include/karlin.h File Reference

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Functions
void	BlastKarlinBlkCalc (double *scoreProbabilities, int4 min, int4 max)
int4	BlastComputeLengthAdjustment (float K, float logK, float alpha_d_lambda, float beta, int4 query_length, uint4 db_length, int4 db_num_seqs, int4 *length_adjustment)
Variables
float	BlastKarlin_lambda
float	BlastKarlin_K
float	BlastKarlin_H

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Function Documentation

int4 BlastComputeLengthAdjustment	(	float	K,
		float	logK,
		float	alpha_d_lambda,
		float	beta,
		int4	query_length,
		uint4	db_length,
		int4	db_num_seqs,
		int4 *	length_adjustment
	)

Definition at line 457 of file karlin.c.

References int4, and maximum.

Referenced by statistics_calcLengthAdjustNew().

{
    int4 i;                     /* iteration index */
    const int4 maxits = 20;     /* maximum allowed iterations */
    double m = query_length, n = db_length, N = db_num_seqs;

    double ell;            /* A float value of the length adjustment */
    double ss;             /* effective size of the search space */
    double ell_min = 0, ell_max;   /* At each iteration i,
                                         * ell_min <= ell <= ell_max. */
    char converged = 0;       /* True if the iteration converged */
    double ell_next = 0;   /* Value the variable ell takes at iteration
                                 * i + 1 */
    /* Choose ell_max to be the largest nonnegative value that satisfies
     *
     *    K * (m - ell) * (n - N * ell) > max(m,n)
     *
     * Use quadratic formula: 2 c /( - b + sqrt( b*b - 4 * a * c )) */
    { /* scope of a, mb, and c, the coefficients in the quadratic formula
       * (the variable mb is -b) */
        double a  = N;
        double mb = m * N + n;
        double c  = n * m - maximum(m, n) / K;

        if(c < 0) {
            *length_adjustment = 0;
            return 1;
        } else {
            ell_max = 2 * c / (mb + sqrt(mb * mb - 4 * a * c));
        }
    } /* end scope of a, mb and c */

    for(i = 1; i <= maxits; i++) {      /* for all iteration indices */
        double ell_bar;    /* proposed next value of ell */
        ell      = ell_next;
        ss       = (m - ell) * (n - N * ell);
        ell_bar  = alpha_d_lambda * (logK + log(ss)) + beta;
        if(ell_bar >= ell) { /* ell is no bigger than the true fixed point */
            ell_min = ell;
            if(ell_bar - ell_min <= 1.0) {
                converged = 1;
                break;
            }
            if(ell_min == ell_max) { /* There are no more points to check */
                break;
            }
        } else { /* else ell is greater than the true fixed point */
            ell_max = ell;
        }
        if(ell_min <= ell_bar && ell_bar <= ell_max) {
          /* ell_bar is in range. Accept it */
            ell_next = ell_bar;
        } else { /* else ell_bar is not in range. Reject it */
            ell_next = (i == 1) ? ell_max : (ell_min + ell_max) / 2;
        }
    } /* end for all iteration indices */
    if(converged) { /* the iteration converged */
        /* If ell_fixed is the (unknown) true fixed point, then we
         * wish to set (*length_adjustment) to floor(ell_fixed).  We
         * assume that floor(ell_min) = floor(ell_fixed) */
        *length_adjustment = (int4) ell_min;
        /* But verify that ceil(ell_min) != floor(ell_fixed) */
        ell = ceil(ell_min);
        if( ell <= ell_max ) {
          ss = (m - ell) * (n - N * ell);
          if(alpha_d_lambda * (logK + log(ss)) + beta >= ell) {
            /* ceil(ell_min) == floor(ell_fixed) */
            *length_adjustment = (int4) ell;
          }
        }
    } else { /* else the iteration did not converge. */
        /* Use the best value seen so far */
        *length_adjustment = (int4) ell_min;
    }

    return converged ? 0 : 1;
}

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void BlastKarlinBlkCalc	(	double *	scoreProbabilities,
		int4	min,
		int4	max
	)

Definition at line 84 of file karlin.c.

References BlastKarlin_H, BlastKarlin_K, BlastKarlin_lambda, BlastKarlinLambdaNR(), BlastKarlinLHtoK(), and BlastKarlinLtoH().

Referenced by statistics_calculateUngappedKarlinParameters().

{
        /* Calculate the parameter Lambda */
        BlastKarlin_lambda = BlastKarlinLambdaNR(scoreProbabilities, min, max);

        /* Calculate H */
        BlastKarlin_H = BlastKarlinLtoH(scoreProbabilities, min, max, BlastKarlin_lambda);

        /* Calculate K */
        BlastKarlin_K = BlastKarlinLHtoK(scoreProbabilities, min, max, BlastKarlin_lambda,
                                         BlastKarlin_H);
}

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Variable Documentation

float BlastKarlin_H

Definition at line 7 of file karlin.h.

Referenced by BlastKarlinBlkCalc(), and statistics_calculateUngappedKarlinParameters().

float BlastKarlin_K

Definition at line 6 of file karlin.h.

Referenced by BlastKarlinBlkCalc(), and statistics_calculateUngappedKarlinParameters().

float BlastKarlin_lambda

Definition at line 5 of file karlin.h.

Referenced by BlastKarlinBlkCalc(), and statistics_calculateUngappedKarlinParameters().

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