GtScoreMatrix* gt_score_matrix_new_read(const char *path, GtAlphabet *alphabet,
GtError *err)
{
GtScoreMatrix *sm;
gt_error_check(err);
gt_assert(path && alphabet);
sm = gt_score_matrix_new(alphabet);
if (parse_score_matrix(sm, path, err)) {
gt_score_matrix_delete(sm);
return NULL;
}
return sm;
}
static GtScoreFunction* gt_dna_scorefunc_new(GtAlphabet *a, int match,
int mismatch, int insertion,
int deletion)
{
GtScoreMatrix *sm = gt_score_matrix_new(a);
GtScoreFunction *sf = gt_score_function_new(sm, insertion, deletion);
unsigned int m,n;
for (m=0;m<gt_alphabet_size(a);m++)
{
for (n=0;n<gt_alphabet_size(a);n++)
{
gt_score_matrix_set_score(sm, m, n, (n==m ? match : mismatch));
}
}
/* make N-N a mismatch! */
gt_score_matrix_set_score(sm, gt_alphabet_size(a) - 1,
gt_alphabet_size(a) - 1, mismatch);
return sf;
}
GtScoreMatrix* gt_score_matrix_new_read_protein(const char *path, GtError *err)
{
GtAlphabet *protein_alpha;
GtScoreMatrix *sm;
int had_err;
gt_error_check(err);
gt_assert(path);
/* create score matrix */
protein_alpha = gt_alphabet_new_protein();
sm = gt_score_matrix_new(protein_alpha);
gt_alphabet_delete(protein_alpha);
/* parse matrix file */
had_err = parse_score_matrix(sm, path, err);
if (had_err) {
gt_score_matrix_delete(sm);
return NULL;
}
return sm;
}
