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 */
