lib/seqStats.c File Reference

#include "common.h"
#include "dnautil.h"
#include "seqStats.h"

Include dependency graph for seqStats.c:

Go to the source code of this file.

Defines
#define	log4   1.386294
#define	invLog4   (1.0/log4)
Functions
double	dnaMatchEntropy (DNA *query, DNA *target, int baseCount)

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Define Documentation

#define invLog4   (1.0/log4)

Referenced by dnaMatchEntropy().

#define log4   1.386294

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Function Documentation

double dnaMatchEntropy	(	DNA *	query,
		DNA *	target,
		int	baseCount
	)

Definition at line 5 of file seqStats.c.

References invLog4, and ntVal.

{
#define log4 1.386294
#define invLog4 (1.0/log4)
double p, q, e = 0, invTotal;
int c, count[4], total;
int i, qVal, tVal;
count[0] = count[1] = count[2] = count[3] = 0;
for (i=0; i<baseCount; ++i)
    {
    qVal = ntVal[(int)query[i]];
    tVal = ntVal[(int)target[i]];
    if (qVal == tVal && qVal >= 0)
        count[qVal] += 1;
    }
total = count[0] + count[1] + count[2] + count[3];
invTotal = 1.0/total;
for (i=0; i<4; ++i)
    {
    if ((c = count[i]) > 0)
        {
        p = c * invTotal;
        q = log(p);
        e -= p*q;
        }
    }
e *= invLog4;
return e;
}

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