Search Toolkit Book for CGather_Iter
#include <objtools/format/gather_iter.hpp>
Inheritance diagram for CGather_Iter:
Collaboration diagram for CGather_Iter:
Public Member Functions | |
| CGather_Iter (const CSeq_entry_Handle &top_seq_entry, const CFlatFileConfig &config) | |
| operator bool (void) const | |
| CGather_Iter & | operator++ (void) |
| const CBioseq_Handle & | operator* (void) const |
| 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 |
Private Member Functions | |
| bool | x_AddSeqEntryToStack (const CSeq_entry_Handle &seq_entry) |
| bool | x_IsBioseqHandleOkay (const CBioseq_Handle &bioseq) |
Private Attributes | |
| std::vector< CSeq_entry_CI > | m_SeqEntryIterStack |
| unique_ptr< CBioseq_CI > | m_BioseqIter |
| const CFlatFileConfig & | m_Config |
| bool | x_found |
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... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Detailed Description
Definition at line 52 of file gather_iter.hpp.
Constructor & Destructor Documentation
◆ CGather_Iter()
| CGather_Iter::CGather_Iter | ( | const CSeq_entry_Handle & | top_seq_entry, |
| const CFlatFileConfig & | config | ||
| ) |
Definition at line 47 of file gather_iter.cpp.
Member Function Documentation
◆ operator bool()
| CGather_Iter::operator bool | ( | void | ) | const |
Definition at line 56 of file gather_iter.cpp.
◆ operator*()
| const CBioseq_Handle & CGather_Iter::operator* | ( | void | ) | const |
Definition at line 96 of file gather_iter.cpp.
References _ASSERT, and m_BioseqIter.
◆ operator++()
| CGather_Iter & CGather_Iter::operator++ | ( | void | ) |
Definition at line 62 of file gather_iter.cpp.
References _ASSERT, m_BioseqIter, m_SeqEntryIterStack, x_AddSeqEntryToStack(), and x_IsBioseqHandleOkay().
◆ x_AddSeqEntryToStack()
|
private |
Definition at line 102 of file gather_iter.cpp.
References _ASSERT, CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_mut_set, CBioseq_set_Base::eClass_phy_set, CBioseq_set_Base::eClass_pop_set, CBioseq_set_Base::eClass_wgs_set, CBioseq_CI::eLevel_Mains, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), CFlatFileConfig::IsViewAll(), CFlatFileConfig::IsViewFirst(), CFlatFileConfig::IsViewNuc(), CFlatFileConfig::IsViewProt(), m_BioseqIter, m_Config, m_SeqEntryIterStack, x_found, and x_IsBioseqHandleOkay().
Referenced by operator++().
◆ x_IsBioseqHandleOkay()
|
private |
Definition at line 159 of file gather_iter.cpp.
References eGetId_Best, GetId(), m_Config, and CFlatFileConfig::SuppressLocalId().
Referenced by operator++(), and x_AddSeqEntryToStack().
Member Data Documentation
◆ m_BioseqIter
|
private |
Definition at line 78 of file gather_iter.hpp.
Referenced by operator*(), operator++(), and x_AddSeqEntryToStack().
◆ m_Config
|
private |
Definition at line 80 of file gather_iter.hpp.
Referenced by x_AddSeqEntryToStack(), and x_IsBioseqHandleOkay().
◆ m_SeqEntryIterStack
|
private |
Definition at line 77 of file gather_iter.hpp.
Referenced by operator++(), and x_AddSeqEntryToStack().
◆ x_found
|
private |
Definition at line 92 of file gather_iter.hpp.
Referenced by x_AddSeqEntryToStack().
The documentation for this class was generated from the following files:
- include/objtools/format/gather_iter.hpp
- src/objtools/format/gather_iter.cpp
