Search Toolkit Book for CCompartApp::CCompartment
#include "compart.hpp"
(Private to src/app/compart.)
Inheritance diagram for CCompartApp::CCompartment:
Collaboration diagram for CCompartApp::CCompartment:
Public Types | |
| typedef pair< THit::TCoord, THit::TCoord > | TRange |
| 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... | |
Public Member Functions | |
| CCompartment (const THitRefs &hitrefs, size_t length) | |
| TRange | GetSpan (void) const |
| bool | GetStrand (void) const |
| bool | operator< (const CCompartment &rhs) const |
| size_t | GetIdentityBin (void) const |
| size_t | GetExonCount (void) const |
| size_t | GetMatchCount (void) const |
| size_t | GetHitCount (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 |
Protected Member Functions | |
| void | x_AddHit (const THitRef &hitref) |
| void | x_EvalExons (void) |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Protected Attributes | |
| THitRefs | m_HitRefs |
| size_t | m_SeqLength |
| size_t | m_IdentityBin |
| size_t | m_ExonCount |
| size_t | m_MatchCount |
Friends | |
| ostream & | operator<< (ostream &ostr, const CCompartment &rhs) |
Additional Inherited Members | |
| 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
Definition at line 58 of file compart.hpp.
Member Typedef Documentation
◆ TRange
| typedef pair<THit::TCoord, THit::TCoord> CCompartApp::CCompartment::TRange |
Definition at line 63 of file compart.hpp.
Constructor & Destructor Documentation
◆ CCompartment()
Definition at line 518 of file compart.cpp.
References eUnknown, NCBI_THROW, x_AddHit(), and x_EvalExons().
Member Function Documentation
◆ GetExonCount()
|
inline |
Definition at line 73 of file compart.hpp.
References m_ExonCount.
◆ GetHitCount()
|
inline |
Definition at line 81 of file compart.hpp.
References m_HitRefs.
◆ GetIdentityBin()
|
inline |
Definition at line 69 of file compart.hpp.
References m_IdentityBin.
◆ GetMatchCount()
|
inline |
Definition at line 77 of file compart.hpp.
References m_MatchCount.
◆ GetSpan()
| CCompartApp::CCompartment::TRange CCompartApp::CCompartment::GetSpan | ( | void | ) | const |
Definition at line 502 of file compart.cpp.
References a, b, eUnknown, m_HitRefs, and NCBI_THROW.
Referenced by operator<().
◆ GetStrand()
| bool CCompartApp::CCompartment::GetStrand | ( | void | ) | const |
Definition at line 552 of file compart.cpp.
References eUnknown, and NCBI_THROW.
Referenced by operator<().
◆ operator<()
| bool CCompartApp::CCompartment::operator< | ( | const CCompartment & | rhs | ) | const |
Definition at line 562 of file compart.cpp.
References GetSpan(), GetStrand(), GetStrand(), and m_HitRefs.
◆ x_AddHit()
Definition at line 533 of file compart.cpp.
References eUnknown, and NCBI_THROW.
Referenced by CCompartment().
◆ x_EvalExons()
|
protected |
Definition at line 611 of file compart.cpp.
References GetStrand(), ITERATE, max(), prev(), and round().
Referenced by CCompartment().
Friends And Related Function Documentation
◆ operator<<
|
friend |
Definition at line 676 of file compart.cpp.
Member Data Documentation
◆ m_ExonCount
|
protected |
Definition at line 94 of file compart.hpp.
Referenced by GetExonCount().
◆ m_HitRefs
|
protected |
Definition at line 89 of file compart.hpp.
Referenced by GetHitCount(), GetSpan(), operator<(), and operator<<().
◆ m_IdentityBin
|
protected |
Definition at line 93 of file compart.hpp.
Referenced by GetIdentityBin().
◆ m_MatchCount
|
protected |
Definition at line 95 of file compart.hpp.
Referenced by GetMatchCount().
◆ m_SeqLength
|
protected |
Definition at line 91 of file compart.hpp.
The documentation for this class was generated from the following files:
- src/app/compart/compart.hpp
- src/app/compart/compart.cpp
