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 */
