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 doinput(int argc, Char *argv[])
{ /* reads the input data */
getoptions();
seqboot_inputnumbers();
allocrest();
if (weights)
openfile(&weightfile,WEIGHTFILE,"input weight file",
"r",argv[0],weightfilename);
if (mixture){
openfile(&mixfile,MIXFILE,"mixture file", "r",argv[0],mixfilename);
openfile(&outmixfile,"outmixture","output mixtures file","w",argv[0],
outmixfilename);
seqboot_inputaux(mixdata, mixfile);
}
if (ancvar){
openfile(&ancfile,ANCFILE,"ancestor file", "r",argv[0],ancfilename);
openfile(&outancfile,"outancestors","output ancestors file","w",argv[0],
outancfilename);
seqboot_inputaux(ancdata, ancfile);
}
if (categories) {
openfile(&catfile,CATFILE,"input category file","r",argv[0],catfilename);
openfile(&outcatfile,"outcategories","output category file","w",argv[0],
outcatfilename);
inputcategs(0, sites, category, 9, "SeqBoot");
}
if (factors){
openfile(&factfile,FACTFILE,"factors file","r",argv[0],factfilename);
openfile(&outfactfile,"outfactors","output factors file","w",argv[0],
outfactfilename);
}
if (justwts && !permute)
openfile(&outweightfile,"outweights","output weight file",
"w",argv[0],outweightfilename);
else {
openfile(&outfile,OUTFILE,"output data file","w",argv[0],outfilename);
}
inputoptions();
seqboot_inputdata();
} /* doinput */
