NCBI C++ ToolKit
Public Types | Public Member Functions | Public Attributes | Private Member Functions | List of all members
CFastaReader::SGap Struct Reference

Search Toolkit Book for CFastaReader::SGap

#include <objtools/readers/fasta.hpp>

+ Inheritance diagram for CFastaReader::SGap:
+ Collaboration diagram for CFastaReader::SGap:

Public Types

enum  EKnownSize { eKnownSize_No, eKnownSize_Yes }
 
typedef CObjectFor< CSeq_gap::ETypeTGapTypeObj
 
typedef CConstRef< TGapTypeObjTNullableGapType
 
typedef set< CLinkage_evidence::ETypeTLinkEvidSet
 
- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 SGap (TSeqPos pos, TSignedSeqPos len, EKnownSize eKnownSize, TSeqPos uLineNumber, TNullableGapType pGapType=TNullableGapType(), const set< CLinkage_evidence::EType > &setOfLinkageEvidence=set< CLinkage_evidence::EType >())
 
- 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
 

Public Attributes

const TSeqPos m_uPos
 
const TSeqPos m_uLen
 
const EKnownSize m_eKnownSize
 
const TSeqPos m_uLineNumber
 
const TNullableGapType m_pGapType
 
const TLinkEvidSet m_setOfLinkageEvidence
 

Private Member Functions

SGapoperator= (const SGap &)
 
 SGap (const SGap &rhs)
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 307 of file fasta.hpp.

Member Typedef Documentation

Definition at line 316 of file fasta.hpp.

Definition at line 340 of file fasta.hpp.

Definition at line 317 of file fasta.hpp.

Constructor & Destructor Documentation

CFastaReader::SGap::SGap ( TSeqPos  pos,
TSignedSeqPos  len,
EKnownSize  eKnownSize,
TSeqPos  uLineNumber,
TNullableGapType  pGapType = TNullableGapType(),
const set< CLinkage_evidence::EType > &  setOfLinkageEvidence = set<CLinkage_evidence::EType>() 
)

Definition at line 2218 of file fasta.cpp.

CFastaReader::SGap::SGap ( const SGap rhs)
private

Member Function Documentation

SGap& CFastaReader::SGap::operator= ( const SGap )
private

Member Data Documentation

const EKnownSize CFastaReader::SGap::m_eKnownSize

Definition at line 336 of file fasta.hpp.

const TNullableGapType CFastaReader::SGap::m_pGapType

Definition at line 339 of file fasta.hpp.

const TLinkEvidSet CFastaReader::SGap::m_setOfLinkageEvidence

Definition at line 341 of file fasta.hpp.

const TSeqPos CFastaReader::SGap::m_uLen

Definition at line 335 of file fasta.hpp.

const TSeqPos CFastaReader::SGap::m_uLineNumber

Definition at line 337 of file fasta.hpp.

const TSeqPos CFastaReader::SGap::m_uPos

Definition at line 332 of file fasta.hpp.


The documentation for this struct was generated from the following files:
Modified on Wed Apr 26 17:44:49 2017 by modify_doxy.py rev. 533848