void inputoptions()
{
/* read options information */
long i;
if (!firstset && !justwts) {
samenumsp(&sites, ith);
reallocsites();
}
for (i = 0; i < sites; i++) {
category[i] = 1;
oldweight[i] = 1;
}
if (justwts || weights)
inputweights(sites, oldweight, &weights);
if (printdata)
putc('\n', outfile);
if (jukes && printdata)
fprintf(outfile, " Jukes-Cantor Distance\n");
if (kimura && printdata)
fprintf(outfile, " Kimura 2-parameter Distance\n");
if (f84 && printdata)
fprintf(outfile, " F84 Distance\n");
if (similarity)
fprintf(outfile, " \n Table of similarity between sequences\n");
if (firstset && printdata && (kimura || f84))
fprintf(outfile, "\nTransition/transversion ratio = %10.6f\n", ttratio);
if (ctgry && categs > 1) {
inputcategs(0, sites, category, categs, "DnaDist");
if (printdata)
printcategs(outfile, sites, category, "Site categories");
} else if (printdata && (categs > 1)) {
fprintf(outfile, "\nSite category Rate of change\n\n");
for (i = 1; i <= categs; i++)
fprintf(outfile, "%12ld%13.3f\n", i, rate[i - 1]);
putc('\n', outfile);
printcategories();
}
if ((jukes || kimura || logdet) && freqsfrom) {
printf(" WARNING: CANNOT USE EMPIRICAL BASE FREQUENCIES");
printf(" WITH JUKES-CANTOR, KIMURA, JIN/NEI OR LOGDET DISTANCES\n");
exxit(-1);
}
if (jukes)
ttratio = 0.5000001;
if (weights && printdata)
printweights(outfile, 0, sites, oldweight, "Sites");
} /* inputoptions */
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 */
void inputoptions()
{
/* input the information on the options */
long weightsum, maxfactsize, i, j, k, l, m;
if (data == genefreqs) {
k = 0;
l = 0;
for (i = 0; i < (loci); i++) {
m = alleles[i];
k++;
for (j = 1; j <= m; j++) {
l++;
factorr[l - 1] = k;
}
}
} else {
for (i = 1; i <= (sites); i++)
factorr[i - 1] = i;
}
for (i = 0; i < (sites); i++)
oldweight[i] = 1;
if (weights)
inputweightsstr2(phyloweights->Str[0],0, sites, &weightsum, oldweight, &weights, "seqboot");
if (factors && printdata) {
for(i = 0; i < sites; i++)
factor[i] = (char)('0' + (factorr[i]%10));
printfactors(outfile, sites, factor, " (least significant digit)");
}
if (weights && printdata)
printweights(outfile, 0, sites, oldweight, "Sites");
for (i = 0; i < (loci); i++)
how_many[i] = 0;
for (i = 0; i < (loci); i++)
where[i] = 0;
for (i = 1; i <= (sites); i++) {
how_many[factorr[i - 1] - 1]++;
if (where[factorr[i - 1] - 1] == 0)
where[factorr[i - 1] - 1] = i;
}
groups = factorr[sites - 1];
newgroups = 0;
newsites = 0;
maxfactsize = 0;
for(i = 0 ; i < loci ; i++){
if(how_many[i] > maxfactsize){
maxfactsize = how_many[i];
}
}
maxnewsites = groups * maxfactsize;
allocnew();
for (i = 0; i < (groups); i++) {
if (oldweight[where[i] - 1] > 0) {
newgroups++;
newsites += how_many[i];
newwhere[newgroups - 1] = where[i];
newhowmany[newgroups - 1] = how_many[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 */