int main(void)
{
Sequence L;
L = (Sequence)malloc(sizeof(struct seqlist));
CreatSequence(L);
PrintSequence(L);
reverse(L);
PrintSequence(L);
}
static void LIBCALLBACK GetSeqFeat (AsnExpOptStructPtr aeosp)
{
BioseqPtr bsp;
ExpStructPtr esp;
SeqFeatPtr sfp;
if (aeosp->dvp->intvalue == START_STRUCT) {
esp = (ExpStructPtr) aeosp->data;
sfp = (SeqFeatPtr) aeosp->the_struct;
if (esp != NULL && esp->fp != NULL && sfp != NULL &&
sfp->data.choice == esp->feat) {
bsp = BioseqFind (SeqLocId (sfp->location));
if (bsp != NULL) {
PrintSequence (bsp, sfp, esp->fp, esp->is_na);
}
}
}
}
void NormSequence(Input *xlst, int n, int dim){
int i,j,d;
fprintf(stderr, "Normalize sequences (0:%f) ... \n", MAXVAL);
for(d=0;d<dim;d++){
float min = INF, max=-INF;
for(i=0;i<n;i++){
Input *x = &xlst[i];
/// find min & max values
for(j=0;j<x->m;j++)
if(x->O[j][d] > max)
max = x->O[j][d];
else if(x->O[j][d] < min)
min = x->O[j][d];
}//i
for(i=0;i<n;i++){
Input *x = &xlst[i];
/// normalize -> [0:MAXVAL]
for(j=0;j<x->m;j++)
x->O[j][d] = MAXVAL*(x->O[j][d]-min) / (max-min);
}//i
}//d
PrintSequence(stdout, xlst[0].m, dim, xlst[0].O);
}
int main (int argc, char **argv)
{
HMM hmm; /* the HMM */
int T = 100; /* length of observation sequence */
int *O; /* the observation sequence O[1..T]*/
int *q; /* the state sequence q[1..T] */
FILE *fp; /* HMM parameters in this file */
int sflg=0, tflg=0, errflg = 0;
int seed; /* random number seed */
int c;
extern char *optarg;
extern int optind, opterr, optopt;
while ((c= getopt(argc, argv, "S:T:")) != EOF)
switch (c) {
case 'S':
/* set random number generator seed */
if (sflg)
errflg++;
else {
sflg++;
sscanf(optarg, "%d", &seed);
}
break;
case 'T':
/* set sequence length */
if (tflg)
errflg++;
else {
tflg++;
sscanf(optarg, "%d", &T);
}
break;
case '?':
errflg++;
}
if ((argc - optind) != 1) errflg++; /* number or arguments not
okay */
if (errflg || !tflg ) {
Usage(argv[0]);
exit(1);
}
/* read HMM file */
fp = fopen(argv[optind],"r");
if (fp == NULL) {
fprintf(stderr, "Error: File %s not found \n", argv[optind]);
exit (1);
}
ReadHMM(fp, &hmm);
fclose(fp);
/* length of observation sequence, T */
O = ivector(1,T); /* alloc space for observation sequence O */
q = ivector(1,T); /* alloc space for state sequence q */
if (!sflg) seed = hmmgetseed();
fprintf(stderr, "RandomSeed: %d\n", seed);
GenSequenceArray(&hmm, seed, T, O, q);
PrintSequence(stdout, T, O);
free_ivector(O, 1, T);
free_ivector(q, 1, T);
FreeHMM(&hmm);
}
