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

{1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22};

* matrix_name,

** posPrivateMatrix,

retval->

= queryLength;

( !compactSearch ) {

(compactSearch);

* queryProbArray,

minScore, maxScore;

(

= 0;

< matrixLength;

++) {

&& (matrix[

][k] < minScore))

minScore = matrix[

][k];

(matrix[

][k] > maxScore)

maxScore = matrix[

][k];

return_sfp->

= minScore;

return_sfp->

= maxScore;

scoreArray[

] = 0.0;

return_sfp->

= &(scoreArray[-minScore]);

onePosFrac = 1.0 / ((double) matrixLength);

(

= 0;

< matrixLength;

++) {

(matrix[

][k] >= minScore) {

return_sfp->

[matrix[

][k]] +=

(onePosFrac * queryProbArray[k]);

(

= minScore;

<= maxScore;

++)

** posPrivateMatrix,

scalingFactor,

factor, factor_low = 1.0, factor_high = 1.0;

, new_lambda;

** private_matrix;

private_matrix = posPrivateMatrix;

dim1 = compactSearch->

;

(doBinarySearch) {

(c = 0; c < dim1; c++) {

(

= 0;

< dim2;

++) {

matrix[c][

] = (

)

((factor * private_matrix[c][

]) / divFactor);

scoreArray, return_sfp);

(new_lambda >

) {

factor = factor_high;

(too_high ==

)

factor_high += (factor_high - 1.0);

factor = factor_high;

(too_high ==

)

factor_low += (factor_low - 1.0);

factor = 0.5 * (factor_high + factor_low);

(c = 0; c < dim1; c++) {

(

= 0;

< dim2;

++) {

matrix[c][

] = (

)

((factor * private_matrix[c][

]) / divFactor);

scoreArray, return_sfp);

(new_lambda >

) {

factor_high = factor;

(c = 0; c < dim1; c++) {

(

= 0;

< dim2;

++) {

matrix[c][

] = (

)

((

) private_matrix[c][

] *

compactSearch->

,

(c = 0; c < dim1; c++) {

(

= 0;

< dim2;

++) {

private_matrix[c][

] =

scalingFactor,

sbp) ==

)? 0 : 1);

#define sfree(x)

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

int Kappa_impalaScaling(Kappa_posSearchItems *posSearch, Kappa_compactSearchItems *compactSearch, double scalingFactor, Boolean doBinarySearch, BlastScoreBlk *sbp)

Copied from posit2.c.

const Int4 trueCharPositions[20]

positions of true characters in protein alphabet

Kappa_compactSearchItems * Kappa_compactSearchItemsNew(const Uint1 *query, unsigned int queryLength, BlastScoreBlk *sbp)

Creates a new Kappa_compactSearchItems structure.

Kappa_posSearchItems * Kappa_posSearchItemsFree(Kappa_posSearchItems *posSearch)

Deallocates the Kappa_posSearchItems structure.

static Blast_ScoreFreq * fillSfp(int **matrix, int matrixLength, double *queryProbArray, double *scoreArray, Blast_ScoreFreq *return_sfp)

Replace/refactor with either one of the already existing variants of this function: posfillSfp (blast...

Kappa_compactSearchItems * Kappa_compactSearchItemsFree(Kappa_compactSearchItems *compactSearch)

Deallocates the Kappa_compactSearchItems structure.

static Boolean impalaScaleMatrix(Kappa_compactSearchItems *compactSearch, int **posMatrix, int **posPrivateMatrix, double scalingFactor, Boolean doBinarySearch, BlastScoreBlk *sbp)

Copy of posit2.c's impalaScaleMatrix.

Kappa_posSearchItems * Kappa_posSearchItemsNew(unsigned int queryLength, const char *matrix_name, int **posPrivateMatrix, double **posFreqs)

Allocates a new Kappa_posSearchItems structure.

Port of posit.h structures and impalaScaling for implementing composition based statistics for PSI-BL...

#define PRO_TRUE_ALPHABET_SIZE

number of real aminoacids (i.e.

#define kScoreMatrixScoreRange

range of scores in a matrix

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

Generic 2 dimensional matrix allocator.

const int kPSIScaleFactor

Successor to POSIT_SCALE_FACTOR.

const Uint4 kPositScalingNumIterations

Constant used in scaling PSSM routines: Successor to POSIT_NUM_ITERATIONS.

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

Generic 2 dimensional matrix deallocator.

void _PSIUpdateLambdaK(const int **pssm, const Uint1 *query, Uint4 query_length, const double *std_probs, BlastScoreBlk *sbp)

Updates the Karlin-Altschul parameters based on the query sequence and PSSM's score frequencies.

const double kPositScalingPercent

Constant used in scaling PSSM routines: Successor to POSIT_PERCENT.

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

#define BLAST_SCORE_MIN

minimum allowed score (for one letter comparison).

double Blast_KarlinLambdaNR(Blast_ScoreFreq *sfp, double initialLambdaGuess)

Calculates the parameter Lambda given an initial guess for its value.

Blast_ScoreFreq * Blast_ScoreFreqFree(Blast_ScoreFreq *sfp)

Deallocates the score frequencies structure.

#define BLAST_SCORE_MAX

maximum allowed score (for one letter comparison).

Various auxiliary BLAST utility functions.

double * BLAST_GetStandardAaProbabilities(void)

Get the standard amino acid probabilities.

#define BLASTAA_SIZE

Size of aminoacid alphabet.

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

unsigned int

A callback function used to compare two keys in a database.

SFreqRatios * _PSIMatrixFrequencyRatiosFree(SFreqRatios *freq_ratios)

Deallocate the frequency ratios structure.

SFreqRatios * _PSIMatrixFrequencyRatiosNew(const char *matrix_name)

Retrive the matrix's frequency ratios.

Prototypes for portable math library (ported from C Toolkit)

long BLAST_Nint(double x)

Nearest 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.

double lambda(size_t dimMatrix_, const Int4 *const *scoreMatrix_, const double *q_)

Structure used for scoring calculations.

Boolean protein_alphabet

TRUE if alphabet_code is for a protein alphabet (e.g., ncbistdaa etc.), FALSE for nt.

Blast_KarlinBlk ** kbp_psi

K-A parameters for position-based alignments.

Int2 alphabet_size

size of alphabet.

Uint1 alphabet_code

NCBI alphabet code.

SBlastScoreMatrix * matrix

scoring matrix data

Blast_KarlinBlk * kbp_ideal

Ideal values (for query with average database composition).

Blast_KarlinBlk ** kbp_gap_std

K-A parameters for std (not position-based) alignments.

Blast_KarlinBlk ** kbp_std

K-A parameters for ungapped alignments.

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.

Holds score frequencies used in calculation of Karlin-Altschul parameters for an ungapped search.

double score_avg

average score, must be negative for local alignment.

Int4 obs_min

lowest observed (actual) scores

double * sprob

arrays for frequency of given score, shifted down by score_min.

Int4 obs_max

highest observed (actual) scores

Structure used to pass data into the scaling routines.

Blast_KarlinBlk ** kbp_gap_std

Gapped Karlin-Altschul parameters [alias].

double lambda_ideal

Lambda calculated using standard residue compositions for the query and database sequences.

double * standardProb

Array of standard residue probabilities, as those returned by BLAST_GetStandardAaProbabilities.

Blast_KarlinBlk ** kbp_gap_psi

Gapped PSI-BLAST Karlin-Altschul parameters [alias].

Blast_KarlinBlk ** kbp_psi

Ungapped PSI-BLAST Karlin-Altschul parameters [alias].

int ** matrix

Standard substitution scoring matrix [alias].

Blast_KarlinBlk ** kbp_std

Ungapped Karlin-Altschul parameters [alias].

Uint1 * query

Query sequence data in ncbistdaa format without sentinel bytes [alias].

int qlength

Length of the sequence above.

int alphabetSize

Size of the alphabet.

double K_ideal

K calculated using standard residue compositions for the query and database sequences.

Structure used to pass data into the scaling routines.

unsigned int queryLength

Length of the query sequence, specifies the number of columns in the matrices in this structure.

SFreqRatios * stdFreqRatios

Frequecy ratios for underlying scoring matrix.

double ** posFreqs

PSSM's frequency ratios [alias].

int ** posPrivateMatrix

Scaled PSSM [alias].

int ** data

actual scoring matrix data, stored in row-major form

voidp calloc(uInt items, uInt size)

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