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#include "libc.h"
#include "types.h"
#include "seq.h"
#include "misc.h"
#include "args.h"
#include "dna.h"
#ifndef __lint
static const char rcsid[] =
"$Id: dna.c,v 1.2 2000/06/05 22:48:19 florea Exp $";
#endif
static const argv_scores_t EIMOV = {
DEFAULT_E,
DEFAULT_I,
DEFAULT_M,
DEFAULT_O,
DEFAULT_V
};
static void set_argv_scores(argv_scores_t *s, const argv_scores_t *const dflt)
{
*s = *dflt;
}
/* DNA_scores ----------------------------------- set scoring matrix for DNA */
void DNA_scores_dflt(argv_scores_t *ds, ss_t ss, const argv_scores_t *dflt)
{
int i, j, bad;
ck_argc("DNA_scores");
set_argv_scores(ds, dflt);
for (i = 0; i < NACHARS; ++i)
for (j = 0; j < NACHARS; ++j)
ss[i][j] = ds->V;
bad = -100*ds->M;
for (i = 0; i < NACHARS; ++i)
ss['X'][i] = ss[i]['X'] = bad;
ss['a']['a'] = ss['c']['c'] = ss['g']['g'] = ss['t']['t'] = ds->M;
ss['a']['A'] = ss['c']['C'] = ss['g']['G'] = ss['t']['T'] = ds->M;
ss['A']['a'] = ss['C']['c'] = ss['G']['g'] = ss['T']['t'] = ds->M;
ss['A']['A'] = ss['C']['C'] = ss['G']['G'] = ss['T']['T'] = ds->M;
ss['a']['g'] = ss['g']['a'] = ss['c']['t'] = ss['t']['c'] = ds->I;
ss['a']['G'] = ss['g']['A'] = ss['c']['T'] = ss['t']['C'] = ds->I;
ss['A']['g'] = ss['G']['a'] = ss['C']['t'] = ss['T']['c'] = ds->I;
ss['A']['G'] = ss['G']['A'] = ss['C']['T'] = ss['T']['C'] = ds->I;
}
void DNA_scores(argv_scores_t *ds, ss_t ss)
{
DNA_scores_dflt(ds, ss, &EIMOV);
}
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