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CSequenceIStream::CSeqData Struct Reference

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Type containing the sequence itself along with the masking information. More...

#include <algo/blast/dbindex/sequence_istream.hpp>

+ Inheritance diagram for CSequenceIStream::CSeqData:
+ Collaboration diagram for CSequenceIStream::CSeqData:

Public Types

typedef std::vector< CConstRef< objects::CSeq_loc > > TMask
 Type representing masked portions of a sequence. More...
 
- 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

 CSeqData ()
 Object constructor. More...
 
 operator bool () const
 Conversion to bool. More...
 
- 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

CRef< objects::CSeq_entry > seq_entry_
 Sequence data. More...
 
TMask mask_locs_
 Masked portion of the sequence. More...
 

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

Type containing the sequence itself along with the masking information.

Definition at line 57 of file sequence_istream.hpp.

Member Typedef Documentation

typedef std::vector< CConstRef< objects::CSeq_loc > > CSequenceIStream::CSeqData::TMask

Type representing masked portions of a sequence.

Definition at line 60 of file sequence_istream.hpp.

Constructor & Destructor Documentation

CSequenceIStream::CSeqData::CSeqData ( )
inline

Object constructor.

Definition at line 66 of file sequence_istream.hpp.

Member Function Documentation

CSequenceIStream::CSeqData::operator bool ( ) const
inline

Conversion to bool.

Returns
true if the object contains a valid sequence; false otherwise

Definition at line 74 of file sequence_istream.hpp.

References CRef< C, Locker >::GetPointerOrNull().

Member Data Documentation

TMask CSequenceIStream::CSeqData::mask_locs_
mutable

Masked portion of the sequence.

Definition at line 63 of file sequence_istream.hpp.

Referenced by CSubjectMap_Factory_Base::NewSequenceInit(), CSequenceIStreamBlastDB::next(), and CSequenceIStreamFasta::next().

CRef< objects::CSeq_entry > CSequenceIStream::CSeqData::seq_entry_

The documentation for this struct was generated from the following file:
Modified on Fri Apr 20 12:41:26 2018 by modify_doxy.py rev. 546573