CQuerySplitter Class Reference
[BLAST (Basic Local Alignment Search Tool)]

Search Toolkit Book for CQuerySplitter

#include <split_query.hpp>

Inheritance diagram for CQuerySplitter:

[legend]Collaboration diagram for CQuerySplitter:

Detailed Description

Class responsible for splitting query sequences and providing data to the BLAST search class to search a split query chunk.

Definition at line 65 of file split_query.hpp.

Public Types

typedef vector< CRef< objects::CScope > > TScopeVector

Defines a vector of CScope objects.

typedef vector< CRef< CBlastQueryVector > > TSplitQueryVector

Definition of a vector of CBlastQueryVectors, each element corresponds to a query chunk.

Public Member Functions

CQuerySplitter (CRef< IQueryFactory > query_factory, const CBlastOptions *options)

Parametrized constructor.

size_t GetChunkSize () const

Returns the number of bases/residues that make up a query chunk.

Uint4 GetNumberOfChunks () const

Returns the number of chunks the query/queries will be split into.

bool IsQuerySplit () const

Determines whether the query sequence(s) are split or not.

CRef< CSplitQueryBlk > Split ()

Split the query sequence(s).

CRef< IQueryFactory > GetQueryFactoryForChunk (Uint4 chunk_num)

Returns a IQueryFactory suitable to be executed by a BLAST search class.

Private Member Functions

void x_ExtractCScopesAndMasks ()

Auxiliary method to extract the CScope objects from the query factory.

void x_ComputeChunkRanges ()

Compute all chunk ranges.

void x_ComputeQueryIndicesForChunks ()

Compute query indices that correspond to each chunk.

void x_ComputeQueryContextsForChunks ()

Compute query contexts that correspond to each chunk.

void x_ComputeContextOffsetsForChunks ()

Compute the context offsets which are used to adjust the results.

void x_ComputeContextOffsets_TranslatedQueries ()

Compute the context offsets which are used to adjust the results for translated queries.

void x_ComputeContextOffsets_NonTranslatedQueries ()

Compute the context offsets which are used to adjust the results for non-translated queries.

CQuerySplitter (const CQuerySplitter &rhs)

Prohibit copy constructor.

CQuerySplitter & operator= (const CQuerySplitter &rhs)

Prohibit assignment operator.

Private Attributes

CRef< IQueryFactory > m_QueryFactory

The original, unsplit query factory.

const CBlastOptions * m_Options

BLAST options.

Uint4 m_NumChunks

Number of chunks, if this is 1, no splitting occurs.

CRef< CSplitQueryBlk > m_SplitBlk

Split query block structure.

vector< CRef< IQueryFactory > > m_QueryChunkFactories

Vector of query factories, each element corresponds to a chunk.

CRef< ILocalQueryData > m_LocalQueryData

Source of local query data.

size_t m_TotalQueryLength

Length of the concatenated query.

size_t m_ChunkSize

Size of the query chunks.

TScopeVector m_Scopes

Vector of CScope objects.

TSeqLocInfoVector m_UserSpecifiedMasks

Vector of masking locations.

TSplitQueryVector m_SplitQueriesInChunk

Vector of split queries.

Friends

class ::CSplitQueryTestFixture

Declare unit test class as a friend.

ostream & operator<< (ostream &out, const CQuerySplitter &rhs)

Print this object so that its contents can be directly used to update split_query.ini (for unit testing).

Member Typedef Documentation

typedef vector< CRef<objects::CScope> > CQuerySplitter::TScopeVector

Defines a vector of CScope objects.

Definition at line 69 of file split_query.hpp.

typedef vector< CRef<CBlastQueryVector> > CQuerySplitter::TSplitQueryVector

Definition of a vector of CBlastQueryVectors, each element corresponds to a query chunk.

Definition at line 73 of file split_query.hpp.

Constructor & Destructor Documentation

CQuerySplitter::CQuerySplitter ( CRef< IQueryFactory > query_factory,

const CBlastOptions * options

)

Parametrized constructor.

Parameters:

query_factory Object containing query sequence(s) [in]

options BLAST options for the search [in]

Definition at line 53 of file split_query_cxx.cpp.
References SplitQuery_CalculateNumChunks(), and SplitQuery_GetChunkSize().

CQuerySplitter::CQuerySplitter ( const CQuerySplitter & rhs ) [private]

Prohibit copy constructor.

Member Function Documentation

size_t CQuerySplitter::GetChunkSize ( void ) const [inline]

Returns the number of bases/residues that make up a query chunk.

Definition at line 82 of file split_query.hpp.

Uint4 CQuerySplitter::GetNumberOfChunks ( ) const [inline]

Returns the number of chunks the query/queries will be split into.

Definition at line 85 of file split_query.hpp.
Referenced by operator<<().

CRef< IQueryFactory > CQuerySplitter::GetQueryFactoryForChunk ( Uint4 chunk_num )

Returns a IQueryFactory suitable to be executed by a BLAST search class.

Parameters:

chunk_num chunk number to retrieve (< GetNumberOfChunks())

Definition at line 878 of file split_query_cxx.cpp.
References CRef< C, Locker >::Empty(), NStr::IntToString(), m_SplitBlk, and Split().

bool CQuerySplitter::IsQuerySplit ( ) const [inline]

Determines whether the query sequence(s) are split or not.

Definition at line 88 of file split_query.hpp.

CQuerySplitter& CQuerySplitter::operator= ( const CQuerySplitter & rhs ) [private]

Prohibit assignment operator.

CRef< CSplitQueryBlk > CQuerySplitter::Split ( )

Split the query sequence(s).

Definition at line 845 of file split_query_cxx.cpp.
References m_SplitBlk, and CRef< C, Locker >::NotEmpty().
Referenced by GetQueryFactoryForChunk().

void CQuerySplitter::x_ComputeChunkRanges ( ) [private]

Compute all chunk ranges.

Definition at line 135 of file split_query_cxx.cpp.
References _ASSERT, CBlastOptions::GetProgramType(), m_ChunkSize, m_NumChunks, m_Options, m_SplitBlk, m_TotalQueryLength, CRef< C, Locker >::NotEmpty(), and SplitQuery_GetOverlapChunkSize().

void CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries ( ) [private]

Compute the context offsets which are used to adjust the results for non-translated queries.

Definition at line 567 of file split_query_cxx.cpp.
References _ASSERT, Blast_QueryIsTranslated(), CBlastOptions::GetProgramType(), INT4_MAX, m_LocalQueryData, m_Options, m_QueryChunkFactories, m_SplitBlk, and SplitQuery_GetOverlapChunkSize().
Referenced by x_ComputeContextOffsetsForChunks().

void CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries ( ) [private]

Compute the context offsets which are used to adjust the results for translated queries.

Definition at line 673 of file split_query_cxx.cpp.
References _ASSERT, Blast_QueryIsTranslated(), CODON_LENGTH, CBlastOptions::GetProgramType(), INT4_MAX, m_LocalQueryData, m_Options, m_QueryChunkFactories, m_SplitBlk, and SplitQuery_GetOverlapChunkSize().
Referenced by x_ComputeContextOffsetsForChunks().

void CQuerySplitter::x_ComputeContextOffsetsForChunks ( ) [private]

Compute the context offsets which are used to adjust the results.

Definition at line 555 of file split_query_cxx.cpp.
References Blast_QueryIsTranslated(), CBlastOptions::GetProgramType(), m_Options, x_ComputeContextOffsets_NonTranslatedQueries(), and x_ComputeContextOffsets_TranslatedQueries().

void CQuerySplitter::x_ComputeQueryContextsForChunks ( ) [private]

Compute query contexts that correspond to each chunk.

Definition at line 326 of file split_query_cxx.cpp.
References _ASSERT, Blast_QueryIsTranslated(), BlastSetup_GetStrand(), CODON_LENGTH, eNa_strand_minus, GetNumberOfContexts(), CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), kInvalidContext, m_LocalQueryData, m_Options, m_SplitBlk, NUM_FRAMES, auto_ptr< X >::reset(), and s_GetShiftForTranslatedNegStrand().

void CQuerySplitter::x_ComputeQueryIndicesForChunks ( ) [private]

Compute query indices that correspond to each chunk.

Definition at line 211 of file split_query_cxx.cpp.
References _TRACE, CBlastOptions::GetProgramType(), CBlastOptions::GetStrandOption(), m_LocalQueryData, and m_Options.

void CQuerySplitter::x_ExtractCScopesAndMasks ( ) [private]

Auxiliary method to extract the CScope objects from the query factory.

Definition at line 113 of file split_query_cxx.cpp.
References _ASSERT, CObjMgr_QueryFactory::ExtractScopes(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), m_LocalQueryData, m_NumChunks, m_QueryFactory, m_Scopes, m_UserSpecifiedMasks, and CRef< C, Locker >::NotEmpty().

Friends And Related Function Documentation

friend class ::CSplitQueryTestFixture [friend]

Declare unit test class as a friend.

Definition at line 153 of file split_query.hpp.

ostream& operator<< ( ostream & out,

const CQuerySplitter & rhs

) [friend]

Print this object so that its contents can be directly used to update split_query.ini (for unit testing).

Parameters:

out stream to print this object [in|out]

rhs object to print [in]

Definition at line 66 of file split_query_cxx.cpp.

Member Data Documentation

size_t CQuerySplitter::m_ChunkSize [private]

Size of the query chunks.

Definition at line 119 of file split_query.hpp.
Referenced by x_ComputeChunkRanges().

CRef<ILocalQueryData> CQuerySplitter::m_LocalQueryData [private]

Source of local query data.

Definition at line 115 of file split_query.hpp.
Referenced by operator<<(), x_ComputeContextOffsets_NonTranslatedQueries(), x_ComputeContextOffsets_TranslatedQueries(), x_ComputeQueryContextsForChunks(), x_ComputeQueryIndicesForChunks(), and x_ExtractCScopesAndMasks().

Uint4 CQuerySplitter::m_NumChunks [private]

Number of chunks, if this is 1, no splitting occurs.

Definition at line 109 of file split_query.hpp.
Referenced by x_ComputeChunkRanges(), and x_ExtractCScopesAndMasks().

const CBlastOptions* CQuerySplitter::m_Options [private]

BLAST options.

Definition at line 107 of file split_query.hpp.
Referenced by x_ComputeChunkRanges(), x_ComputeContextOffsets_NonTranslatedQueries(), x_ComputeContextOffsets_TranslatedQueries(), x_ComputeContextOffsetsForChunks(), x_ComputeQueryContextsForChunks(), and x_ComputeQueryIndicesForChunks().

vector< CRef<IQueryFactory> > CQuerySplitter::m_QueryChunkFactories [private]

Vector of query factories, each element corresponds to a chunk.

Definition at line 113 of file split_query.hpp.
Referenced by x_ComputeContextOffsets_NonTranslatedQueries(), and x_ComputeContextOffsets_TranslatedQueries().

CRef<IQueryFactory> CQuerySplitter::m_QueryFactory [private]

The original, unsplit query factory.

Definition at line 105 of file split_query.hpp.
Referenced by x_ExtractCScopesAndMasks().

TScopeVector CQuerySplitter::m_Scopes [private]

Vector of CScope objects.

Definition at line 121 of file split_query.hpp.
Referenced by x_ExtractCScopesAndMasks().

CRef<CSplitQueryBlk> CQuerySplitter::m_SplitBlk [private]

Split query block structure.

Definition at line 111 of file split_query.hpp.
Referenced by GetQueryFactoryForChunk(), Split(), x_ComputeChunkRanges(), x_ComputeContextOffsets_NonTranslatedQueries(), x_ComputeContextOffsets_TranslatedQueries(), and x_ComputeQueryContextsForChunks().

TSplitQueryVector CQuerySplitter::m_SplitQueriesInChunk [private]

Vector of split queries.

Definition at line 125 of file split_query.hpp.
Referenced by operator<<().

size_t CQuerySplitter::m_TotalQueryLength [private]

Length of the concatenated query.

Definition at line 117 of file split_query.hpp.
Referenced by x_ComputeChunkRanges().

TSeqLocInfoVector CQuerySplitter::m_UserSpecifiedMasks [private]

Vector of masking locations.

Definition at line 123 of file split_query.hpp.
Referenced by x_ExtractCScopesAndMasks().

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

src/algo/blast/api/split_query.hpp
src/algo/blast/api/split_query_cxx.cpp

Generated on Mon Dec 7 13:42:09 2009 for NCBI C++ ToolKit by

1.4.6

Modified on Mon Dec 07 16:23:49 2009 by modify_doxy.py rev. 173732


Public Types
typedef vector< CRef< objects::CScope > >	TScopeVector
	Defines a vector of CScope objects.
typedef vector< CRef< CBlastQueryVector > >	TSplitQueryVector
	Definition of a vector of CBlastQueryVectors, each element corresponds to a query chunk.
Public Member Functions
	CQuerySplitter (CRef< IQueryFactory > query_factory, const CBlastOptions *options)
	Parametrized constructor.
size_t	GetChunkSize () const
	Returns the number of bases/residues that make up a query chunk.
Uint4	GetNumberOfChunks () const
	Returns the number of chunks the query/queries will be split into.
bool	IsQuerySplit () const
	Determines whether the query sequence(s) are split or not.
CRef< CSplitQueryBlk >	Split ()
	Split the query sequence(s).
CRef< IQueryFactory >	GetQueryFactoryForChunk (Uint4 chunk_num)
	Returns a IQueryFactory suitable to be executed by a BLAST search class.
Private Member Functions
void	x_ExtractCScopesAndMasks ()
	Auxiliary method to extract the CScope objects from the query factory.
void	x_ComputeChunkRanges ()
	Compute all chunk ranges.
void	x_ComputeQueryIndicesForChunks ()
	Compute query indices that correspond to each chunk.
void	x_ComputeQueryContextsForChunks ()
	Compute query contexts that correspond to each chunk.
void	x_ComputeContextOffsetsForChunks ()
	Compute the context offsets which are used to adjust the results.
void	x_ComputeContextOffsets_TranslatedQueries ()
	Compute the context offsets which are used to adjust the results for translated queries.
void	x_ComputeContextOffsets_NonTranslatedQueries ()
	Compute the context offsets which are used to adjust the results for non-translated queries.
	CQuerySplitter (const CQuerySplitter &rhs)
	Prohibit copy constructor.
CQuerySplitter &	operator= (const CQuerySplitter &rhs)
	Prohibit assignment operator.
Private Attributes
CRef< IQueryFactory >	m_QueryFactory
	The original, unsplit query factory.
const CBlastOptions *	m_Options
	BLAST options.
Uint4	m_NumChunks
	Number of chunks, if this is 1, no splitting occurs.
CRef< CSplitQueryBlk >	m_SplitBlk
	Split query block structure.
vector< CRef< IQueryFactory > >	m_QueryChunkFactories
	Vector of query factories, each element corresponds to a chunk.
CRef< ILocalQueryData >	m_LocalQueryData
	Source of local query data.
size_t	m_TotalQueryLength
	Length of the concatenated query.
size_t	m_ChunkSize
	Size of the query chunks.
TScopeVector	m_Scopes
	Vector of CScope objects.
TSeqLocInfoVector	m_UserSpecifiedMasks
	Vector of masking locations.
TSplitQueryVector	m_SplitQueriesInChunk
	Vector of split queries.
Friends
class	::CSplitQueryTestFixture
	Declare unit test class as a friend.
ostream &	operator<< (ostream &out, const CQuerySplitter &rhs)
	Print this object so that its contents can be directly used to update split_query.ini (for unit testing).

CQuerySplitter Class Reference [BLAST (Basic Local Alignment Search Tool)]

Detailed Description

Public Types

Public Member Functions

Private Member Functions