Search Toolkit Book for IRawSequenceSource

Interface to a source of raw sequence data. More...

#include <objtools/blast/seqdb_writer/build_db.hpp>

Inheritance diagram for IRawSequenceSource:

Collaboration diagram for IRawSequenceSource:

Public Member Functions
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...

virtual void	GetColumnNames (vector< string > &names)=0
	Get the names of all columns defined by this sequence source. More...

virtual int	GetColumnId (const string &name)=0
	Get the column ID for a column mentioned by name. More...

virtual const map< string, string > &	GetColumnMetaData (int id)=0
	Get metadata for the column with the specified Column ID. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (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

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< Uint8 >	TCounter
	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

Interface to a source of raw sequence data.

This interface provides raw data, including column data, from a BlastDB-like data source.

Definition at line 70 of file build_db.hpp.

Member Function Documentation

◆ GetColumnId()

virtual int IRawSequenceSource::GetColumnId ( const string & name )

pure virtual

Get the column ID for a column mentioned by name.

Parameters

name	The name (column title) of the column. [in]

Returns: The corresponding Column-ID.

Implemented in CClusterDBSource, and CRawSeqDBSource.

Referenced by CBuildDatabase::AddSequences().

◆ GetColumnMetaData()

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

pure virtual

Get metadata for the column with the specified Column ID.

Parameters

id	The column-id for which to get meta-data. [in]

Returns: All meta-data for this column-id.

Implemented in CClusterDBSource, and CRawSeqDBSource.

Referenced by CBuildDatabase::AddSequences().

◆ GetColumnNames()

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

pure virtual

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

Parameters

names A list of column names. [out]

Implemented in CClusterDBSource, and CRawSeqDBSource.

Referenced by CBuildDatabase::AddSequences().

◆ GetNext()

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

pure virtual

Get a raw sequence.

This method provides information about a sequence, including the header, zero or more columns, and (raw) sequence data.

The sequence data is split into the sequence + ambiguities strings, which should be in the format used by BlastDB databases. (If the database type is protein, "ambiguities" should be an empty string.)

For each column of the database for which this OID has blob data, the column index should be found in column_ids, and a reference to the blob data should be stored at the same index in the column_blob vector. If this OID does not have a data object for this column, either the column may be missing from the list, or the blob data string should be empty.

Parameters

sequence	Sequence data packed in BlastDB disk format. [out]
ambiguities	Ambiguities packed in BlastDB disk format. [out]
deflines	This OID's headers as a Blast-def-line-set. [out]
column_ids	Column IDs of this OID's nonempty blobs. [out]
column_blobs	All non-empty blobs for this OID. [out]

Referenced by CBuildDatabase::AddSequences().

The documentation for this class was generated from the following file:

include/objtools/blast/seqdb_writer/build_db.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ GetColumnId()

◆ GetColumnMetaData()

◆ GetColumnNames()

◆ GetNext()