void inputoptions(void)
{
/* input the information on the options */
long i;
if(justwts){
if(firstset){
if (ancvar) {
inputancestorsstr(phyloanc->Str[0], anczero0, ancone0);
}
}
for (i = 0; i < (chars); i++)
weight[i] = 1;
inputweightsstr(phyloweights->Str[0], chars, weight, &weights);
}
else {
if (!firstset) {
samenumspstate(phylostates[ith-1], &chars, ith);
reallocchars();
}
for (i = 0; i < (chars); i++)
weight[i] = 1;
if (ancvar)
inputancestorsstr(phyloanc->Str[0], anczero0, ancone0);
if (weights)
inputweightsstr(phyloweights->Str[ith-1], chars, weight, &weights);
}
if ((weights || justwts) && printdata)
printweights(outfile, 0, chars, weight, "Characters");
for (i = 0; i < (chars); i++) {
if (!ancvar) {
anczero[i] = true;
ancone[i] = false;
} else {
anczero[i] = anczero0[i];
ancone[i] = ancone0[i];
}
}
if (ancvar && printdata)
printancestors(outfile, anczero, ancone);
questions = false;
for (i = 0; i < (chars); i++) {
questions = (questions || (ancone[i] && anczero[i]));
threshwt[i] = threshold * weight[i];
}
} /* inputoptions */
void inputoptions()
{
/* input the information on the options */
long i;
scan_eoln(infile);
for (i = 0; i < (chars); i++)
weight[i] = 1;
if (ancvar)
inputancestors(anczero0, ancone0);
if (factors)
inputfactors(chars, factor, &factors);
if (weights)
inputweights(chars, weight, &weights);
putchar('\n');
if (weights)
printweights(stdout, 0, chars, weight, "Characters");
if (factors)
printfactors(stdout, chars, factor, "");
for (i = 0; i < (chars); i++) {
if (!ancvar) {
anczero[i] = true;
ancone[i] = false;
} else {
anczero[i] = anczero0[i];
ancone[i] = ancone0[i];
}
}
if (ancvar)
printancestors(stdout, anczero, ancone);
if (!thresh)
threshold = spp;
questions = false;
for (i = 0; i < (chars); i++) {
questions = (questions || (ancone[i] && anczero[i]));
threshwt[i] = threshold * weight[i];
}
} /* inputoptions */
int main(int argc, Char *argv[])
{ /* Penny's branch-and-bound method */
/* Reads in the number of species, number of characters,
options and data. Then finds all most parsimonious trees */
#ifdef MAC
argc = 1; /* macsetup("Penny",""); */
argv[0] = "Penny";
#endif
init(argc,argv);
openfile(&infile,INFILE,"input file", "r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file", "w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
msets = 1;
firstset = true;
garbage = NULL;
bits = 8*sizeof(long) - 1;
doinit();
if (weights || justwts)
openfile(&weightfile,WEIGHTFILE,"weights file","r",argv[0],weightfilename);
if (trout)
openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
if(ancvar)
openfile(&ancfile,ANCFILE,"ancestors file", "r",argv[0],ancfilename);
if(mixture)
openfile(&mixfile,MIXFILE,"mixture file", "r",argv[0],mixfilename);
for (ith = 1; ith <= msets; ith++) {
if(firstset) {
if (allsokal && !mixture)
fprintf(outfile, "Camin-Sokal parsimony method\n\n");
if (allwagner && !mixture)
fprintf(outfile, "Wagner parsimony method\n\n");
}
doinput();
if (msets > 1 && !justwts) {
fprintf(outfile, "Data set # %ld:\n\n",ith);
if (progress)
printf("\nData set # %ld:\n",ith);
}
if (justwts) {
if(firstset && mixture && printdata)
printmixture(outfile, wagner);
fprintf(outfile, "Weights set # %ld:\n\n", ith);
if (progress)
printf("\nWeights set # %ld:\n\n", ith);
}
else if (mixture && printdata)
printmixture(outfile, wagner);
if (printdata) {
if (weights || justwts)
printweights(outfile, 0, chars, weight, "Characters");
if (ancvar)
printancestors(outfile, anczero, ancone);
}
if (ith == 1)
firstset = false;
maketree();
}
FClose(infile);
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
} /* Penny's branch-and-bound method */
