NCBI C++ ToolKit
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CRawSeqDBSource Class Reference

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+ Inheritance diagram for CRawSeqDBSource:
+ Collaboration diagram for CRawSeqDBSource:

Public Member Functions

 CRawSeqDBSource (const string &name, bool protein, CBuildDatabase *outdb)
 
virtual ~CRawSeqDBSource ()
 
virtual bool GetNext (CTempString &sequence, CTempString &ambiguities, CRef< CBlast_def_line_set > &deflines, vector< SBlastDbMaskData > &mask_range, vector< int > &column_ids, vector< CTempString > &column_blobs)
 
virtual void GetColumnNames (vector< string > &names)
 Get the names of all columns defined by this sequence source. More...
 
virtual int GetColumnId (const string &name)
 Get the column ID for a column mentioned by name. More...
 
virtual const map< string, string > & GetColumnMetaData (int id)
 Get metadata for the column with the specified Column ID. More...
 
void ClearSequence ()
 
- Public Member Functions inherited from IRawSequenceSource
virtual bool GetNext (CTempString &sequence, CTempString &ambiguities, CRef< objects::CBlast_def_line_set > &deflines, vector< SBlastDbMaskData > &mask_ranges, vector< int > &column_ids, vector< CTempString > &column_blobs)=0
 Get a raw sequence. 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
 

Private Attributes

CRef< CSeqDBExpertm_Source
 
const char * m_Sequence
 
int m_Oid
 
vector< CBlastDbBlobm_Blobs
 
vector< intm_ColumnIds
 
vector< stringm_ColumnNames
 
vector< intm_MaskIds
 
map< int, intm_MaskIdMap
 

Additional Inherited Members

- 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 CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 575 of file makeblastdb.cpp.

Constructor & Destructor Documentation

◆ CRawSeqDBSource()

CRawSeqDBSource::CRawSeqDBSource ( const string name,
bool  protein,
CBuildDatabase outdb 
)

◆ ~CRawSeqDBSource()

virtual CRawSeqDBSource::~CRawSeqDBSource ( )
inlinevirtual

Definition at line 579 of file makeblastdb.cpp.

References m_Sequence, m_Source, NULL, and CSeqDB::RetSequence().

Member Function Documentation

◆ ClearSequence()

void CRawSeqDBSource::ClearSequence ( )
inline

◆ GetColumnId()

virtual int CRawSeqDBSource::GetColumnId ( const string name)
inlinevirtual

Get the column ID for a column mentioned by name.

Parameters
nameThe name (column title) of the column. [in]
Returns
The corresponding Column-ID.

Implements IRawSequenceSource.

Definition at line 601 of file makeblastdb.cpp.

References CSeqDB::GetColumnId(), and m_Source.

◆ GetColumnMetaData()

virtual const map<string,string>& CRawSeqDBSource::GetColumnMetaData ( int  id)
inlinevirtual

Get metadata for the column with the specified Column ID.

Parameters
idThe column-id for which to get meta-data. [in]
Returns
All meta-data for this column-id.

Implements IRawSequenceSource.

Definition at line 606 of file makeblastdb.cpp.

References CSeqDB::GetColumnMetaData(), and m_Source.

◆ GetColumnNames()

virtual void CRawSeqDBSource::GetColumnNames ( vector< string > &  names)
inlinevirtual

Get the names of all columns defined by this sequence source.

Parameters
namesA list of column names. [out]

Implements IRawSequenceSource.

Definition at line 596 of file makeblastdb.cpp.

References m_ColumnNames, and names.

◆ GetNext()

bool CRawSeqDBSource::GetNext ( CTempString sequence,
CTempString ambiguities,
CRef< CBlast_def_line_set > &  deflines,
vector< SBlastDbMaskData > &  mask_range,
vector< int > &  column_ids,
vector< CTempString > &  column_blobs 
)
virtual

Member Data Documentation

◆ m_Blobs

vector<CBlastDbBlob> CRawSeqDBSource::m_Blobs
private

Definition at line 626 of file makeblastdb.cpp.

Referenced by GetNext().

◆ m_ColumnIds

vector<int> CRawSeqDBSource::m_ColumnIds
private

Definition at line 627 of file makeblastdb.cpp.

Referenced by CRawSeqDBSource(), and GetNext().

◆ m_ColumnNames

vector<string> CRawSeqDBSource::m_ColumnNames
private

Definition at line 628 of file makeblastdb.cpp.

Referenced by CRawSeqDBSource(), and GetColumnNames().

◆ m_MaskIdMap

map<int, int> CRawSeqDBSource::m_MaskIdMap
private

Definition at line 630 of file makeblastdb.cpp.

Referenced by CRawSeqDBSource(), and GetNext().

◆ m_MaskIds

vector<int> CRawSeqDBSource::m_MaskIds
private

Definition at line 629 of file makeblastdb.cpp.

Referenced by CRawSeqDBSource(), and GetNext().

◆ m_Oid

int CRawSeqDBSource::m_Oid
private

Definition at line 623 of file makeblastdb.cpp.

Referenced by GetNext().

◆ m_Sequence

const char* CRawSeqDBSource::m_Sequence
private

Definition at line 622 of file makeblastdb.cpp.

Referenced by ClearSequence(), GetNext(), and ~CRawSeqDBSource().

◆ m_Source

CRef<CSeqDBExpert> CRawSeqDBSource::m_Source
private

The documentation for this class was generated from the following file:
Modified on Wed Apr 17 13:10:49 2024 by modify_doxy.py rev. 669887