void emboss_getoptions(char *pgm, int argc, char *argv[]) { AjPStr test = NULL; AjPStr outputformat = NULL; AjPStr typeofseq = NULL; AjPStr justweights = NULL; AjBool rewrite = false; long inseed, inseed0; data = genefreqs; seq = dna; bootstrap = false; jackknife = false; permute = false; ild = false; lockhart = false; blocksize = 1; regular = true; fracsample = 1.0; all = true; reps = 100; weights = false; mixture = false; ancvar = false; categories = false; justwts = false; printdata = false; dotdiff = true; progress = true; interleaved = true; xml = false; nexus = false; factors = false; enzymes = false; embInitPV(pgm, argc, argv, "PHYLIPNEW",VERSION); phylofreqs = ajAcdGetFrequencies("infile"); test = ajAcdGetListSingle("test"); if(ajStrMatchC(test, "b")) { bootstrap = true; regular = ajAcdGetToggle("regular"); if(regular) fracsample = 1.0; else { fracsample = ajAcdGetFloat("fracsample"); fracsample = fracsample/100.0; } blocksize = ajAcdGetInt("blocksize"); } else if(ajStrMatchC(test, "j")) { jackknife = true; regular = ajAcdGetToggle("regular"); if(regular) fracsample = 0.5; else { fracsample = ajAcdGetFloat("fracsample"); fracsample = fracsample/100.0; } } else if(ajStrMatchC(test, "c")) permute = true; else if(ajStrMatchC(test, "o")) ild = true; else if(ajStrMatchC(test, "s")) lockhart = true; else if(ajStrMatchC(test, "r")) rewrite = true; if(rewrite) { if (data == seqs) { outputformat = ajAcdGetListSingle("rewriteformat"); if(ajStrMatchC(outputformat, "n")) nexus = true; else if(ajStrMatchC(outputformat, "x")) xml = true; if( (nexus) || (xml) ) { typeofseq = ajAcdGetListSingle("seqtype"); if(ajStrMatchC(typeofseq, "d")) seq = dna; else if(ajStrMatchC(typeofseq, "r")) seq = rna; else if(ajStrMatchC(typeofseq, "p")) seq = protein; } } } else{ reps = ajAcdGetInt("reps"); inseed = ajAcdGetInt("seed"); emboss_initseed(inseed, &inseed0, seed); if(jackknife || bootstrap || permute) { phyloweights = ajAcdGetProperties("weights"); if(phyloweights) weights = true; } if(!permute) { justweights = ajAcdGetListSingle("justweights"); if(ajStrMatchC(justweights, "j")) justwts = true; } } printdata = ajAcdGetBoolean("printdata"); if(printdata) dotdiff = ajAcdGetBoolean("dotdiff"); progress = ajAcdGetBoolean("progress"); embossoutfile = ajAcdGetOutfile("outfile"); emboss_openfile(embossoutfile, &outfile, &outfilename); printf("\n bootstrap: %s",(bootstrap ? "true" : "false")); printf("\njackknife: %s",(jackknife ? "true" : "false")); printf("\n permute: %s",(permute ? "true" : "false")); printf("\n lockhart: %s",(lockhart ? "true" : "false")); printf("\n ild: %s",(ild ? "true" : "false")); printf("\n justwts: %s \n",(justwts ? "true" : "false")); } /* emboss_getoptions */
void emboss_getoptions(char *pgm, int argc, char *argv[]) { AjPStr datatype = NULL; global = false; jumble = false; njumble = 1; lengths = false; outgrno = 1; outgropt = false; all = true; contchars = false; trout = true; usertree = false; printdata = false; progress = true; treeprint = true; mulsets = false; datasets = 1; embInitPV (pgm, argc, argv, "PHYLIPNEW",VERSION); phylofreq = ajAcdGetFrequencies("infile"); phylotrees = ajAcdGetTree("intreefile"); if (phylotrees) { numtrees = 0; while (phylotrees[numtrees]) numtrees++; usertree = true; lengths = ajAcdGetBoolean("lengths"); } datatype = ajAcdGetListSingle("datatype"); if(ajStrMatchC(datatype, "c")) contchars = true; outgrno = ajAcdGetInt("outgrno"); if(outgrno != 0) outgropt = true; else outgrno = 1; if(!usertree) { global = ajAcdGetBoolean("global"); njumble = ajAcdGetInt("njumble"); if(njumble >0) { inseed = ajAcdGetInt("seed"); jumble = true; emboss_initseed(inseed, &inseed0, seed); } else njumble = 1; } printdata = ajAcdGetBoolean("printdata"); progress = ajAcdGetBoolean("progress"); treeprint = ajAcdGetBoolean("treeprint"); trout = ajAcdGetToggle("trout"); embossoutfile = ajAcdGetOutfile("outfile"); embossouttree = ajAcdGetOutfile("outtreefile"); emboss_openfile(embossoutfile, &outfile, &outfilename); if(trout) emboss_openfile(embossouttree, &outtree, &outtreename); fprintf(outfile, "\nContinuous character Maximum Likelihood"); fprintf(outfile, " method version %s\n\n",VERSION); ajStrDel(&datatype); } /* emboss_getoptions */