static int bioScoreMatch(boolean isProt, char *a, char *b, int size)
/* Return score of match (no inserts) between two bio-polymers. */
{
if (isProt)
{
return dnaOrAaScoreMatch(a, b, size, 2, -1, 'X');
}
else
{
return dnaOrAaScoreMatch(a, b, size, 1, -1, 'n');
}
}
int dnaScoreMatch(DNA *a, DNA *b, int size)
/* Compare two pieces of DNA base by base. Total mismatches are
* subtracted from total matches and returned as score. 'N's
* neither hurt nor help score. */
{
return dnaOrAaScoreMatch(a, b, size, 1, -1, 'n');
}
int aaScoreMatch(AA *a, AA *b, int size)
/* Compare two peptides aa by aa. */
{
return dnaOrAaScoreMatch(a, b, size, 2, -1, 'X');
}