High level definitions and declarations for the PSSM engine of PSI-BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_stat.h>

Include dependency graph for blast_psi.h:

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Go to the source code of this file.

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Classes
struct	PSIMsaCell
	Structure to describe the characteristics of a position in the multiple sequence alignment data structure. More...

struct	PSIMsaDimensions
	Structure representing the dimensions of the multiple sequence alignment data structure. More...

struct	PSIMsa
	Multiple sequence alignment (msa) data structure containing the raw data needed by the PSSM engine to create a PSSM. More...

struct	PSICdMsaCellData
	Data needed for PSSM computation stored in MSA cell for single column in CD aligned to a position in the query. More...

struct	PSICdMsaCell
	Alignment cell that represents one column of CD aligned to a position in the query. More...

struct	PSICdMsa
	Data structure representing multiple alignemnt of CDs and query sequence along with data needed for PSSM computation. More...

struct	PSIMatrix
	This is the main return value from the PSSM engine. More...

struct	PSIDiagnosticsRequest
	Structure to allow requesting various diagnostics data to be collected by PSSM engine. More...

struct	PSIDiagnosticsResponse
	This structure contains the diagnostics information requested using the PSIDiagnosticsRequest structure. More...

Typedefs
typedef struct PSIMsaCell	PSIMsaCell
	Structure to describe the characteristics of a position in the multiple sequence alignment data structure. More...

typedef struct PSIMsaDimensions	PSIMsaDimensions
	Structure representing the dimensions of the multiple sequence alignment data structure. More...

typedef struct PSIMsa	PSIMsa
	Multiple sequence alignment (msa) data structure containing the raw data needed by the PSSM engine to create a PSSM. More...

typedef struct PSICdMsaCellData	PSICdMsaCellData
	Data needed for PSSM computation stored in MSA cell for single column in CD aligned to a position in the query. More...

typedef struct PSICdMsaCell	PSICdMsaCell
	Alignment cell that represents one column of CD aligned to a position in the query. More...

typedef struct PSICdMsa	PSICdMsa
	Data structure representing multiple alignemnt of CDs and query sequence along with data needed for PSSM computation. More...

typedef struct PSIMatrix	PSIMatrix
	This is the main return value from the PSSM engine. More...

typedef struct PSIDiagnosticsRequest	PSIDiagnosticsRequest
	Structure to allow requesting various diagnostics data to be collected by PSSM engine. More...

typedef struct PSIDiagnosticsResponse	PSIDiagnosticsResponse
	This structure contains the diagnostics information requested using the PSIDiagnosticsRequest structure. More...

Functions
PSIMsa *	PSIMsaNew (const PSIMsaDimensions *dimensions)
	Allocates and initializes the multiple sequence alignment data structure for use as input to the PSSM engine. More...

PSIMsa *	PSIMsaFree (PSIMsa *msa)
	Deallocates the PSIMsa structure. More...

PSIMatrix *	PSIMatrixNew (Uint4 query_length, Uint4 alphabet_size)
	Allocates a new PSIMatrix structure. More...

PSIMatrix *	PSIMatrixFree (PSIMatrix *matrix)
	Deallocates the PSIMatrix structure passed in. More...

PSIDiagnosticsRequest *	PSIDiagnosticsRequestNew (void)
	Allocates a PSIDiagnosticsRequest structure, setting all fields to false. More...

PSIDiagnosticsRequest *	PSIDiagnosticsRequestNewEx (Boolean save_ascii_pssm)
	Allocates a PSIDiagnosticsRequest structure, setting fields to their default values for their use in the context of the PSI-BLAST application. More...

PSIDiagnosticsRequest *	PSIDiagnosticsRequestFree (PSIDiagnosticsRequest *diags_request)
	Deallocates the PSIDiagnosticsRequest structure passed in. More...

PSIDiagnosticsResponse *	PSIDiagnosticsResponseNew (Uint4 query_length, Uint4 alphabet_size, const PSIDiagnosticsRequest *request)
	Allocates a new PSI-BLAST diagnostics structure based on which fields of the PSIDiagnosticsRequest structure are TRUE. More...

PSIDiagnosticsResponse *	PSIDiagnosticsResponseFree (PSIDiagnosticsResponse *diags)
	Deallocates the PSIDiagnosticsResponse structure passed in. More...

int	PSICreatePssm (const PSIMsa msap, const PSIBlastOptions options, BlastScoreBlk sbp, PSIMatrix *pssm)
	Main entry point to core PSSM engine to calculate the PSSM. More...

int	PSICreatePssmWithDiagnostics (const PSIMsa msap, const PSIBlastOptions options, BlastScoreBlk sbp, const PSIDiagnosticsRequest request, PSIMatrix pssm, PSIDiagnosticsResponse diagnostics)
	Main entry point to core PSSM engine which allows to request diagnostics information. More...

int	PSICreatePssmFromCDD (const PSICdMsa cd_msa, const PSIBlastOptions options, BlastScoreBlk sbp, const PSIDiagnosticsRequest request, PSIMatrix pssm, PSIDiagnosticsResponse diagnostics)
	Main entry point to core PSSM engine for computing CDD-based PSSMs. More...

int	PSICreatePssmFromFrequencyRatios (const Uint1 query, Uint4 query_length, BlastScoreBlk sbp, double freq_ratios, double impala_scaling_factor, PSIMatrix pssm)
	Top-level function to create a PSSM given a matrix of frequency ratios and perform scaling on the resulting PSSM (i.e. More...

Detailed Description

High level definitions and declarations for the PSSM engine of PSI-BLAST.

Definition in file blast_psi.h.

Typedef Documentation

◆ PSICdMsa

typedef struct PSICdMsa PSICdMsa

Data structure representing multiple alignemnt of CDs and query sequence along with data needed for PSSM computation.

◆ PSICdMsaCell

typedef struct PSICdMsaCell PSICdMsaCell

Alignment cell that represents one column of CD aligned to a position in the query.

◆ PSICdMsaCellData

typedef struct PSICdMsaCellData PSICdMsaCellData

Data needed for PSSM computation stored in MSA cell for single column in CD aligned to a position in the query.

◆ PSIDiagnosticsRequest

typedef struct PSIDiagnosticsRequest PSIDiagnosticsRequest

Structure to allow requesting various diagnostics data to be collected by PSSM engine.

◆ PSIDiagnosticsResponse

typedef struct PSIDiagnosticsResponse PSIDiagnosticsResponse

This structure contains the diagnostics information requested using the PSIDiagnosticsRequest structure.

◆ PSIMatrix

typedef struct PSIMatrix PSIMatrix

This is the main return value from the PSSM engine.

◆ PSIMsa

typedef struct PSIMsa PSIMsa

Multiple sequence alignment (msa) data structure containing the raw data needed by the PSSM engine to create a PSSM.

By convention, the first row of the data field contains the query sequence

◆ PSIMsaCell

typedef struct PSIMsaCell PSIMsaCell

Structure to describe the characteristics of a position in the multiple sequence alignment data structure.

◆ PSIMsaDimensions

typedef struct PSIMsaDimensions PSIMsaDimensions

Structure representing the dimensions of the multiple sequence alignment data structure.

Function Documentation

◆ PSICreatePssm()

int PSICreatePssm	(	const PSIMsa *	msap,
		const PSIBlastOptions *	options,
		BlastScoreBlk *	sbp,
		PSIMatrix **	pssm
	)

Main entry point to core PSSM engine to calculate the PSSM.

Parameters

msap	multiple sequence alignment data structure [in]
options	options to the PSSM engine [in]
sbp	BLAST score block structure [in\|out]
pssm	PSSM and statistical information (the latter is also returned in the sbp->kbp_gap_psi[0])

Returns: PSI_SUCCESS on success, otherwise one of the PSIERR_* constants

Definition at line 95 of file blast_psi.c.

References NULL, and PSICreatePssmWithDiagnostics().

◆ PSICreatePssmFromCDD()

int PSICreatePssmFromCDD	(	const PSICdMsa *	cd_msa,
		const PSIBlastOptions *	options,
		BlastScoreBlk *	sbp,
		const PSIDiagnosticsRequest *	request,
		PSIMatrix **	pssm,
		PSIDiagnosticsResponse **	diagnostics
	)

Main entry point to core PSSM engine for computing CDD-based PSSMs.

Parameters

cd_msa	information about CDs that match to query sequence [in]
options	options to PSSM engine [in]
sbp	BLAST score block structure [in\|out]
request	diagnostics information request [in]
pssm	PSSM [out]
diagnostics	diagnostics information response, expects a pointer to uninitialized structure [in\|out]

Definition at line 229 of file blast_psi.c.

References _PSIComputeFreqRatiosFromCDs(), _PSIComputeFrequenciesFromCDs(), _PSICreateAndScalePssmFromFrequencyRatios(), _PSIInternalPssmDataNew(), _PSISaveCDDiagnostics(), _PSISequenceWeightsNew(), _PSIValidateCdMSA(), BlastScoreBlk::alphabet_size, PSICdMsa::dimensions, PSIBlastOptions::impala_scaling_factor, NULL, PSIBlastOptions::pseudo_count, PSI_SUCCESS, PSIDiagnosticsResponseFree(), PSIDiagnosticsResponseNew(), PSIERR_BADPARAM, PSIERR_OUTOFMEM, PSIMatrixNew(), PSICdMsa::query, PSIMsaDimensions::query_length, s_PSICreatePssmCleanUp(), s_PSISavePssm(), and _PSISequenceWeights::std_prob.

Referenced by CPssmEngine::x_CreatePssmFromCDD().

◆ PSICreatePssmFromFrequencyRatios()

int PSICreatePssmFromFrequencyRatios	(	const Uint1 *	query,
		Uint4	query_length,
		BlastScoreBlk *	sbp,
		double **	freq_ratios,
		double	impala_scaling_factor,
		PSIMatrix **	pssm
	)

Top-level function to create a PSSM given a matrix of frequency ratios and perform scaling on the resulting PSSM (i.e.

: performs the last two stages of the algorithm) Note that no diagnostics can be returned as those are calculated in earlier stages of the algorithm.

Parameters

query	query sequence in ncbistdaa format, no sentinels needed [in]
query_length	length of the query sequence [in]
sbp	BLAST score block structure [in\|out]
freq_ratios	matrix of frequency ratios, dimensions are query_length by BLASTAA_SIZE [in]
impala_scaling_factor	scaling factor used in IMPALA-style scaling if its value is NOT kPSSM_NoImpalaScaling (otherwise it performs standard PSI-BLAST scaling) [in]
pssm	PSSM and statistical information [in\|out]

Returns: PSI_SUCCESS on success, otherwise one of the PSIERR_* constants

Definition at line 344 of file blast_psi.c.

References _PSICopyMatrix_double(), _PSICreateAndScalePssmFromFrequencyRatios(), _PSIInternalPssmDataNew(), BlastScoreBlk::alphabet_size, BLAST_GetStandardAaProbabilities(), _PSIInternalPssmData::freq_ratios, _PSIInternalPssmData::ncols, _PSIInternalPssmData::nrows, NULL, PSI_SUCCESS, PSIERR_OUTOFMEM, PSIMatrixNew(), query, s_PSICreatePssmFromFrequencyRatiosCleanUp(), and s_PSISavePssm().

Referenced by CPssmEngine::x_CreatePssmFromFreqRatios().

◆ PSICreatePssmWithDiagnostics()

int PSICreatePssmWithDiagnostics	(	const PSIMsa *	msap,
		const PSIBlastOptions *	options,
		BlastScoreBlk *	sbp,
		const PSIDiagnosticsRequest *	request,
		PSIMatrix **	pssm,
		PSIDiagnosticsResponse **	diagnostics
	)

Main entry point to core PSSM engine which allows to request diagnostics information.

Parameters

msap	multiple sequence alignment data structure [in]
options	options to the PSSM engine [in]
sbp	BLAST score block structure [in\|out]
request	diagnostics information request [in]
pssm	PSSM and statistical information (the latter is also returned in the sbp->kbp_gap_psi[0]) [out]
diagnostics	diagnostics information response, expects a pointer to an uninitialized structure which will be populated with data requested in requests [in\|out]

Returns: PSI_SUCCESS on success, otherwise one of the PSIERR_* constants

Definition at line 105 of file blast_psi.c.

References _PSIAlignedBlockNew(), _PSIComputeAlignmentBlocks(), _PSIComputeFreqRatios(), _PSIComputeSequenceWeights(), _PSICreateAndScalePssmFromFrequencyRatios(), _PSIInternalPssmDataNew(), _PSIMsaNew(), _PSIPackedMsaFree(), _PSIPackedMsaNew(), _PSIPurgeBiasedSegments(), _PSISaveDiagnostics(), _PSISequenceWeightsNew(), _PSIStructureGroupCustomization(), _PSIValidateMSA(), _PSIValidateMSA_StructureGroup(), BlastScoreBlk::alphabet_size, _PSIMsa::dimensions, PSIBlastOptions::ignore_unaligned_positions, PSIBlastOptions::impala_scaling_factor, PSIBlastOptions::nsg_compatibility_mode, NULL, PSIBlastOptions::pseudo_count, PSI_SUCCESS, PSIDiagnosticsResponseFree(), PSIDiagnosticsResponseNew(), PSIERR_BADPARAM, PSIERR_OUTOFMEM, PSIMatrixNew(), _PSIMsa::query, PSIMsaDimensions::query_length, s_PSICreatePssmCleanUp(), s_PSISavePssm(), and _PSISequenceWeights::std_prob.

Referenced by PSICreatePssm(), and CPssmEngine::x_CreatePssmFromMsa().

◆ PSIDiagnosticsRequestFree()

PSIDiagnosticsRequest* PSIDiagnosticsRequestFree ( PSIDiagnosticsRequest * diags_request )

Deallocates the PSIDiagnosticsRequest structure passed in.

Parameters

diags_request structure to deallocate [in]

Returns: NULL

Definition at line 611 of file blast_psi.c.

References NULL, and sfree.

Referenced by CPsiBlastInputClustalW::~CPsiBlastInputClustalW().

◆ PSIDiagnosticsRequestNew()

PSIDiagnosticsRequest* PSIDiagnosticsRequestNew ( void )

Allocates a PSIDiagnosticsRequest structure, setting all fields to false.

Returns: newly allocated structure or NULL in case of memory allocation failure

Definition at line 585 of file blast_psi.c.

References calloc().

Referenced by CPsiBlastInputClustalW::CPsiBlastInputClustalW(), PSIDiagnosticsRequestNewEx(), and CPsiBlastTestFixture::x_ComputePssmForNextIteration().

◆ PSIDiagnosticsRequestNewEx()

PSIDiagnosticsRequest* PSIDiagnosticsRequestNewEx ( Boolean save_ascii_pssm )

Allocates a PSIDiagnosticsRequest structure, setting fields to their default values for their use in the context of the PSI-BLAST application.

Parameters

save_ascii_pssm corresponds to the command line argument to save the PSSM in ASCII format [in]

Returns: newly allocated structure or NULL in case of memory allocation failure

Definition at line 591 of file blast_psi.c.

References PSIDiagnosticsRequest::frequency_ratios, PSIDiagnosticsRequest::gapless_column_weights, PSIDiagnosticsRequest::information_content, PSIDiagnosticsRequest::interval_sizes, NULL, PSIDiagnosticsRequest::num_matching_seqs, PSIDiagnosticsRequestNew(), PSIDiagnosticsRequest::sigma, TRUE, and PSIDiagnosticsRequest::weighted_residue_frequencies.

Referenced by BOOST_AUTO_TEST_CASE(), CPsiBlastApp::ComputePssmForNextIteration(), CDeltaBlastApp::ComputePssmForNextPsiBlastIteration(), CDeltaBlast::Run(), and CPsiBlastArgs::x_CreatePssmFromMsa().

◆ PSIDiagnosticsResponseFree()

PSIDiagnosticsResponse* PSIDiagnosticsResponseFree ( PSIDiagnosticsResponse * diags )

Deallocates the PSIDiagnosticsResponse structure passed in.

Parameters

diags structure to deallocate [in]

Returns: NULL

Definition at line 717 of file blast_psi.c.

References _PSIDeallocateMatrix(), PSIDiagnosticsResponse::frequency_ratios, PSIDiagnosticsResponse::gapless_column_weights, PSIDiagnosticsResponse::independent_observations, PSIDiagnosticsResponse::information_content, PSIDiagnosticsResponse::interval_sizes, NULL, PSIDiagnosticsResponse::num_matching_seqs, PSIDiagnosticsResponse::query_length, PSIDiagnosticsResponse::residue_freqs, sfree, PSIDiagnosticsResponse::sigma, and PSIDiagnosticsResponse::weighted_residue_freqs.

Referenced by PSICreatePssmFromCDD(), PSICreatePssmWithDiagnostics(), and PSIDiagnosticsResponseNew().

◆ PSIDiagnosticsResponseNew()

PSIDiagnosticsResponse* PSIDiagnosticsResponseNew	(	Uint4	query_length,
		Uint4	alphabet_size,
		const PSIDiagnosticsRequest *	request
	)

Allocates a new PSI-BLAST diagnostics structure based on which fields of the PSIDiagnosticsRequest structure are TRUE.

Note: this is declared here for consistency - this does not need to be called by client code of this API, it is called in the PSICreatePssm* functions to allocate the diagnostics response structure.

Parameters

query_length	length of the query sequence [in]
alphabet_size	length of the alphabet [in]
request	diagnostics to retrieve from PSSM engine [in]

Returns: pointer to allocated PSIDiagnosticsResponse or NULL if dimensions or request are NULL

Definition at line 618 of file blast_psi.c.

Referenced by PSICreatePssmFromCDD(), and PSICreatePssmWithDiagnostics().

◆ PSIMatrixFree()

PSIMatrix* PSIMatrixFree ( PSIMatrix * matrix )

Deallocates the PSIMatrix structure passed in.

Parameters

matrix structure to deallocate [in]

Returns: NULL

Definition at line 569 of file blast_psi.c.

References _PSIDeallocateMatrix(), PSIMatrix::ncols, NULL, PSIMatrix::pssm, and sfree.

Referenced by PSIMatrixNew(), s_PSICreatePssmCleanUp(), and s_PSICreatePssmFromFrequencyRatiosCleanUp().

◆ PSIMatrixNew()

PSIMatrix* PSIMatrixNew	(	Uint4	query_length,
		Uint4	alphabet_size
	)

Allocates a new PSIMatrix structure.

Parameters

query_length	number of columns allocated for the PSSM [in]
alphabet_size	number of rows allocated for the PSSM [in]

Returns: pointer to allocated PSIMatrix structure or NULL if out of memory

Definition at line 541 of file blast_psi.c.

References _PSIAllocateMatrix(), PSIMatrix::h, PSIMatrix::kappa, PSIMatrix::lambda, malloc(), PSIMatrix::ncols, PSIMatrix::nrows, NULL, PSIMatrixFree(), PSIMatrix::pssm, PSIMatrix::ung_h, PSIMatrix::ung_kappa, and PSIMatrix::ung_lambda.

Referenced by PSICreatePssmFromCDD(), PSICreatePssmFromFrequencyRatios(), and PSICreatePssmWithDiagnostics().

◆ PSIMsaFree()

PSIMsa* PSIMsaFree ( PSIMsa * msa )

Deallocates the PSIMsa structure.

Parameters

msa	multiple sequence alignment structure to deallocate [in]

Returns: NULL

Definition at line 513 of file blast_psi.c.

References _PSIDeallocateMatrix(), PSIMsa::data, PSIMsa::dimensions, NULL, PSIMsaDimensions::num_seqs, and sfree.

Referenced by CPssmInputTestData::CPssmInputTestData(), PSIMsaNew(), CdPssmInput::~CdPssmInput(), CPsiBlastInputClustalW::~CPsiBlastInputClustalW(), CPsiBlastInputData::~CPsiBlastInputData(), CPssmInputFlankingGaps::~CPssmInputFlankingGaps(), CPssmInputTestData::~CPssmInputTestData(), and SU_PSSMInput::~SU_PSSMInput().

◆ PSIMsaNew()

PSIMsa* PSIMsaNew ( const PSIMsaDimensions * dimensions )

Allocates and initializes the multiple sequence alignment data structure for use as input to the PSSM engine.

Parameters

dimensions dimensions of multiple sequence alignment data structure to allocate [in]

Returns: allocated PSIMsa structure or NULL if out of memory.

Definition at line 462 of file blast_psi.c.

References _PSIAllocateMatrix(), calloc(), PSIMsa::data, PSIMsa::dimensions, FALSE, PSIMsaCell::is_aligned, PSIMsaCell::letter, malloc(), NULL, PSIMsaDimensions::num_seqs, PSIMsaFree(), and PSIMsaDimensions::query_length.

Referenced by BOOST_AUTO_TEST_CASE(), CdPssmInput::CdPssmInput(), CPssmInputFlankingGaps::CPssmInputFlankingGaps(), CPsiBlastInputClustalW::Process(), CPsiBlastInputData::Process(), CPssmInputTestData::SetupDuplicateHit(), CPssmInputTestData::SetupHenikoffsPositionBasedSequenceWeights(), CPssmInputTestData::SetupMsaHasUnalignedRegion(), CPssmInputTestData::SetupQueryAlignedWithInternalGaps(), CPssmInputTestData::SetupSelfHit(), and SU_PSSMInput::SU_PSSMInput().

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ PSICdMsa

◆ PSICdMsaCell

◆ PSICdMsaCellData

◆ PSIDiagnosticsRequest

◆ PSIDiagnosticsResponse

◆ PSIMatrix

◆ PSIMsa

◆ PSIMsaCell

◆ PSIMsaDimensions

Function Documentation

◆ PSICreatePssm()

◆ PSICreatePssmFromCDD()

◆ PSICreatePssmFromFrequencyRatios()

◆ PSICreatePssmWithDiagnostics()

◆ PSIDiagnosticsRequestFree()

◆ PSIDiagnosticsRequestNew()

◆ PSIDiagnosticsRequestNewEx()

◆ PSIDiagnosticsResponseFree()

◆ PSIDiagnosticsResponseNew()

◆ PSIMatrixFree()

◆ PSIMatrixNew()

◆ PSIMsaFree()

◆ PSIMsaNew()