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[]) { ajint numseqs=0; ajint numwts=0; AjPStr method = NULL; ancvar = false; dollo = true; jumble = false; njumble = 1; trout = true; usertree = false; goteof = false; weights = false; justwts = false; printdata = false; progress = true; treeprint = true; stepbox = false; ancseq = false; mulsets = false; msets = 1; embInitPV(pgm, argc, argv, "PHYLIPNEW",VERSION); phylostates = ajAcdGetDiscretestates("infile"); while (phylostates[numseqs]) numseqs++; phylotrees = ajAcdGetTree("intreefile"); if (phylotrees) { numtrees = 0; while (phylotrees[numtrees]) numtrees++; usertree = true; } phyloweights = ajAcdGetProperties("weights"); if (phyloweights) { weights = true; numwts = ajPhyloPropGetSize(phyloweights); } if (numseqs > 1) { mulsets = true; msets = numseqs; } else if (numwts > 1) { mulsets = true; msets = numwts; justwts = true; } method = ajAcdGetListSingle("method"); if(ajStrMatchC(method, "d")) dollo = true; else dollo = false; if(!usertree) { njumble = ajAcdGetInt("njumble"); if(njumble >0) { inseed = ajAcdGetInt("seed"); jumble = true; emboss_initseed(inseed, &inseed0, seed); } else njumble = 1; } if((mulsets) && (!jumble)) { jumble = true; inseed = ajAcdGetInt("seed"); emboss_initseed(inseed, &inseed0, seed); } phyloanc = ajAcdGetProperties("ancfile"); if(phyloanc) ancvar = true; threshold = ajAcdGetFloat("threshold"); printdata = ajAcdGetBoolean("printdata"); progress = ajAcdGetBoolean("progress"); treeprint = ajAcdGetBoolean("treeprint"); trout = ajAcdGetToggle("trout"); stepbox = ajAcdGetBoolean("stepbox"); ancseq = ajAcdGetBoolean("ancseq"); embossoutfile = ajAcdGetOutfile("outfile"); emboss_openfile(embossoutfile, &outfile, &outfilename); if(trout) { embossouttree = ajAcdGetOutfile("outtreefile"); emboss_openfile(embossouttree, &outtree, &outtreename); } printf("\nDollo and polymorphism parsimony algorithm, version %s\n\n", VERSION); fprintf(outfile,"\nDollo and polymorphism parsimony algorithm,"); fprintf(outfile," version %s\n\n",VERSION); } /* emboss_getoptions */
void emboss_getoptions(char *pgm, int argc, char *argv[]) { /* get from user the relevant parameters for the plotter and diagram */ boolean getgrows; int m, n; AjPStr getstyle = NULL; AjPStr plottercode = NULL; AjPStr getpreviewer = NULL; AjPStr getnodeposition = NULL; embInitPV(pgm, argc, argv, "PHYLIPNEW",VERSION); n = (int)((pagex-hpmargin-0.01)/(paperx-hpmargin)+1.0); m = (int)((pagey-vpmargin-0.01)/(papery-vpmargin)+1.0); phylotrees = ajAcdGetTree("intreefile"); plottercode = ajAcdGetListSingle("plotter"); getplotter(ajStrGetCharFirst(plottercode)); preview = true; getpreviewer = ajAcdGetListSingle("previewer"); /* sets plotter variable */ if(ajStrMatchC(getpreviewer, "n")) { preview = false; previewer = other; /* Added by Dan F. */ } else if(ajStrMatchC(getpreviewer, "i")) previewer = ibm; else if(ajStrMatchC(getpreviewer, "m")) previewer = mac; else if(ajStrMatchC(getpreviewer, "x")) previewer = xpreview; else if(ajStrMatchC(getpreviewer, "w")) previewer = winpreview; else if(ajStrMatchC(getpreviewer, "i")) previewer = tek; else if(ajStrMatchC(getpreviewer, "i")) previewer = decregis; else if(ajStrMatchC(getpreviewer, "o")) previewer = other; getgrows = ajAcdGetBoolean("grows"); if(getgrows) grows = horizontal; else grows = vertical; getstyle = ajAcdGetListSingle("style"); if(ajStrMatchC(getstyle, "c")) style = cladogram; else if(ajStrMatchC(getstyle, "p")) style = phenogram; else if(ajStrMatchC(getstyle, "e")) style = eurogram; else if(ajStrMatchC(getstyle, "s")) style = swoopogram; else if(ajStrMatchC(getstyle, "v")) style = curvogram; else if(ajStrMatchC(getstyle, "o")) { style = circular; treedepth = 1.0; } uselengths = ajAcdGetBoolean("lengths"); labelrotation = ajAcdGetFloat("labelrotation"); if(plotter==ray) { xmargin = ajAcdGetFloat("xrayshade"); ymargin = ajAcdGetFloat("yrayshade"); } else { xmargin = ajAcdGetFloat("xmargin"); ymargin = ajAcdGetFloat("ymargin"); } rescaled = ajAcdGetToggle("rescaled"); if(rescaled) bscale = ajAcdGetFloat("bscale"); treedepth = ajAcdGetFloat("treedepth"); stemlength = ajAcdGetFloat("stemlength"); nodespace = ajAcdGetFloat("nodespace"); nodespace = 1.0 / nodespace; m = ajAcdGetFloat("pagesheight"); n = ajAcdGetFloat("pageswidth"); paperx = ajAcdGetFloat("paperx"); papery = ajAcdGetFloat("papery"); hpmargin = ajAcdGetFloat("hpmargin"); vpmargin = ajAcdGetFloat("vpmargin"); pagex = ((double)n * (paperx-hpmargin)+hpmargin); pagey = ((double)m * (papery-vpmargin)+vpmargin); getnodeposition = ajAcdGetListSingle("nodeposition"); if(ajStrMatchC(getnodeposition, "i")) nodeposition = intermediate; else if(ajStrMatchC(getnodeposition, "w")) nodeposition = weighted; else if(ajStrMatchC(getnodeposition, "c")) nodeposition = centered; else if(ajStrMatchC(getnodeposition, "i")) nodeposition = inner; else if(ajStrMatchC(getnodeposition, "v")) nodeposition = vshaped; embossplotfile = ajAcdGetOutfile("plotfile"); emboss_openfile(embossplotfile, &plotfile, &pltfilename); } /* getparms */
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 */
void emboss_getoptions(char *pgm, int argc, char *argv[]) { AjPStr disttype = NULL; AjPStr tree_p = NULL; AjPStr style = NULL; dtype = PHYLIPBSD; tree_pairing = ADJACENT_PAIRS; output_scheme = VERBOSE; ibmpc = IBMCRT; ansi = ANSICRT; didreroot = false; spp = 0; grbg = NULL; col = 0; noroot = true; numopts = 0; outgrno = 1; outgropt = false; progress = true; /* The following are not used by treedist, but may be used in functions in cons.c, so we set them here. */ treeprint = false; trout = false; prntsets = false; embInitPV(pgm, argc, argv, "PHYLIPNEW",VERSION); phylotrees = ajAcdGetTree("intreefile"); trees_in_1 = 0; while (phylotrees[trees_in_1]) trees_in_1++; progress = ajAcdGetBoolean("progress"); outgrno = ajAcdGetInt("outgrno"); if(outgrno != 0) outgropt = true; else outgrno = 1; disttype = ajAcdGetListSingle("dtype"); if(ajStrMatchC(disttype, "s")) dtype = PHYLIPSYMMETRIC; else dtype = PHYLIPBSD; noroot = !ajAcdGetBoolean("noroot"); tree_p = ajAcdGetListSingle("pairing"); if(ajStrMatchC(tree_p, "a")) tree_pairing = ADJACENT_PAIRS; else if(ajStrMatchC(tree_p, "p")) tree_pairing = ALL_IN_FIRST; style = ajAcdGetListSingle("style"); if(ajStrMatchC(style, "f")) output_scheme = FULL_MATRIX; else if(ajStrMatchC(style, "s")) output_scheme = SPARSE; else if(ajStrMatchC(style, "v")) output_scheme = VERBOSE; embossoutfile = ajAcdGetOutfile("outfile"); emboss_openfile(embossoutfile, &outfile, &outfilename); } /* embosss_getoptions */