, CEditingActionFeatException, CEditingActionFeatComment, CEditingActionDescComment, CEditingActionDescLocalId, CEditingActionDescAuthorNameList, CEditingActionDescStatus, CEditingActionDescPages, CEditingActionDescIssue, CEditingActionDescVolume, CEditingActionDescJournal, CEditingActionDescAuthorInitials, CEditingActionDescAuthorConsortium, CEditingActionDescAuthorSuffix, CEditingActionDescAuthorLastName, CEditingActionDescAuthorFirstName, CEditingActionDescEmail, CEditingActionDescCountry, CEditingActionDescState, CEditingActionDescCity, CEditingActionDescStreet, CEditingActionDescDepartment, CEditingActionDescAffil, CEditingActionDescPubPmid, CEditingActionDescPubTitle, CEditingActionMolInfoStrand, CEditingActionMolInfoTopology, CEditingActionMolInfoClass, CEditingActionMolInfoCompletedness, CEditingActionMolInfoTechnique, CEditingActionMolInfoMolecule, CEditingActionDescStructCommFieldName, CEditingActionDescStructCommDbName, CEditingActionDescUserObject, CEditingActionDescGenomeProjectId, CEditingActionDescKeyword, CEditingActionDescDefline, CEditingActionDescCommentDescriptor, CEditingActionBiosourceDbxref, CEditingActionBiosourceStructuredVoucher, CEditingActionBiosourceAllNotes, CEditingActionBiosourceSubSource, CEditingActionBiosourceOrgMod, CEditingActionBiosourcePrimers, CEditingActionBiosourceOrigin, CEditingActionBiosourceLocation, CEditingActionBiosourceLineage, CEditingActionBiosourceDivision, CEditingActionBiosourceCommonName, CEditingActionBiosourceTaxnameAfterBinomial, and CEditingActionBiosourceTaxname.

Referenced by DoConvertFrom(), DoParseFrom(), and DoRemove().

◆ SameObject()

virtual bool IEditingAction::SameObject ( )
protectedpure virtual

◆ SetConstraint()

void IEditingAction::SetConstraint ( CRef< CEditingActionConstraint constraint)

◆ SetCurrentSeqEntry()

void IEditingAction::SetCurrentSeqEntry ( CSeq_entry_Handle  seh)

◆ SetExistingText()

void IEditingAction::SetExistingText ( edit::EExistingText  existing_text)

Definition at line 370 of file editing_actions.cpp.

References m_existing_text.

◆ SetMaxRecords()

void IEditingAction::SetMaxRecords ( size_t  max)
inline

Definition at line 117 of file editing_actions.hpp.

References m_max_records, and max().

◆ SetRetranslateCds()

void IEditingAction::SetRetranslateCds ( bool  value)
inline

Definition at line 115 of file editing_actions.hpp.

References m_retranslate_cds, and rapidjson::value.

◆ SetTopSeqEntry()

void IEditingAction::SetTopSeqEntry ( CSeq_entry_Handle  seh)

◆ SetUpdateMRNAProduct()

void IEditingAction::SetUpdateMRNAProduct ( bool  value)
inline

Definition at line 114 of file editing_actions.hpp.

References m_update_mrna, and rapidjson::value.

◆ SetValue()

virtual void IEditingAction::SetValue ( const string value)
protectedpure virtual

Implemented in CEditingActionSeqid, CEditingActionFlatFile, CEditingActionFeatTranscriptId, CEditingActionFeatGeneLocus, CEditingActionFeatProduct, CEditingActionFeatFunction, CEditingActionFeatEcNumber, CEditingActionFeatTranslation, CEditingActionFeatPartial, CEditingActionFeatActivity, CEditingActionFeatAllele, CEditingActionFeatSynonym, CEditingActionFeatMaploc, CEditingActionFeatLocus_tag, CEditingActionFeatNcRnaClass, CEditingActionFeatDesc, CEditingActionFeatTranslTable, CEditingActionFeatCodonStart, CEditingActionFeatRegion, CEditingActionFeatRnaQual, CEditingActionFeatTranslExcept, CEditingActionFeatAnticodon, CEditingActionFeatCodonsRecognized, CEditingActionFeatPseudo, CEditingActionFeatEvidence, CEditingActionFeatDbxref, CEditingActionFeatDualVal2, CEditingActionFeatDualVal1, CEditingActionFeatGbQual, CEditingActionFeatException, CEditingActionFeatComment, CEditingActionDescComment, CEditingActionDescLocalId, CEditingActionDescAuthorNameList, CEditingActionDescStatus, CEditingActionDescPages, CEditingActionDescIssue, CEditingActionDescVolume, CEditingActionDescJournal, CEditingActionDescAuthorInitials, CEditingActionDescAuthorConsortium, CEditingActionDescAuthorSuffix, CEditingActionDescAuthorLastName, CEditingActionDescAuthorFirstName, CEditingActionDescEmail, CEditingActionDescCountry, CEditingActionDescState, CEditingActionDescCity, CEditingActionDescStreet, CEditingActionDescDepartment, CEditingActionDescAffil, CEditingActionDescPubPmid, CEditingActionDescPubTitle, CEditingActionMolInfoStrand, CEditingActionMolInfoTopology, CEditingActionMolInfoClass, CEditingActionMolInfoCompletedness, CEditingActionMolInfoTechnique, CEditingActionMolInfoMolecule, CEditingActionDescStructCommFieldName, CEditingActionDescStructCommDbName, CEditingActionDescUserObject, CEditingActionDescGenomeProjectId, CEditingActionDescKeyword, CEditingActionDescDefline, CEditingActionDescCommentDescriptor, CEditingActionBiosourceDbxref, CEditingActionBiosourceStructuredVoucher, CEditingActionBiosourceAllNotes, CEditingActionBiosourceSubSource, CEditingActionBiosourceOrgMod, CEditingActionBiosourcePrimers, CEditingActionBiosourceOrigin, CEditingActionBiosourceLocation, CEditingActionBiosourceLineage, CEditingActionBiosourceDivision, CEditingActionBiosourceCommonName, CEditingActionBiosourceTaxnameAfterBinomial, and CEditingActionBiosourceTaxname.

Referenced by DoEdit(), DoParseFrom(), DoRemoveOutside(), DoSwapFrom(), DoSwapTo(), and HandleValue().

◆ SwapContext()

void IEditingAction::SwapContext ( IEditingAction source)
protectedvirtual

◆ SwapFrom()

void IEditingAction::SwapFrom ( IEditingAction destination)

Definition at line 500 of file editing_actions.cpp.

References eActionType_SwapFrom, Find(), and m_Other.

◆ SwapTo()

void IEditingAction::SwapTo ( const string value,
IEditingAction source 
)

Member Data Documentation

◆ m_cap_change

ECapChange IEditingAction::m_cap_change
protected

Definition at line 181 of file editing_actions.hpp.

Referenced by ConvertFrom(), and DoConvertFrom().

◆ m_case_insensitive

bool IEditingAction::m_case_insensitive
protected

Definition at line 178 of file editing_actions.hpp.

Referenced by DoEdit(), and Edit().

◆ m_ChangedDescriptors

map<const CSeqdesc*, CRef<CSeqdesc> > IEditingAction::m_ChangedDescriptors
protected

◆ m_ChangedFeatures

map<CSeq_feat_Handle, CRef<CSeq_feat> > IEditingAction::m_ChangedFeatures
protected

◆ m_ChangedIds

bool IEditingAction::m_ChangedIds
protected

◆ m_ChangedInstances

map<CBioseq_Handle, CRef<CSeq_inst> > IEditingAction::m_ChangedInstances
protected

◆ m_ChangedSubmitBlock

CRef<CSubmit_block> IEditingAction::m_ChangedSubmitBlock
protected

◆ m_ChangedValues

vector<string> IEditingAction::m_ChangedValues
protected

◆ m_constraint

CRef<CEditingActionConstraint> IEditingAction::m_constraint
protected

◆ m_ContextForDescriptors

map<const CSeqdesc*, CSeq_entry_Handle> IEditingAction::m_ContextForDescriptors
protected

◆ m_CreatedDescriptors

map<const CSeqdesc*, CSeq_entry_Handle> IEditingAction::m_CreatedDescriptors
protected

◆ m_CreatedFeatures

map<CSeq_feat_Handle, CSeq_entry_Handle> IEditingAction::m_CreatedFeatures
protected

◆ m_CurrentSeqEntry

CSeq_entry_Handle IEditingAction::m_CurrentSeqEntry
protected

◆ m_DeletedDescriptors

map<const CSeqdesc*, CSeq_entry_Handle> IEditingAction::m_DeletedDescriptors
protected

◆ m_edit_loc

macro::CMacroFunction_EditStringQual::ESearchLoc IEditingAction::m_edit_loc
protected

Definition at line 177 of file editing_actions.hpp.

Referenced by DoEdit(), and Edit().

◆ m_existing_text

edit::EExistingText IEditingAction::m_existing_text
protected

Definition at line 185 of file editing_actions.hpp.

Referenced by HandleValue(), IsCreateNew(), and SetExistingText().

◆ m_find

string IEditingAction::m_find
protected

Definition at line 176 of file editing_actions.hpp.

Referenced by DoEdit(), and Edit().

◆ m_is_regex

bool IEditingAction::m_is_regex
protected

Definition at line 179 of file editing_actions.hpp.

Referenced by DoEdit(), and Edit().

◆ m_leave_on_original

bool IEditingAction::m_leave_on_original
protected

Definition at line 182 of file editing_actions.hpp.

Referenced by ConvertFrom(), and DoConvertFrom().

◆ m_max_records

size_t IEditingAction::m_max_records
protected

◆ m_modified

bool IEditingAction::m_modified
protected

◆ m_Name

string IEditingAction::m_Name
protected

◆ m_Other

IEditingAction* IEditingAction::m_Other
protected

◆ m_parse_options

edit::CParseTextOptions IEditingAction::m_parse_options
protected

Definition at line 183 of file editing_actions.hpp.

Referenced by DoParseFrom(), and ParseFrom().

◆ m_remove_options

CRef<macro::CRemoveTextOptions> IEditingAction::m_remove_options
protected

Definition at line 180 of file editing_actions.hpp.

Referenced by DoRemoveOutside(), and RemoveOutside().

◆ m_replace

string IEditingAction::m_replace
protected

Definition at line 176 of file editing_actions.hpp.

Referenced by DoEdit(), and Edit().

◆ m_retranslate_cds

bool IEditingAction::m_retranslate_cds
protected

Definition at line 188 of file editing_actions.hpp.

Referenced by GetActionCommand(), and SetRetranslateCds().

◆ m_SeqSubmit

CConstRef<objects::CSeq_submit> IEditingAction::m_SeqSubmit
protected

Definition at line 170 of file editing_actions.hpp.

Referenced by IEditingActionDesc::Find(), GetActionCommand(), and GetSeqSubmit().

◆ m_strip_name

string IEditingAction::m_strip_name
protected

Definition at line 176 of file editing_actions.hpp.

Referenced by ConvertFrom(), and DoConvertFrom().

◆ m_TopSeqEntry

CSeq_entry_Handle IEditingAction::m_TopSeqEntry
protected

◆ m_update_mrna

bool IEditingAction::m_update_mrna
protected

Definition at line 187 of file editing_actions.hpp.

Referenced by GetActionCommand(), and SetUpdateMRNAProduct().

◆ m_value

string IEditingAction::m_value
protected

The documentation for this class was generated from the following files:
Modified on Tue Apr 23 07:38:04 2024 by modify_doxy.py rev. 669887