Search Toolkit Book for CBioseqGaps_CI
This iterates over the runs of Ns of each sequence. More...
#include <objmgr/util/sequence.hpp>
Inheritance diagram for CBioseqGaps_CI:
Collaboration diagram for CBioseqGaps_CI:
Classes | |
| struct | Params |
| The params that control the behavior of CBioseqGaps_CI. More... | |
| struct | SCurrentGapInfo |
| This indicates the state of the iterator right now. More... | |
Public Member Functions | |
| CBioseqGaps_CI (const CSeq_entry_Handle &entry_h, const Params ¶ms=Params()) | |
| This constructor initializes the iterator. More... | |
| CBioseqGaps_CI & | operator++ (void) |
| Move the iterator forward to next gap (or the end, if there are no more to return) More... | |
| DECLARE_OPERATOR_BOOL (m_bioseq_CI) | |
| const SCurrentGapInfo & | operator* (void) const |
| Get information about the gap we're currently on. More... | |
| const SCurrentGapInfo * | operator-> (void) const |
| Get information about the gap we're currently on. More... | |
| 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 Types | |
| enum | EFindNext { eFindNext_NotFound , eFindNext_Found } |
| This indicates what happened when we tried to run x_FindNextGapOnBioseq. More... | |
Protected Member Functions | |
| virtual const SCurrentGapInfo & | x_GetCurrent (void) const |
| This gives info on the gap we're currently on. More... | |
| virtual void | x_Next (void) |
| This moves this iterator to the next relevant gap. More... | |
| virtual void | x_NextBioseq (void) |
| This advances m_bioseq_CI although it has extra logic to terminate m_bioseq_CI if we've exceeded the number of bioseqs we can look for. More... | |
| virtual EFindNext | x_FindNextGapOnBioseq (const CBioseq_Handle &bioseq_h, const TSeqPos pos_to_start_looking, TSeqPos &out_pos_of_gap, TSeqPos &out_len_of_gap) const |
| This finds the next gap on the bioseq, starting at given pos. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Protected Attributes | |
| CBioseq_CI | m_bioseq_CI |
| This points to the bioseq we're currently on. More... | |
| SCurrentGapInfo | m_infoOnCurrentGap |
| This indicates information about the gap we're currently on. More... | |
| Params | m_Params |
| This holds the params the caller gave when this object was initially created. More... | |
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
This iterates over the runs of Ns of each sequence.
Definition at line 1572 of file sequence.hpp.
The documentation for this class was generated from the following files:
- include/objmgr/util/sequence.hpp
- src/objmgr/util/bioseqgaps_ci.cpp
