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NCBI C++ ToolKit: src/algo/blast/core/blast_psi.c Source File

impala_scaling_factor);

( !msap || !options || !sbp || !pssm ) {

seq_weights, internal_pssm);

( !msa || ! aligned_block || !seq_weights || !internal_pssm || !*pssm ) {

seq_weights, internal_pssm);

seq_weights, internal_pssm);

seq_weights, internal_pssm);

seq_weights, internal_pssm);

seq_weights, internal_pssm);

seq_weights, internal_pssm);

(request && diagnostics) {

( !*diagnostics ) {

seq_weights, internal_pssm);

internal_pssm, *diagnostics);

seq_weights, internal_pssm);

( !cd_msa || !options || !sbp || !pssm ) {

( !seq_weights || !internal_pssm || !*pssm ) {

(request && diagnostics) {

( !*diagnostics ) {

** freq_ratios,

impala_scaling_factor,

* std_prob =

;

( !std_prob || !*pssm || !internal_pssm ) {

internal_pssm->

, internal_pssm->

);

, query_length,

impala_scaling_factor);

impala_scaling_factor)

impala_scaling_factor);

(

*) dimensions,

( !retval->

) {

(s = 0; s < dimensions->

+ 1; s++) {

retval->seqinfo = (PSISeqInfo*)

(dimensions->

+ 1,

(PSISeqInfo));

( !retval->seqinfo ) {

( msa->seqinfo ) {

(msa->seqinfo);

retval->

= query_length;

retval->

= alphabet_size;

( !(retval->

) ) {

retval->

= 0.0;

retval->

= 0.0;

(matrix->

) {

(save_ascii_pssm) {

(diags_request);

(query_length,

(

));

(query_length,

(

));

(wants->

) {

retval->

= (

*)

(query_length,

(

));

( !retval->

) {

(

*)

(query_length,

(

));

(diags->

) {

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

const double kPSSM_NoImpalaScaling

Value used to indicate that no IMPALA-style scaling should be performed when scaling a PSSM.

PSIDiagnosticsResponse * PSIDiagnosticsResponseFree(PSIDiagnosticsResponse *diags)

Deallocates the PSIDiagnosticsResponse structure passed in.

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.

PSIMatrix * PSIMatrixFree(PSIMatrix *matrix)

Deallocates the PSIMatrix structure passed in.

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

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

PSIMsa * PSIMsaFree(PSIMsa *msa)

Deallocates the PSIMsa structure.

static void s_PSICreatePssmCleanUp(PSIMatrix **pssm, _PSIPackedMsa *packed_msa, _PSIMsa *msa, _PSIAlignedBlock *aligned_block, _PSISequenceWeights *seq_weights, _PSIInternalPssmData *internal_pssm)

Convenience function to deallocate data structures allocated in PSICreatePssmWithDiagnostics.

PSIDiagnosticsRequest * PSIDiagnosticsRequestNew(void)

Allocates a PSIDiagnosticsRequest structure, setting all fields to false.

static int _PSICreateAndScalePssmFromFrequencyRatios(_PSIInternalPssmData *internal_pssm, const Uint1 *query, Uint4 query_length, double *std_prob, BlastScoreBlk *sbp, double impala_scaling_factor)

Private function which performs the last 2 stages of the PSSM creation: conversion of PSSM frequecy r...

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 res...

PSIDiagnosticsRequest * PSIDiagnosticsRequestNewEx(Boolean save_ascii_pssm)

Allocates a PSIDiagnosticsRequest structure, setting fields to their default values for their use in ...

PSIMatrix * PSIMatrixNew(Uint4 query_length, Uint4 alphabet_size)

Allocates a new PSIMatrix structure.

static void s_PSICreatePssmFromFrequencyRatiosCleanUp(PSIMatrix **pssm, _PSIInternalPssmData *internal_pssm, double *std_prob)

Convenience function to deallocate data structures allocated in PSICreatePssmFromFrequencyRatios.

static void s_PSISavePssm(const _PSIInternalPssmData *internal_pssm, const BlastScoreBlk *sbp, PSIMatrix *pssm)

Copies pssm data from internal_pssm and sbp into pssm.

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

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

PSIMsa * PSIMsaNew(const PSIMsaDimensions *dimensions)

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

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.

PSIDiagnosticsRequest * PSIDiagnosticsRequestFree(PSIDiagnosticsRequest *diags_request)

Deallocates the PSIDiagnosticsRequest structure passed in.

int _PSIComputeAlignmentBlocks(const _PSIMsa *msa, _PSIAlignedBlock *aligned_blocks)

Main function to compute aligned blocks' properties for each position within multiple alignment (stag...

int _PSIConvertFreqRatiosToPSSM(_PSIInternalPssmData *internal_pssm, const Uint1 *query, const BlastScoreBlk *sbp, const double *std_probs)

Converts the PSSM's frequency ratios obtained in the previous stage to a PSSM of scores.

int _PSIComputeFreqRatios(const _PSIMsa *msa, const _PSISequenceWeights *seq_weights, const BlastScoreBlk *sbp, const _PSIAlignedBlock *aligned_blocks, Int4 pseudo_count, Boolean nsg_compatibility_mode, _PSIInternalPssmData *internal_pssm)

Main function to compute the PSSM's frequency ratios (stage 5).

void ** _PSIAllocateMatrix(unsigned int ncols, unsigned int nrows, unsigned int data_type_sz)

Generic 2 dimensional matrix allocator.

void _PSIStructureGroupCustomization(_PSIMsa *msa)

Enable NCBI structure group customization to discard the query sequence, as this really isn't the res...

int _PSIComputeFreqRatiosFromCDs(const PSICdMsa *cd_msa, const _PSISequenceWeights *seq_weights, const BlastScoreBlk *sbp, Int4 pseudo_count, _PSIInternalPssmData *internal_pssm)

Main function to compute CD-based PSSM's frequency ratios.

_PSISequenceWeights * _PSISequenceWeightsNew(const PSIMsaDimensions *dimensions, const BlastScoreBlk *sbp)

Allocates and initializes the _PSISequenceWeights structure.

_PSIInternalPssmData * _PSIInternalPssmDataNew(Uint4 query_length, Uint4 alphabet_size)

Allocates a new _PSIInternalPssmData structure.

_PSIAlignedBlock * _PSIAlignedBlockNew(Uint4 query_length)

Allocates and initializes the _PSIAlignedBlock structure.

int _PSIComputeSequenceWeights(const _PSIMsa *msa, const _PSIAlignedBlock *aligned_blocks, Boolean nsg_compatibility_mode, _PSISequenceWeights *seq_weights)

Main function to calculate the sequence weights.

int _PSISaveDiagnostics(const _PSIMsa *msa, const _PSIAlignedBlock *aligned_block, const _PSISequenceWeights *seq_weights, const _PSIInternalPssmData *internal_pssm, PSIDiagnosticsResponse *diagnostics)

Collects diagnostic information from the process of creating the PSSM.

int _PSIPurgeBiasedSegments(_PSIPackedMsa *msa)

Main function for keeping only those selected sequences for PSSM construction (stage 2).

int _PSIComputeFrequenciesFromCDs(const PSICdMsa *cd_msa, BlastScoreBlk *sbp, const PSIBlastOptions *options, _PSISequenceWeights *seq_weights)

Main function to calculate CD weights and combine weighted residue counts from matched CDs.

_PSIMsa * _PSIMsaNew(const _PSIPackedMsa *msa, Uint4 alphabet_size)

Allocates and initializes the internal version of the PSIMsa structure (makes a deep copy) for intern...

_PSISequenceWeights * _PSISequenceWeightsFree(_PSISequenceWeights *seq_weights)

Deallocates the _PSISequenceWeights structure.

void ** _PSIDeallocateMatrix(void **matrix, unsigned int ncols)

Generic 2 dimensional matrix deallocator.

void _PSICopyMatrix_int(int **dest, int **src, unsigned int ncols, unsigned int nrows)

Copies src matrix into dest matrix, both of which must be int matrices with dimensions ncols by nrows...

_PSIInternalPssmData * _PSIInternalPssmDataFree(_PSIInternalPssmData *pssm_data)

Deallocates the _PSIInternalPssmData structure.

void _PSICopyMatrix_double(double **dest, double **src, unsigned int ncols, unsigned int nrows)

Copies src matrix into dest matrix, both of which must be double matrices with dimensions ncols by nr...

int _PSIValidateMSA_StructureGroup(const _PSIMsa *msa)

Structure group validation function for multiple sequence alignment structure.

int _PSIScaleMatrix(const Uint1 *query, const double *std_probs, _PSIInternalPssmData *internal_pssm, BlastScoreBlk *sbp)

Scales the PSSM (stage 7)

_PSIMsa * _PSIMsaFree(_PSIMsa *msa)

Deallocates the _PSIMsa data structure.

_PSIAlignedBlock * _PSIAlignedBlockFree(_PSIAlignedBlock *aligned_blocks)

Deallocates the _PSIAlignedBlock structure.

int _PSISaveCDDiagnostics(const PSICdMsa *cd_msa, const _PSISequenceWeights *seq_weights, const _PSIInternalPssmData *internal_pssm, PSIDiagnosticsResponse *diagnostics)

Collects diagnostic information from the process of creating the CDD-based PSSM.

int _PSIValidateCdMSA(const PSICdMsa *cd_msa, Uint4 alphabet_size)

Validation of multiple alignment of conserved domains structure.

_PSIPackedMsa * _PSIPackedMsaNew(const PSIMsa *msa)

Allocates and initializes the compact version of the PSIMsa structure (makes a deep copy) for interna...

int _IMPALAScaleMatrix(const Uint1 *query, const double *std_probs, _PSIInternalPssmData *internal_pssm, BlastScoreBlk *sbp, double scaling_factor)

Provides a similar function to _PSIScaleMatrix but it performs the scaling as IMPALA did,...

_PSIPackedMsa * _PSIPackedMsaFree(_PSIPackedMsa *msa)

Deallocates the _PSIMsa data structure.

int _PSIValidateMSA(const _PSIMsa *msa, Boolean ignore_unaligned_positions)

Main validation function for multiple sequence alignment structure.

Private interface for Position Iterated BLAST API, contains the PSSM generation engine.

#define PSIERR_BADPARAM

Bad parameter used in function.

#define PSIERR_OUTOFMEM

Out of memory.

#define PSI_SUCCESS

Successful operation.

Various auxiliary BLAST utility functions.

double * BLAST_GetStandardAaProbabilities(void)

Get the standard amino acid probabilities.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define ASSERT

macro for assert.

Structure used for scoring calculations.

Blast_KarlinBlk ** kbp_psi

K-A parameters for position-based alignments.

Int2 alphabet_size

size of alphabet.

Blast_KarlinBlk ** kbp_gap_psi

K-A parameters for psi alignments.

double K

K value used in statistics.

double Lambda

Lambda value used in statistics.

double H

H value used in statistics.

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

Boolean nsg_compatibility_mode

Compatibility option for the NCBI's structure group (note nsg_ prefix, stands for NCBI's structure gr...

double impala_scaling_factor

Scaling factor as used in IMPALA to do the matrix rescaling.

Boolean ignore_unaligned_positions

This turns off a validation for the multiple sequence alignment in the PSSM engine for unaligned posi...

Int4 pseudo_count

Pseudocount constant.

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

PSIMsaDimensions * dimensions

Query length and number of aligned cds.

unsigned char * query

Query sequence as Ncbistdaa.

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

Boolean information_content

request information content

Boolean frequency_ratios

request frequency ratios

Boolean independent_observations

request number of independent observations

Boolean weighted_residue_frequencies

request observed weighted residue frequencies

Boolean gapless_column_weights

request gapless column weights

Boolean num_matching_seqs

request number of matching sequences

Boolean sigma

request sigma

Boolean residue_frequencies

request observed residue frequencies

Boolean interval_sizes

request interval sizes

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

double * information_content

position information content (query_length elements)

Uint4 ** residue_freqs

observed residue frequencies per position of the PSSM (Dimensions are query_length by alphabet_size)

double ** weighted_residue_freqs

Weighted observed residue frequencies per position of the PSSM.

Uint4 * interval_sizes

interval sizes of aligned regions (query_length elements)

Uint4 alphabet_size

Specifies length of alphabet.

Uint4 query_length

Specifies the number of positions in the PSSM.

double * gapless_column_weights

Weights for columns without gaps (query_length elements)

double * independent_observations

Effective number of observations per column.

Uint4 * num_matching_seqs

number of matching sequences per query position (query_length elements)

double * sigma

sigma (query_length elements)

double ** frequency_ratios

PSSM's frequency ratios (Dimensions are query_length by alphabet_size)

This is the main return value from the PSSM engine.

double ung_lambda

Ungapped Lambda Karlin-Altschul parameter.

double kappa

Kappa Karlin-Altschul parameter.

int ** pssm

Position-specific score matrix.

double ung_kappa

Ungapped Kappa Karlin-Altschul parameter.

Uint4 ncols

Number of columns in PSSM (query_length)

double ung_h

Ungapped H Karlin-Altschul parameter.

double lambda

Lambda Karlin-Altschul parameter.

Uint4 nrows

Number of rows in PSSM (alphabet_size)

double h

H Karlin-Altschul parameter.

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

Boolean is_aligned

Is this letter part of the alignment?

Uint1 letter

Preferred letter at this position, in ncbistdaa encoding.

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

Uint4 num_seqs

Number of distinct sequences aligned with the query (does not include the query)

Uint4 query_length

Length of the query.

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

PSIMsaCell ** data

actual data, dimensions are (dimensions->num_seqs+1) by (dimensions->query_length)

PSIMsaDimensions * dimensions

dimensions of the msa

This structure keeps track of the regions aligned between the query sequence and those that were not ...

Internal representation of a PSSM in various stages of its creation and its dimensions.

Uint4 nrows

number of rows (alphabet_size)

int ** pssm

PSSM (scores)

Uint4 ncols

number of columns (query_length)

double ** freq_ratios

frequency ratios

Internal multiple alignment data structure used by the PSSM engine.

Uint1 * query

query sequence (length: query_length)

PSIMsaDimensions * dimensions

dimensions of field below

Compact version of PSIMsa structure.

Internal data structure to keep computed sequence weights.

double * std_prob

standard amino acid probabilities

voidp calloc(uInt items, uInt size)

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