NCBI C++ ToolKit
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CPhrap_Sequence Class Reference

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+ Inheritance diagram for CPhrap_Sequence:
+ Collaboration diagram for CPhrap_Sequence:

Public Member Functions

 CPhrap_Sequence (const string &name, TPhrapReaderFlags flags)
 
virtual void ReadTag (CNcbiIstream &in, char tag)
 
bool IsContig (void) const
 
CRef< CPhrap_ContigGetContig (void)
 
bool IsRead (void) const
 
CRef< CPhrap_ReadGetRead (void)
 
void SetRead (CPhrap_Read &read)
 
- Public Member Functions inherited from CPhrap_Seq
 CPhrap_Seq (TPhrapReaderFlags flags)
 
 CPhrap_Seq (const string &name, TPhrapReaderFlags flags)
 
virtual ~CPhrap_Seq (void)
 
void Read (CNcbiIstream &in)
 
void ReadData (CNcbiIstream &in)
 
void SetComplemented (bool value)
 
bool IsComplemented (void) const
 
TPhrapReaderFlags GetFlags (void) const
 
bool FlagSet (EPhrapReaderFlags value) const
 
const stringGetName (void) const
 
TSeqPos GetPaddedLength (void) const
 
TSeqPos GetUnpaddedLength (void) const
 
const stringGetData (void) const
 
CRef< CSeq_idGetId (void) const
 
TSeqPos GetPaddedPos (TSeqPos unpadded) const
 
TSeqPos GetUnpaddedPos (TSeqPos padded, TSeqPos *link=0) const
 
CRef< CBioseqCreateBioseq (void) const
 
const TPadMapGetPadMap (void) const
 
TSeqPos GetAlignedFrom (void) const
 
TSeqPos GetAlignedTo (void) const
 
- 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
 

Private Attributes

CRef< CPhrap_Seqm_Seq
 

Additional Inherited Members

- Public Types inherited from CPhrap_Seq
typedef map< TSeqPos, TSeqPosTPadMap
 
- 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< Uint8TCounter
 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 CPhrap_Seq
void CreateComplementedDescr (CRef< CSeq_descr > &descr) const
 
void CreatePadsFeat (CRef< CSeq_annot > &annot) const
 
void SetAligned (TSeqPos from, TSeqPos to)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 1607 of file phrap.cpp.

Constructor & Destructor Documentation

◆ CPhrap_Sequence()

CPhrap_Sequence::CPhrap_Sequence ( const string name,
TPhrapReaderFlags  flags 
)

Definition at line 1626 of file phrap.cpp.

References IsOldComplementedName(), and CPhrap_Seq::SetComplemented().

Member Function Documentation

◆ GetContig()

CRef< CPhrap_Contig > CPhrap_Sequence::GetContig ( void  )

◆ GetRead()

CRef< CPhrap_Read > CPhrap_Sequence::GetRead ( void  )

◆ IsContig()

bool CPhrap_Sequence::IsContig ( void  ) const

◆ IsRead()

bool CPhrap_Sequence::IsRead ( void  ) const

◆ ReadTag()

void CPhrap_Sequence::ReadTag ( CNcbiIstream in,
char  tag 
)
virtual

Implements CPhrap_Seq.

Definition at line 1636 of file phrap.cpp.

References CT_POS_TYPE, in(), and NCBI_THROW2.

◆ SetRead()

void CPhrap_Sequence::SetRead ( CPhrap_Read read)

Member Data Documentation

◆ m_Seq

CRef<CPhrap_Seq> CPhrap_Sequence::m_Seq
mutableprivate

Definition at line 1622 of file phrap.cpp.

Referenced by GetContig(), GetRead(), IsContig(), IsRead(), and SetRead().


The documentation for this class was generated from the following file:
Modified on Wed Feb 21 09:57:15 2024 by modify_doxy.py rev. 669887