Search Toolkit Book for CAlnMap::CAlnChunkVec
#include <objtools/alnmgr/alnmap.hpp>
Inheritance diagram for CAlnMap::CAlnChunkVec:
Collaboration diagram for CAlnMap::CAlnChunkVec:
Public Member Functions | |
| CAlnChunkVec (const CAlnMap &aln_map, TNumrow row) | |
| CConstRef< CAlnChunk > | operator[] (TNumchunk i) const |
| TNumchunk | size (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 | |
| CAlnChunkVec (void) | |
Private Attributes | |
| const CAlnMap & | m_AlnMap |
| TNumrow | m_Row |
| vector< TNumseg > | m_StartSegs |
| vector< TNumseg > | m_StopSegs |
| TSeqPos | m_LeftDelta |
| TSeqPos | m_RightDelta |
Friends | |
| CRef< CAlnChunkVec > | CAlnMap::GetAlnChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags) const |
| CRef< CAlnChunkVec > | CAlnMap::GetSeqChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags) const |
| void | CAlnMap::x_GetChunks (CAlnChunkVec *vec, TNumrow row, TNumseg left_seg, TNumseg right_seg, TGetChunkFlags flags) const |
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 247 of file alnmap.hpp.
Constructor & Destructor Documentation
◆ CAlnChunkVec() [1/2]
Definition at line 250 of file alnmap.hpp.
◆ CAlnChunkVec() [2/2]
|
private |
Member Function Documentation
◆ operator[]()
| CConstRef< CAlnMap::CAlnChunk > CAlnMap::CAlnChunkVec::operator[] | ( | CAlnMap::TNumchunk | i | ) | const |
Definition at line 1210 of file alnmap.cpp.
References CAlnMap::fEndOnLeft, CAlnMap::fEndOnRight, CAlnMap::fInsert, CAlnMap::fNoSeqOnLeft, CAlnMap::fNoSeqOnRight, CAlnMap::fNotAlignedToSeqOnAnchor, CAlnMap::fSeq, CAlnMap::fUnaligned, CAlnMap::fUnalignedOnLeft, CAlnMap::fUnalignedOnRight, CAlnMap::CNumSegWithOffset::GetAlnSeg(), CAlnMap::GetAlnStart(), CAlnMap::GetAlnStop(), CAlnMap::CNumSegWithOffset::GetOffset(), CAlnMap::GetWidth(), i, CAlnMap::IsPositiveStrand(), m_AlnMap, m_LeftDelta, CAlnMap::m_NumRows, CAlnMap::m_NumSegs, m_RightDelta, m_Row, CAlnMap::m_Starts, m_StartSegs, m_StopSegs, size(), type, CAlnMap::x_GetLen(), CAlnMap::x_GetRawSegType(), and CAlnMap::x_GetSegFromRawSeg().
◆ size()
|
inline |
Friends And Related Function Documentation
◆ CAlnMap::GetAlnChunks
|
friend |
◆ CAlnMap::GetSeqChunks
|
friend |
◆ CAlnMap::x_GetChunks
|
friend |
Member Data Documentation
◆ m_AlnMap
Definition at line 285 of file alnmap.hpp.
Referenced by operator[]().
◆ m_LeftDelta
|
private |
Definition at line 289 of file alnmap.hpp.
Referenced by operator[](), and CAlnMap::x_GetChunks().
◆ m_RightDelta
|
private |
Definition at line 290 of file alnmap.hpp.
Referenced by operator[](), and CAlnMap::x_GetChunks().
◆ m_Row
|
private |
Definition at line 286 of file alnmap.hpp.
Referenced by operator[]().
◆ m_StartSegs
|
private |
Definition at line 287 of file alnmap.hpp.
Referenced by operator[](), size(), and CAlnMap::x_GetChunks().
◆ m_StopSegs
|
private |
Definition at line 288 of file alnmap.hpp.
Referenced by operator[](), and CAlnMap::x_GetChunks().
The documentation for this class was generated from the following files:
- include/objtools/alnmgr/alnmap.hpp
- src/objtools/alnmgr/alnmap.cpp
