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[])
{
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 maketree()
{
/* constructs a binary tree from the pointers in treenode.
adds each node at location which yields highest "likelihood"
then rearranges the tree for greatest "likelihood" */
long i, j, nextnode;
double gotlike;
node *item, *nufork, *dummy, *p;
char *treestr;
fullset = (1L << (bits + 1)) - (1L << 1);
if (!usertree) {
for (i = 1; i <= (spp); i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
root = treenode[enterorder[0] - 1];
add(treenode[enterorder[0] - 1], treenode[enterorder[1] - 1],
treenode[spp], &root, treenode);
if (progress) {
printf("Adding species:\n");
writename(0, 2, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
lastrearr = false;
for (i = 3; i <= (spp); i++) {
bestyet = -350.0 * spp * chars;
item = treenode[enterorder[i - 1] - 1];
nufork = treenode[spp + i - 2];
addpreorder(root, item, nufork);
add(there, item, nufork, &root, treenode);
like = bestyet;
rearrange(&root);
if (progress) {
writename(i - 1, 1, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
lastrearr = (i == spp);
if (lastrearr) {
if (progress) {
printf("\nDoing global rearrangements\n");
printf(" !");
for (j = 1; j <= (nonodes); j++)
if ( j % (( nonodes / 72 ) + 1 ) == 0 )
putchar('-');
printf("!\n");
#ifdef WIN32
phyFillScreenColor();
#endif
}
bestlike = bestyet;
if (jumb == 1) {
bstlike2 = bestlike;
nextree = 1;
}
do {
if (progress)
printf(" ");
gotlike = bestlike;
for (j = 0; j < (nonodes); j++) {
bestyet = - 350.0 * spp * chars;
item = treenode[j];
if (item != root) {
nufork = treenode[j]->back;
re_move(&item, &nufork, &root, treenode);
there = root;
addpreorder(root, item, nufork);
add(there, item, nufork, &root, treenode);
}
if (progress) {
if ( j % (( nonodes / 72 ) + 1 ) == 0 )
putchar('.');
fflush(stdout);
}
}
if (progress) {
putchar('\n');
#ifdef WIN32
phyFillScreenColor();
#endif
}
} while (bestlike > gotlike);
}
}
if (progress)
putchar('\n');
for (i = spp - 1; i >= 1; i--)
re_move(&treenode[i], &dummy, &root, treenode);
if (jumb == njumble) {
if (treeprint) {
putc('\n', outfile);
if (nextree == 2)
fprintf(outfile, "One most parsimonious tree found:\n");
else
fprintf(outfile, "%6ld trees in all found\n", nextree - 1);
}
if (nextree > maxtrees + 1) {
if (treeprint)
fprintf(outfile, "here are the first%4ld of them\n", (long)maxtrees);
nextree = maxtrees + 1;
}
if (treeprint)
putc('\n', outfile);
for (i = 0; i <= (nextree - 2); i++) {
root = treenode[0];
add(treenode[0], treenode[1], treenode[spp], &root, treenode);
for (j = 3; j <= spp; j++) {
add(treenode[bestrees[i].btree[j - 1] - 1], treenode[j - 1],
treenode[spp + j - 2], &root, treenode);}
evaluate(root);
printree(1.0, treeprint, root);
describe();
for (j = 1; j < (spp); j++)
re_move(&treenode[j], &dummy, &root, treenode);
}
}
} else {
if (numtrees > 2) {
emboss_initseed(inseed, &inseed0, seed);
printf("\n");
}
if (treeprint) {
fprintf(outfile, "User-defined tree");
if (numtrees > 1)
putc('s', outfile);
fprintf(outfile, ":\n");
}
names = (boolean *)Malloc(spp*sizeof(boolean));
which = 1;
firsttree = true; /**/
nodep = NULL; /**/
nextnode = 0; /**/
haslengths = 0; /**/
phirst = 0; /**/
zeros = (long *)Malloc(chars*sizeof(long)); /**/
for (i = 0; i < chars; i++) /**/
zeros[i] = 0; /**/
while (which <= numtrees) {
treestr = ajStrGetuniquePtr(&phylotrees[which-1]->Tree);
treeread(&treestr, &root, treenode, &goteof, &firsttree,
nodep, &nextnode, &haslengths,
&grbg, initdollopnode,false,nonodes);
for (i = spp; i < (nonodes); i++) {
p = treenode[i];
for (j = 1; j <= 3; j++) {
p->stateone = (bitptr)Malloc(words*sizeof(long));
p->statezero = (bitptr)Malloc(words*sizeof(long));
p = p->next;
}
} /* debug: see comment at initdollopnode() */
if (treeprint)
fprintf(outfile, "\n\n");
evaluate(root);
printree(1.0, treeprint, root);
describe();
which++;
}
FClose(intree);
fprintf(outfile, "\n\n");
if (numtrees > 1 && chars > 1)
standev(numtrees, minwhich, minsteps, nsteps, fsteps, seed);
free(names);
}
if (jumb == njumble) {
if (progress) {
printf("Output written to file \"%s\"\n\n", outfilename);
if (trout)
printf("Trees also written onto file \"%s\"\n\n", outtreename);
}
if (ancseq)
freegarbage(&garbage);
}
} /* maketree */
void maketree()
{ /* construct the tree */
long i;
char* treestr;
if (usertree) {
if(numtrees > MAXSHIMOTREES)
shimotrees = MAXSHIMOTREES;
else
shimotrees = numtrees;
if (numtrees > 2)
emboss_initseed(inseed, &inseed0, seed);
if (treeprint) {
fprintf(outfile, "User-defined tree");
if (numtrees > 1)
putc('s', outfile);
putc('\n', outfile);
}
setuptree(&curtree, nonodes2);
for (which = 1; which <= spp; which++)
inittip(which, &curtree);
which = 1;
while (which <= numtrees) {
treestr = ajStrGetuniquePtr(&phylotrees[which-1]->Tree);
treeread2 (&treestr, &curtree.start, curtree.nodep,
lengths, &trweight, &goteof, &haslengths, &spp,false,nonodes2);
curtree.start = curtree.nodep[outgrno - 1]->back;
treevaluate();
printree();
summarize();
which++;
}
FClose(intree);
if (numtrees > 1 && loci > 1 ) {
weight = (long *)Malloc(loci*sizeof(long));
for (i = 0; i < loci; i++)
weight[i] = 1;
standev2(numtrees, maxwhich, 0, loci-1, maxlogl, l0gl, l0gf, seed);
free(weight);
fprintf(outfile, "\n\n");
}
} else { /* if ( !usertree ) */
if (jumb == 1) {
setuptree(&curtree, nonodes2);
setuptree(&priortree, nonodes2);
setuptree(&bestree, nonodes2);
if (njumble > 1)
setuptree(&bestree2, nonodes2);
}
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
nextsp = 3;
buildsimpletree(&curtree);
curtree.start = curtree.nodep[enterorder[0] - 1]->back;
if (jumb == 1) numtrees = 1;
nextsp = 4;
if (progress) {
printf("Adding species:\n");
writename(0, 3, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
while (nextsp <= spp) {
buildnewtip(enterorder[nextsp - 1], &curtree, nextsp);
copy_(&curtree, &priortree);
bestree.likelihood = -DBL_MAX;
addtraverse(curtree.nodep[enterorder[nextsp - 1] - 1]->back,
curtree.start, true );
copy_(&bestree, &curtree);
if (progress) {
writename(nextsp - 1, 1, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
if (global && nextsp == spp) {
if (progress) {
printf("\nDoing global rearrangements\n");
printf(" !");
for (i = 1; i <= spp - 2; i++)
if ( (i - spp) % (( nonodes2 / 72 ) + 1 ) == 0 )
putchar('-');
printf("!\n");
printf(" ");
}
}
succeeded = true;
while (succeeded) {
succeeded = false;
if ( global && nextsp == spp )
globrearrange();
else
rearrange(curtree.start);
if (global && nextsp == spp)
putc('\n', outfile);
}
if (global && nextsp == spp && progress)
putchar('\n');
if (njumble > 1) {
if (jumb == 1 && nextsp == spp)
copy_(&bestree, &bestree2);
else if (nextsp == spp) {
if (bestree2.likelihood < bestree.likelihood)
copy_(&bestree, &bestree2);
}
}
if (nextsp == spp && jumb == njumble) {
if (njumble > 1) copy_(&bestree2, &curtree);
curtree.start = curtree.nodep[outgrno - 1]->back;
printree();
summarize();
}
nextsp++;
}
}
if ( jumb < njumble)
return;
if (progress) {
printf("\nOutput written to file \"%s\"\n", outfilename);
if (trout)
printf("\nTree also written onto file \"%s\"\n\n", outtreename);
}
freeview(&curtree, nonodes2);
if (!usertree) {
freeview(&bestree, nonodes2);
freeview(&priortree, nonodes2);
}
for (i = 0; i < spp; i++)
free(x[i]);
if (!contchars) {
free(locus);
free(pbar);
}
} /* maketree */
