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 */