Search Toolkit Book for CMacroBioData_UserObjectIter
CMacroBioData_UserObjectIter - iterates over all user objects in the seq-entry. More...
#include <gui/objutils/macro_biodata_iter.hpp>
Inheritance diagram for CMacroBioData_UserObjectIter:
Collaboration diagram for CMacroBioData_UserObjectIter:
Public Member Functions | |
| CMacroBioData_UserObjectIter (const objects::CSeq_entry_Handle &entry) | |
| virtual | ~CMacroBioData_UserObjectIter () |
| virtual IMacroBioDataIter & | Begin (void) |
| virtual IMacroBioDataIter & | Next (void) |
| virtual bool | IsEnd (void) const |
| virtual bool | IsBegin (void) |
| virtual SConstScopedObject | GetScopedObject () const |
| Dereferences the underlying iterator. More... | |
| virtual string | GetBestDescr () const |
| Used for logging. More... | |
| virtual void | BuildEditedObject () |
| Creates a copy of the object that will be edited. More... | |
| virtual void | RunEditCommand (CMacroCmdComposite *cmd_composite) |
| Constructs and executes the editing command. More... | |
| virtual void | RunDeleteCommand (CMacroCmdComposite *cmd_composite) |
| Constructs and executes the delete command. More... | |
| Public Member Functions inherited from CMacroBioData_SeqdescIter | |
| CMacroBioData_SeqdescIter (const objects::CSeq_entry_Handle &entry) | |
| virtual | ~CMacroBioData_SeqdescIter () |
| virtual bool | IsDescriptor () const |
| virtual bool | IsFeature () const |
| virtual objects::CBioseq_Handle | GetBioseqHandle (void) const |
| Public Member Functions inherited from IMacroBioDataIter | |
| virtual | ~IMacroBioDataIter () |
| virtual size_t | GetCount () const |
| CObjectInfo | GetEditedObject () |
| void | RunCommand (CRef< CCmdComposite > cmd, CMacroCmdComposite *cmd_composite) |
| Method for executing a specific command. More... | |
| bool | IntendToDelete () const |
| virtual void | SetToDelete (bool intent) |
| bool | IsModified () const |
| void | SetModified () |
| bool | GetChoiceType (const string &field_name, string &choice_type) const |
| returns choice type string for a given identifier field_name More... | |
| virtual const vector< string > & | GetTaxnames () const |
| objects::CSeq_entry_Handle | GetSEH () const |
| bool | HasBeenCompleted () const |
| void | SetCompleted () |
| bool | IsSetSeqSubmit (void) const |
| const objects::CSeq_submit & | GetSeqSubmit (void) const |
| void | SetSeqSubmit (const objects::CSeq_submit &submit) |
| void | SetOutputStream (CNcbiOstream *str) |
| bool | IsSetOutputStream () const |
| CNcbiOstream & | GetOutputStream () const |
| void | SetTableToApply (const string &file_name, size_t match_col, const string &delimiter, bool merge_de, bool split_firstcol, bool convert_multi, bool merge_firstcols, bool multiple_sp_only) |
| const string & | GetTableName () const |
| string | GetValueFromTable (size_t col) |
| bool | FindInTable (const CMQueryNodeValue::TObs &objs, bool case_sensitive=true) |
| bool | FindInTable (const vector< string > &strs, bool case_sensitive=true) |
| string | GetUnMatchedTableEntries (int &count) |
| void | SetHugeDataMode (bool value) |
| bool | IsHugeDataMode () const |
| auto & | RemoteUpdater () |
| auto & | DOIUpdater () |
| auto & | ISOJTAUpdater () |
| bool | TopLevelObject () const |
| objects::CObject_id::TId & | MaxFeatureId () |
| void | SetHugeContext (const shared_ptr< CHugeMacroContext > &context) |
| 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 | x_SetDefaultObjectInfo () |
| Initializes member variable m_CurIterOI. More... | |
| Protected Member Functions inherited from CMacroBioData_SeqdescIter | |
| string | x_GetDescription (const string &descr_name) const |
| string | x_GetSeqId () const |
| Protected Member Functions inherited from IMacroBioDataIter | |
| IMacroBioDataIter (const objects::CSeq_entry_Handle &entry) | |
| void | x_Init () |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Protected Attributes | |
| CConstRef< objects::CUser_object > | m_OrigUserObj |
| CRef< objects::CUser_object > | m_EditedUserObj |
| CConstRef< objects::CUser_object > | m_FirstUserObj |
| Protected Attributes inherited from CMacroBioData_SeqdescIter | |
| objects::CBioseq_CI | m_SeqIter |
| objects::CSeq_entry_CI | m_SeqSetIter |
| > provides context information More... | |
| objects::CSeqdesc_CI | m_DescIter |
| Protected Attributes inherited from IMacroBioDataIter | |
| bool | m_Completed { false } |
| flag to be used by actions that need to be completed only once More... | |
| CObjectInfo | m_CurIterOI |
| objects::CSeq_entry_Handle | m_Seh |
| CConstRef< objects::CSeq_submit > | m_SeqSubmit |
| CNcbiOstream * | m_Ostream { nullptr } |
| bool | m_HugeData { false } |
| indicates that the data is large and some macros should take that into account (for example: taxlookup) More... | |
| shared_ptr< objects::edit::CRemoteUpdater > | m_RemoteUpdater |
| shared_ptr< CDoiLookupWithCache > | m_DOIUpdater |
| shared_ptr< CISOJTALookupWithCache > | m_ISOJTAUpdater |
| shared_ptr< CHugeMacroContext > | m_MacroContext |
| vector< string > | m_Taxnames |
| bool | m_DeleteObject |
| indicates the intention to delete the underlying object More... | |
| bool | m_Modified |
| indicates whether the edited object has been modified. When it's TRUE, call RunEditCommand() More... | |
| STableToApply | m_TableToApply |
Private Member Functions | |
| CMacroBioData_UserObjectIter (const CMacroBioData_UserObjectIter &) | |
| CMacroBioData_UserObjectIter & | operator= (const CMacroBioData_UserObjectIter &) |
Additional Inherited Members | |
| 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 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
CMacroBioData_UserObjectIter - iterates over all user objects in the seq-entry.
Definition at line 591 of file macro_biodata_iter.hpp.
The documentation for this class was generated from the following files:
- include/gui/objutils/macro_biodata_iter.hpp
- src/gui/objutils/macro_biodata_iter.cpp
