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CPhrap_Seq Class Referenceabstract

Search Toolkit Book for CPhrap_Seq

+ Inheritance diagram for CPhrap_Seq:
+ Collaboration diagram for CPhrap_Seq:

Public Types

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_Seq (TPhrapReaderFlags flags)
 CPhrap_Seq (const string &name, TPhrapReaderFlags flags)
virtual ~CPhrap_Seq (void)
void Read (CNcbiIstream &in)
void ReadData (CNcbiIstream &in)
virtual void ReadTag (CNcbiIstream &in, char tag)=0
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

Protected Member Functions

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...

Private Member Functions

void x_FillSeqData (CSeq_data &data) const
void CopyFrom (CPhrap_Seq &seq)

Private Attributes

TPhrapReaderFlags m_Flags
string m_Name
TSeqPos m_PaddedLength
TSeqPos m_UnpaddedLength
string m_Data
TPadMap m_PadMap
bool m_Complemented
TSeqPos m_AlignedFrom
TSeqPos m_AlignedTo
CRef< CSeq_idm_Id


class CPhrap_Sequence

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 105 of file phrap.cpp.

Member Typedef Documentation

◆ TPadMap

Definition at line 145 of file phrap.cpp.

Constructor & Destructor Documentation

◆ CPhrap_Seq() [1/2]

CPhrap_Seq::CPhrap_Seq ( TPhrapReaderFlags  flags)

Definition at line 182 of file phrap.cpp.

◆ CPhrap_Seq() [2/2]

CPhrap_Seq::CPhrap_Seq ( const string name,
TPhrapReaderFlags  flags 

Definition at line 193 of file phrap.cpp.

◆ ~CPhrap_Seq()

virtual CPhrap_Seq::~CPhrap_Seq ( void  )

Definition at line 110 of file phrap.cpp.

Member Function Documentation

◆ CopyFrom()

void CPhrap_Seq::CopyFrom ( CPhrap_Seq seq)

◆ CreateBioseq()

CRef< CBioseq > CPhrap_Seq::CreateBioseq ( void  ) const

◆ CreateComplementedDescr()

void CPhrap_Seq::CreateComplementedDescr ( CRef< CSeq_descr > &  descr) const

◆ CreatePadsFeat()

void CPhrap_Seq::CreatePadsFeat ( CRef< CSeq_annot > &  annot) const

◆ FlagSet()

bool CPhrap_Seq::FlagSet ( EPhrapReaderFlags  value) const

◆ GetAlignedFrom()

TSeqPos CPhrap_Seq::GetAlignedFrom ( void  ) const

◆ GetAlignedTo()

TSeqPos CPhrap_Seq::GetAlignedTo ( void  ) const

Definition at line 149 of file phrap.cpp.

References m_AlignedTo.

Referenced by CPhrap_Contig::x_AddAlignRanges(), and CPhrap_Read::x_AddQualityFeat().

◆ GetData()

const string& CPhrap_Seq::GetData ( void  ) const

Definition at line 136 of file phrap.cpp.

References m_Data.

◆ GetFlags()

TPhrapReaderFlags CPhrap_Seq::GetFlags ( void  ) const

◆ GetId()

CRef< CSeq_id > CPhrap_Seq::GetId ( void  ) const

◆ GetName()

const string& CPhrap_Seq::GetName ( void  ) const

◆ GetPaddedLength()

TSeqPos CPhrap_Seq::GetPaddedLength ( void  ) const

◆ GetPaddedPos()

TSeqPos CPhrap_Seq::GetPaddedPos ( TSeqPos  unpadded) const

◆ GetPadMap()

const TPadMap& CPhrap_Seq::GetPadMap ( void  ) const

Definition at line 146 of file phrap.cpp.

References m_PadMap.

Referenced by CPhrap_Contig::x_AddAlignRanges().

◆ GetUnpaddedLength()

TSeqPos CPhrap_Seq::GetUnpaddedLength ( void  ) const

◆ GetUnpaddedPos()

TSeqPos CPhrap_Seq::GetUnpaddedPos ( TSeqPos  padded,
TSeqPos link = 0 
) const

◆ IsComplemented()

bool CPhrap_Seq::IsComplemented ( void  ) const

◆ Read()

void CPhrap_Seq::Read ( CNcbiIstream in)

Definition at line 222 of file phrap.cpp.

References CheckStreamState(), in(), m_Name, and m_PaddedLength.

Referenced by CPhrap_Read::Read(), and CPhrap_Contig::Read().

◆ ReadData()

void CPhrap_Seq::ReadData ( CNcbiIstream in)

◆ ReadTag()

virtual void CPhrap_Seq::ReadTag ( CNcbiIstream in,
char  tag 
pure virtual

◆ SetAligned()

void CPhrap_Seq::SetAligned ( TSeqPos  from,
TSeqPos  to 

Definition at line 154 of file phrap.cpp.

References m_AlignedFrom, and m_AlignedTo.

Referenced by CPhrap_Read::ReadQuality().

◆ SetComplemented()

void CPhrap_Seq::SetComplemented ( bool  value)

◆ x_FillSeqData()

void CPhrap_Seq::x_FillSeqData ( CSeq_data data) const

Friends And Related Function Documentation

◆ CPhrap_Sequence

friend class CPhrap_Sequence

Definition at line 163 of file phrap.cpp.

Member Data Documentation

◆ m_AlignedFrom

TSeqPos CPhrap_Seq::m_AlignedFrom

Definition at line 174 of file phrap.cpp.

Referenced by CopyFrom(), GetAlignedFrom(), and SetAligned().

◆ m_AlignedTo

TSeqPos CPhrap_Seq::m_AlignedTo

Definition at line 175 of file phrap.cpp.

Referenced by CopyFrom(), GetAlignedTo(), ReadData(), and SetAligned().

◆ m_Complemented

bool CPhrap_Seq::m_Complemented

Definition at line 173 of file phrap.cpp.

Referenced by CopyFrom(), CreateComplementedDescr(), IsComplemented(), and SetComplemented().

◆ m_Data

string CPhrap_Seq::m_Data

Definition at line 171 of file phrap.cpp.

Referenced by CopyFrom(), GetData(), ReadData(), and x_FillSeqData().

◆ m_Flags

TPhrapReaderFlags CPhrap_Seq::m_Flags

Definition at line 166 of file phrap.cpp.

Referenced by CopyFrom(), FlagSet(), GetFlags(), and ReadData().

◆ m_Id

CRef<CSeq_id> CPhrap_Seq::m_Id

Definition at line 176 of file phrap.cpp.

Referenced by CopyFrom(), and GetId().

◆ m_Name

string CPhrap_Seq::m_Name

Definition at line 168 of file phrap.cpp.

Referenced by CopyFrom(), CreatePadsFeat(), GetId(), GetName(), Read(), and ReadData().

◆ m_PaddedLength

TSeqPos CPhrap_Seq::m_PaddedLength

Definition at line 169 of file phrap.cpp.

Referenced by CopyFrom(), GetPaddedLength(), Read(), and ReadData().

◆ m_PadMap

TPadMap CPhrap_Seq::m_PadMap

Definition at line 172 of file phrap.cpp.

Referenced by CopyFrom(), CreatePadsFeat(), GetPaddedPos(), GetPadMap(), GetUnpaddedPos(), and ReadData().

◆ m_UnpaddedLength

TSeqPos CPhrap_Seq::m_UnpaddedLength

Definition at line 170 of file phrap.cpp.

Referenced by CopyFrom(), CreateBioseq(), GetUnpaddedLength(), ReadData(), and x_FillSeqData().

The documentation for this class was generated from the following file:
Modified on Thu Apr 11 15:13:50 2024 by rev. 669887