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CMacroBioData_SeqIter Class Reference

Search Toolkit Book for CMacroBioData_SeqIter

CMacroBioData_SeqIter- iterates over sequences (na and aa) More...

#include <gui/objutils/macro_biodata_iter.hpp>

+ Inheritance diagram for CMacroBioData_SeqIter:
+ Collaboration diagram for CMacroBioData_SeqIter:

Public Member Functions

virtual ~CMacroBioData_SeqIter ()
virtual IMacroBioDataIterBegin (void)
virtual IMacroBioDataIterNext (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...
virtual bool IsDescriptor () const
virtual bool IsFeature () const
virtual objects::CBioseq_Handle GetBioseqHandle (void) const
const objects::CAutoDefOptions & GetAutodefOptions () const
objects::CAutoDefOptions & SetAutodefOptions ()
- 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
CNcbiOstreamGetOutputStream () 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 stringGetTableName () 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...
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

Static Public Member Functions

static CMacroBioData_SeqIters_MakeSeqIterator (const objects::CSeq_entry_Handle &entry, objects::CSeq_inst::EMol mol_type)
- 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)

Protected Member Functions

virtual void x_SetDefaultObjectInfo ()
 Initializes member variable m_CurIterOI. More...
 CMacroBioData_SeqIter (const objects::CSeq_entry_Handle &entry)
- 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

objects::CBioseq_CI m_SeqIter
CConstRef< objects::CBioseq > m_OrigSeq
CRef< objects::CSeq_entry > m_EditedEntry
CRef< objects::CBioseq > m_EditedSeq
objects::CAutoDefOptions m_AutodefOptions
- 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
CNcbiOstreamm_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< CDoiLookupWithCachem_DOIUpdater
shared_ptr< CISOJTALookupWithCachem_ISOJTAUpdater
shared_ptr< CHugeMacroContextm_MacroContext
vector< stringm_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_SeqIter (const CMacroBioData_SeqIter &)
CMacroBioData_SeqIteroperator= (const CMacroBioData_SeqIter &)

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< Uint8TCounter
 Counter type is CAtomiCounter. More...
typedef Uint8 TCount
 Alias for value type of counter. More...
- 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_SeqIter- iterates over sequences (na and aa)

Definition at line 730 of file macro_biodata_iter.hpp.

The documentation for this class was generated from the following files:
Modified on Thu Dec 07 10:12:34 2023 by rev. 669887