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

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#include <pssm_engine.hpp>

Inheritance diagram for CPssmEngine:

[legend]Collaboration diagram for CPssmEngine:

[legend]List of all members.

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Detailed Description

Computes a PSSM as specified in PSI-BLAST.

This class must be configured with a concrete strategy for it to obtain its input data. The following example uses the CPsiBlastInputData concrete strategy:

/// ...
/// CPsiBlastInputData pssm_strategy(query, query_length, alignment, 
///                                  object_manager_scope, psi_blast_options);
/// CPssmEngine pssm_engine(&pssm_strategy);
/// CRef<CPssmWithParameters> scoremat = pssm_engine.Run();
/// ...
/// 

Definition at line 98 of file pssm_engine.hpp.

Public Member Functions
	CPssmEngine (IPssmInputData *input)
	Constructor to configure the PSSM engine with a PSSM input data strategy object Checks that no data returned by the IPssmInputData interface is NULL Exceptions: CPssmEngineException  if validation fails.
	CPssmEngine (IPssmInputFreqRatios *input)
	Constructor to perform the last 2 stages of the PSSM creation algorithm Checks that no data returned by the IPssmInputFreqRatios interface is NULL Exceptions: CPssmEngineException  if validation fails.
	~CPssmEngine ()
	Destructor.
void	SetUngappedStatisticalParams (CConstRef< CBlastAncillaryData > ancillary_data)
	Sets the Karlin & Altschul parameters in the BlastScoreBlk to be used in PSSM generation.
CRef< objects::CPssmWithParameters >	Run ()
	Runs the PSSM engine to compute the PSSM.
Private Member Functions
BlastQueryInfo *	x_InitializeQueryInfo (unsigned int query_length)
	Initialiazes the core BlastQueryInfo structure for a single protein sequence.
void	x_InitializeScoreBlock (const unsigned char *query, unsigned int query_length, const char *matrix_name)
	Initializes the BlastScoreBlk data member required to run the PSSM engine.
unsigned char *	x_GetQuery () const
	Private interface to retrieve query sequence from its data source interface.
unsigned int	x_GetQueryLength () const
	Private interface to retrieve query length from its data source interface.
const char *	x_GetMatrixName () const
	Private interface to retrieve matrix name from its data source interface.
CRef< objects::CPssmWithParameters >	x_CreatePssmFromMsa ()
	Using IPssmInputData as a delegate to provide input data in the form of a multiple sequence alignment, creates a PSSM using the CORE C PSSM engine API.
CRef< objects::CPssmWithParameters >	x_CreatePssmFromFreqRatios ()
	Using IPssmInputFreqRatios as a delegate to provide the input PSSM's frequency ratios, creates a PSSM using the CORE C PSSM engine API.
	CPssmEngine ()
	Default constructor available for derived test classes.
	CPssmEngine (const CPssmEngine &rhs)
	Prohibit copy constructor.
CPssmEngine &	operator= (const CPssmEngine &rhs)
	Prohibit assignment operator.
Static Private Member Functions
static unsigned char *	x_GuardProteinQuery (const unsigned char *query, unsigned int query_length)
	Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence.
static CRef< objects::CPssmWithParameters >	x_PSIMatrix2Asn1 (const PSIMatrix *pssm, const char *matrix_name, const PSIBlastOptions *opts=NULL, const PSIDiagnosticsResponse *diagnostics=NULL)
	Converts the PSIMatrix structure into a ASN.1 CPssmWithParameters object.
static std::string	x_ErrorCodeToString (int error_code)
	Convert a PSSM return status into a string.
Private Attributes
IPssmInputData *	m_PssmInput
	Handle to strategy to process raw PSSM input data.
IPssmInputFreqRatios *	m_PssmInputFreqRatios
	Pointer to input data to create PSSM from frequency ratios.
CBlastScoreBlk	m_ScoreBlk
	Blast score block structure.
Friends
class	::CPssmCreateTestFixture
	unit test class

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Constructor & Destructor Documentation

CPssmEngine::CPssmEngine (   )  [inline, private]

Default constructor available for derived test classes. Definition at line 215 of file pssm_engine.hpp.

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

Prohibit copy constructor.

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Member Function Documentation

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

Prohibit assignment operator.

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Friends And Related Function Documentation

friend class ::CPssmCreateTestFixture [friend]

unit test class Definition at line 222 of file pssm_engine.hpp.

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Member Data Documentation

IPssmInputData* CPssmEngine::m_PssmInput [private]

Handle to strategy to process raw PSSM input data. Definition at line 132 of file pssm_engine.hpp. Referenced by Run(), x_CreatePssmFromMsa(), x_GetMatrixName(), x_GetQuery(), and x_GetQueryLength().

IPssmInputFreqRatios* CPssmEngine::m_PssmInputFreqRatios [private]

Pointer to input data to create PSSM from frequency ratios. Definition at line 134 of file pssm_engine.hpp. Referenced by x_CreatePssmFromFreqRatios(), x_GetMatrixName(), x_GetQuery(), and x_GetQueryLength().

CBlastScoreBlk CPssmEngine::m_ScoreBlk [private]

Blast score block structure. Definition at line 136 of file pssm_engine.hpp. Referenced by SetUngappedStatisticalParams(), x_CreatePssmFromFreqRatios(), x_CreatePssmFromMsa(), and x_InitializeScoreBlock().

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

• include/algo/blast/api/pssm_engine.hpp
• src/algo/blast/api/pssm_engine.cpp

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