NCBI C++ ToolKit
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IEditingActionBiosource Class Reference

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

+ Inheritance diagram for IEditingActionBiosource:
+ Collaboration diagram for IEditingActionBiosource:

Public Member Functions

 IEditingActionBiosource (CSeq_entry_Handle seh, bool is_descriptor, bool is_feature, const string &name)
 
void SetFeat (CSeq_feat_Handle fh)
 
void SetDesc (const CSeqdesc *desc)
 
- 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 void Find (EActionType action)
 
virtual void FindRelated (EActionType action)
 
virtual void Modify (EActionType action)
 
virtual void SwapContext (IEditingAction *source)
 
virtual bool SameObject ()
 
- 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)
 
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

CRef< CSeqdescm_EditedDesc
 
CRef< CSeq_featm_EditedFeat
 
CBioSourcem_EditedBiosource
 
const CSeqdescm_Desc
 
CSeq_feat_Handle m_Feat
 
CSeq_entry_Handle m_DescContext
 
bool m_is_descriptor
 
bool m_is_feature
 
- 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
 

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 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 51 of file editing_action_biosource.hpp.

Constructor & Destructor Documentation

◆ IEditingActionBiosource()

IEditingActionBiosource::IEditingActionBiosource ( CSeq_entry_Handle  seh,
bool  is_descriptor,
bool  is_feature,
const string name 
)

Definition at line 55 of file editing_action_biosource.cpp.

Member Function Documentation

◆ Find()

void IEditingActionBiosource::Find ( EActionType  action)
protectedvirtual

◆ FindRelated()

void IEditingActionBiosource::FindRelated ( EActionType  action)
protectedvirtual

Implements IEditingAction.

Definition at line 160 of file editing_action_biosource.cpp.

References Find().

◆ Modify()

void IEditingActionBiosource::Modify ( EActionType  action)
protectedvirtual

◆ SameObject()

bool IEditingActionBiosource::SameObject ( )
protectedvirtual

Implements IEditingAction.

Definition at line 179 of file editing_action_biosource.cpp.

References IEditingAction::m_Other.

◆ SetDesc()

void IEditingActionBiosource::SetDesc ( const CSeqdesc desc)

◆ SetFeat()

void IEditingActionBiosource::SetFeat ( CSeq_feat_Handle  fh)

◆ SwapContext()

void IEditingActionBiosource::SwapContext ( IEditingAction source)
protectedvirtual

Member Data Documentation

◆ m_Desc

const CSeqdesc* IEditingActionBiosource::m_Desc
protected

Definition at line 67 of file editing_action_biosource.hpp.

Referenced by Find(), Modify(), and SwapContext().

◆ m_DescContext

CSeq_entry_Handle IEditingActionBiosource::m_DescContext
protected

Definition at line 69 of file editing_action_biosource.hpp.

Referenced by Find(), Modify(), and SwapContext().

◆ m_EditedBiosource

CBioSource* IEditingActionBiosource::m_EditedBiosource
protected

Definition at line 66 of file editing_action_biosource.hpp.

Referenced by Find(), CEditingActionBiosourceTaxname::GetValue(), CEditingActionBiosourceTaxnameAfterBinomial::GetValue(), CEditingActionBiosourceCommonName::GetValue(), CEditingActionBiosourceDivision::GetValue(), CEditingActionBiosourceLineage::GetValue(), CEditingActionBiosourceLocation::GetValue(), CEditingActionBiosourceOrigin::GetValue(), CEditingActionBiosourceTaxname::IsSetValue(), CEditingActionBiosourceTaxnameAfterBinomial::IsSetValue(), CEditingActionBiosourceCommonName::IsSetValue(), CEditingActionBiosourceDivision::IsSetValue(), CEditingActionBiosourceLineage::IsSetValue(), CEditingActionBiosourceLocation::IsSetValue(), CEditingActionBiosourceOrigin::IsSetValue(), CEditingActionBiosourcePrimers::Modify(), CEditingActionBiosourceOrgMod::Modify(), CEditingActionBiosourceSubSource::Modify(), CEditingActionBiosourceAllNotes::Modify(), CEditingActionBiosourceDbxref::Modify(), CEditingActionBiosourceTaxname::ResetValue(), CEditingActionBiosourceTaxnameAfterBinomial::ResetValue(), CEditingActionBiosourceCommonName::ResetValue(), CEditingActionBiosourceDivision::ResetValue(), CEditingActionBiosourceLineage::ResetValue(), CEditingActionBiosourceLocation::ResetValue(), CEditingActionBiosourceOrigin::ResetValue(), SetDesc(), SetFeat(), CEditingActionBiosourceTaxname::SetValue(), CEditingActionBiosourceTaxnameAfterBinomial::SetValue(), CEditingActionBiosourceCommonName::SetValue(), CEditingActionBiosourceDivision::SetValue(), CEditingActionBiosourceLineage::SetValue(), CEditingActionBiosourceLocation::SetValue(), CEditingActionBiosourceOrigin::SetValue(), CEditingActionBiosourcePrimers::SetValue(), CEditingActionBiosourceOrgMod::SetValue(), CEditingActionBiosourceSubSource::SetValue(), CEditingActionBiosourceStructuredVoucher::SetValue(), CEditingActionBiosourceDbxref::SetValue(), and SwapContext().

◆ m_EditedDesc

CRef<CSeqdesc> IEditingActionBiosource::m_EditedDesc
protected

Definition at line 64 of file editing_action_biosource.hpp.

Referenced by Find(), Modify(), SetDesc(), and SwapContext().

◆ m_EditedFeat

CRef<CSeq_feat> IEditingActionBiosource::m_EditedFeat
protected

Definition at line 65 of file editing_action_biosource.hpp.

Referenced by Find(), Modify(), SetFeat(), and SwapContext().

◆ m_Feat

CSeq_feat_Handle IEditingActionBiosource::m_Feat
protected

Definition at line 68 of file editing_action_biosource.hpp.

Referenced by Find(), Modify(), and SwapContext().

◆ m_is_descriptor

bool IEditingActionBiosource::m_is_descriptor
protected

Definition at line 70 of file editing_action_biosource.hpp.

Referenced by Find().

◆ m_is_feature

bool IEditingActionBiosource::m_is_feature
protected

Definition at line 71 of file editing_action_biosource.hpp.

Referenced by Find().


The documentation for this class was generated from the following files:
Modified on Fri May 24 14:50:54 2024 by modify_doxy.py rev. 669887