void read_parameters_data(parameters *p) {
int i,integertmp=0;
p->genetic_data=readcharintegermatrix(openinputfile(p->datafilename),
&(p->samplesize),&(p->nloci));
p->nSTR=p->nloci-p->ninf;
if (p->samplesize<=1) {
Rprintf("only one individual, unable to analyse this\n\n");
error("error");
}
if (p->labelfilename!=NULL) {
// printf("reading from file %s\n",p->labelfilename);
p->labels=readstrings(p->labelfilename,p->samplesize,20);
for (i=1;i<=p->samplesize;i++) {
Rprintf("%s ",p->labels[i]);
Rprintf("\n");
}
} else {
p->labels=NULL;
}
if (p->locationfilename!=NULL) { /* need to do this because of difficulties with fltk"*/
if (strcmp(p->locationfilename,"")==0) {
FREE(p->locationfilename);
p->locationfilename=NULL;
}
}
if (p->locationfilename==NULL) {
p->location=NULL;
p->npopulations=0;
if (p->migmodel)
myerror("need locations for migration model");
} else {
p->location=readintegervector(openinputfile(p->locationfilename),&(integertmp));
if (p->npopulations==0) {
for (i=1;i<=integertmp;i++) {
if (p->location[i]>p->npopulations)
p->npopulations=p->location[i];
}
}
if (integertmp!=p->samplesize) {
Rprintf("locations %d not the same as # samples %d\n",integertmp,p->samplesize);
error("error");
}
}
if (p->migmodel)
p->propprior.par[0]=(double)p->npopulations;
if (p->npriors==p->locustypes[0]) {
if (p->locustypes[0]==1&&p->locustypes[1]!=1) {
if (p->locustypes[1]!=p->nSTR)
myerror("incorrect locustype - need locustypes equal to number of STR loci");
} else if (p->locustypes[0]!=1) {
integertmp = 0;
for (i=1;i<=p->locustypes[0];i++)
integertmp+=p->locustypes[i];
if (integertmp!=p->nSTR)
myerror("incorrect locustype - sum does not equal number of STR loci");
}
} //else myerror("incorrect number of mutation rate priors");
}
/**
* The example test program creates two pyramid graphs and produces
* the OR-product graph of them. Then it prints the DOT
* representation of such graphs.
*
*/
int main(int argc, char *argv[])
{
int pebbling_bound=0;
int pyramid_height=0;
int tree_height=0;
int chain_length=0;
FILE *input_file=NULL;
int input_directives = 0;
char graph_name[100];
int option_code=0;
/* Parse option to set Pyramid height,
pebbling upper bound. */
while((option_code = getopt(argc,argv,"hb:p:2:c:f:i:g:"))!=-1) {
switch (option_code) {
case 'h':
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_SUCCESS);
break;
case 'b':
pebbling_bound=atoi(optarg);
if (pebbling_bound>0) break;
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_FAILURE);
break;
/* Input */
case 'p':
pyramid_height=atoi(optarg);
if (pyramid_height>0) {input_directives++; break;}
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_FAILURE);
break;
case '2':
tree_height=atoi(optarg);
if (tree_height>0) {input_directives++; break;}
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_FAILURE);
break;
case 'c':
chain_length=atoi(optarg);
if (chain_length>0) {input_directives++; break;}
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_FAILURE);
break;
case 'i':
input_file=openinputfile(optarg);
input_directives++;
break;
case '?':
default:
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_FAILURE);
}
}
/* Test for valid command line */
if (pebbling_bound==0) {
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_FAILURE);
}
/* Only one input */
if (input_directives > 1) {
fprintf(stderr,USAGEMESSAGE,argv[0]);
exit(EXIT_FAILURE);
}
if (input_directives == 0) input_file = stdin;
/* Produce or read input graph */
DAG *C=NULL;
if (pyramid_height>0) {
C=pyramid(pyramid_height);
snprintf(graph_name, 100, "Pyramid of height %d",pyramid_height);
} else if (tree_height>0) {
C=tree(tree_height);
snprintf(graph_name, 100, "Tree of height %d",tree_height);
} else if (chain_length>0) {
C=path(chain_length);
snprintf(graph_name, 100, "Chain of height %d",chain_length);
} else {
C=kthparser(input_file);
fclose(input_file);
snprintf(graph_name, 100, "Input graph");
}
/* Re-output the input graph */
printf("c ===== input DAG ======\n");
printf("c c %s\n", graph_name);
fprint_DAG(stdout,C,"c ");
printf("c ======================\n");
printf("c Dymon-Tompa rounds: %d\n", pebbling_bound);
printf("c ======================\n");
/* Output the QBF */
/* Clean up and exit */
dispose_DAG(C);
exit(EXIT_SUCCESS);
}