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CPhrap_Read Class Reference

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+ Inheritance diagram for CPhrap_Read:
+ Collaboration diagram for CPhrap_Read:

Classes

struct  SReadDS
 
struct  SReadTag
 

Public Types

typedef map< string, CRef< CPhrap_Read > > TReads
 
typedef vector< SReadTagTReadTags
 
typedef TSignedSeqPos TStart
 
typedef CRange< TSignedSeqPosTRange
 
- 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...
 

Public Member Functions

 CPhrap_Read (const string &name, TPhrapReaderFlags flags)
 
virtual ~CPhrap_Read (void)
 
void Read (CNcbiIstream &in)
 
void AddReadLoc (TSignedSeqPos start, bool complemented)
 
TStart GetStart (void) const
 
void ReadQuality (CNcbiIstream &in)
 
void ReadDS (CNcbiIstream &in)
 
virtual void ReadTag (CNcbiIstream &in, char tag)
 
CRef< CSeq_entryCreateRead (void) const
 
bool IsCircular (void) const
 
- 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 Member Functions

void x_CreateFeat (CBioseq &bioseq) const
 
void x_CreateDesc (CBioseq &bioseq) const
 
void x_AddTagFeats (CRef< CSeq_annot > &annot) const
 
void x_AddQualityFeat (CRef< CSeq_annot > &annot) const
 

Private Attributes

size_t m_NumInfoItems
 
size_t m_NumReadTags
 
TRange m_HiQualRange
 
TStart m_Start
 
SReadDSm_DS
 
TReadTags m_Tags
 

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...
 
- 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 402 of file phrap.cpp.

Member Typedef Documentation

◆ TRange

Definition at line 433 of file phrap.cpp.

◆ TReads

Definition at line 405 of file phrap.cpp.

◆ TReadTags

Definition at line 431 of file phrap.cpp.

◆ TStart

Definition at line 432 of file phrap.cpp.

Constructor & Destructor Documentation

◆ CPhrap_Read()

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

Definition at line 462 of file phrap.cpp.

◆ ~CPhrap_Read()

CPhrap_Read::~CPhrap_Read ( void  )
virtual

Definition at line 473 of file phrap.cpp.

References m_DS.

Member Function Documentation

◆ AddReadLoc()

void CPhrap_Read::AddReadLoc ( TSignedSeqPos  start,
bool  complemented 
)
inline

Definition at line 589 of file phrap.cpp.

References _ASSERT, m_Start, and CPhrap_Seq::SetComplemented().

◆ CreateRead()

CRef< CSeq_entry > CPhrap_Read::CreateRead ( void  ) const

◆ GetStart()

TStart CPhrap_Read::GetStart ( void  ) const
inline

◆ IsCircular()

bool CPhrap_Read::IsCircular ( void  ) const

Definition at line 489 of file phrap.cpp.

References CPhrap_Seq::GetAlignedFrom(), and m_Start.

◆ Read()

void CPhrap_Read::Read ( CNcbiIstream in)

Definition at line 481 of file phrap.cpp.

References CheckStreamState(), in(), m_NumInfoItems, m_NumReadTags, and CPhrap_Seq::Read().

◆ ReadDS()

void CPhrap_Read::ReadDS ( CNcbiIstream in)

◆ ReadQuality()

void CPhrap_Read::ReadQuality ( CNcbiIstream in)

◆ ReadTag()

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

◆ x_AddQualityFeat()

void CPhrap_Read::x_AddQualityFeat ( CRef< CSeq_annot > &  annot) const
private

◆ x_AddTagFeats()

void CPhrap_Read::x_AddTagFeats ( CRef< CSeq_annot > &  annot) const
private

◆ x_CreateDesc()

void CPhrap_Read::x_CreateDesc ( CBioseq bioseq) const
private

◆ x_CreateFeat()

void CPhrap_Read::x_CreateFeat ( CBioseq bioseq) const
private

Member Data Documentation

◆ m_DS

SReadDS* CPhrap_Read::m_DS
private

Definition at line 457 of file phrap.cpp.

Referenced by ReadDS(), x_CreateDesc(), and ~CPhrap_Read().

◆ m_HiQualRange

TRange CPhrap_Read::m_HiQualRange
private

Definition at line 455 of file phrap.cpp.

Referenced by ReadQuality(), and x_AddQualityFeat().

◆ m_NumInfoItems

size_t CPhrap_Read::m_NumInfoItems
private

Definition at line 453 of file phrap.cpp.

Referenced by Read().

◆ m_NumReadTags

size_t CPhrap_Read::m_NumReadTags
private

Definition at line 454 of file phrap.cpp.

Referenced by Read(), and x_AddTagFeats().

◆ m_Start

TStart CPhrap_Read::m_Start
private

Definition at line 456 of file phrap.cpp.

Referenced by AddReadLoc(), GetStart(), and IsCircular().

◆ m_Tags

TReadTags CPhrap_Read::m_Tags
private

Definition at line 458 of file phrap.cpp.

Referenced by ReadTag(), and x_AddTagFeats().


The documentation for this class was generated from the following file:
Modified on Mon Mar 04 05:14:05 2024 by modify_doxy.py rev. 669887