void doinit(void)
{
/* initializes variables */
inputnumbersstate(phylostates[0], &spp, &chars, &nonodes, 1);
words = chars / bits + 1;
// if (printdata)
// fprintf(outfile, "%2ld species, %3ld characters\n\n", spp, chars);
alloctree(&treenode);
setuptree(treenode);
allocrest();
} /* doinit */
void maketree()
{
/* construct the tree */
long i ;
inputdata(replicates, printdata, lower, upper, x, reps);
/* if (njoin && (spp < 3)) {
mexPrintf("\nERROR: Neighbor-Joining runs must have at least 3 species\n\n");
exxit(-1);
} */
if (progress)
putchar('\n');
if (ith == 1)
setuptree(&curtree, nonodes2 + 1);
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
for (i = 0; i < spp; i++)
cluster[i] = curtree.nodep[i];
jointree();
if (njoin)
curtree.start = curtree.nodep[outgrno - 1]->back;
printree(curtree.start, treeprint, njoin, (boolean)(!njoin));
if (treeprint)
summarize();
if (trout) {
col = 0;
if (njoin)
treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start);
else
curtree.root = curtree.start,
treeoutr(curtree.start,&col,&curtree);
}
if (progress) {
mexPrintf("\nOutput written on file \"%s\"\n\n", outfilename);
if (trout)
mexPrintf("Tree written on file \"%s\"\n\n", outtreename);
}
} /* maketree */
void doinput()
{
/* reads the input data */
inputnumbers(&spp, &chars, &nonodes, 1);
words = chars / bits + 1;
printf("%2ld species, %3ld characters\n", spp, chars);
printf("\nReading input file ...\n\n");
getoptions();
if (weights)
openfile(&weightfile,WEIGHTFILE,"weights file","r",progname,weightfilename);
if(ancvar)
openfile(&ancfile,ANCFILE,"ancestors file", "r",progname,ancfilename);
if(factors)
openfile(&factfile,FACTFILE,"factors file", "r",progname,factfilename);
alloctree(&treenode);
setuptree(treenode);
allocrest();
inputoptions();
inputdata(treenode, dollo, false, stdout);
} /* doinput */
void maketree()
{
/* construct the tree */
long i ;
inputdata(replicates, printdata, lower, upper, x, reps);
if (progress)
putchar('\n');
if (ith == 1)
setuptree(&curtree, nonodes2 + 1);
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
for (i = 0; i < spp; i++)
cluster[i] = curtree.nodep[i];
jointree();
if (outgropt)
curtree.start = curtree.nodep[outgrno - 1]->back;
printree(&curtree, curtree.start->next,
treeprint, njoin, !njoin);
if (treeprint)
summarize();
if (trout) {
col = 0;
if (njoin)
treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start);
else
curtree.root = curtree.start,
treeoutr(curtree.start,&col,&curtree);
}
if (progress) {
printf("\nOutput written on output file\n\n");
if (trout)
printf("Tree written on tree file\n\n");
}
} /* maketree */
void globrearrange()
{ /* does global rearrangements */
tree globtree;
tree oldtree;
int i,j,k,num_sibs,num_sibs2;
node *where,*sib_ptr,*sib_ptr2;
double oldbestyet = curtree.likelihood;
int success = false;
alloctree(&globtree.nodep,nonodes2);
alloctree(&oldtree.nodep,nonodes2);
setuptree(&globtree,nonodes2);
setuptree(&oldtree,nonodes2);
allocview(&oldtree, nonodes2, totalleles);
allocview(&globtree, nonodes2, totalleles);
copy_(&curtree,&globtree);
copy_(&curtree,&oldtree);
for ( i = spp ; i < nonodes2 ; i++ ) {
num_sibs = count_sibs(curtree.nodep[i]);
sib_ptr = curtree.nodep[i];
if ( (i - spp) % (( nonodes2 / 72 ) + 1 ) == 0 )
putchar('.');
fflush(stdout);
for ( j = 0 ; j <= num_sibs ; j++ ) {
re_move(&sib_ptr,&where);
copy_(&curtree,&priortree);
if (where->tip) {
copy_(&oldtree,&curtree);
copy_(&oldtree,&bestree);
sib_ptr = sib_ptr->next;
continue;
}
else num_sibs2 = count_sibs(where);
sib_ptr2 = where;
for ( k = 0 ; k < num_sibs2 ; k++ ) {
addwhere = NULL;
addtraverse(sib_ptr,sib_ptr2->back,true);
if ( addwhere && where != addwhere && where->back != addwhere
&& bestree.likelihood > globtree.likelihood) {
copy_(&bestree,&globtree);
success = true;
}
sib_ptr2 = sib_ptr2->next;
}
copy_(&oldtree,&curtree);
copy_(&oldtree,&bestree);
sib_ptr = sib_ptr->next;
}
}
copy_(&globtree,&curtree);
copy_(&globtree,&bestree);
if (success && globtree.likelihood > oldbestyet) {
succeeded = true;
}
else {
succeeded = false;
}
freeview(&oldtree, nonodes2);
freeview(&globtree, nonodes2);
freetree(&globtree.nodep,nonodes2);
freetree(&oldtree.nodep,nonodes2);
}
void maketree()
{ /* construct the tree */
long i;
if (usertree) {
/* Open in binary: ftell() is broken for UNIX line-endings under WIN32 */
openfile(&intree,INTREE,"input tree file", "rb",progname,intreename);
numtrees = countsemic(&intree);
if(numtrees > MAXSHIMOTREES)
shimotrees = MAXSHIMOTREES;
else
shimotrees = numtrees;
if (numtrees > 2)
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) {
for (i = 0 ; i < nonodes2 ; i++) {
if ( i > spp) {
/* must do this since not all nodes may be used if an
unrooted tree is read in after a rooted one */
curtree.nodep[i]->back = NULL;
curtree.nodep[i]->next->back = NULL;
curtree.nodep[i]->next->next->back = NULL;
}
else curtree.nodep[i]->back = NULL;
}
treeread2 (intree, &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", 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 */
void maketree()
{
/* contruct the tree */
long nextsp,numtrees;
boolean succeeded=false;
long i, j, which;
if (usertree) {
inputdata(replicates, printdata, lower, upper, x, reps);
setuptree(&curtree, nonodes2);
for (which = 1; which <= spp; which++)
setuptipf(which, &curtree);
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
openfile(&intree,INTREE,"input tree file","r",progname,intreename);
fscanf(intree, "%ld%*[^\n]", &numtrees);
getc(intree);
if (numtrees > MAXNUMTREES) {
printf("\nERROR: number of input trees is read incorrectly from %s\n",
intreename);
exxit(-1);
}
if (treeprint) {
fprintf(outfile, "User-defined tree");
if (numtrees > 1)
putc('s', outfile);
fprintf(outfile, ":\n\n");
}
first = true;
which = 1;
while (which <= numtrees) {
treeread2 (intree, &curtree.start, curtree.nodep,
lengths, &trweight, &goteof, intreename, "Fitch",
&haslengths, &spp);
nums = spp;
curtree.start = curtree.nodep[outgrno - 1]->back;
treevaluate();
printree(&curtree, curtree.start, treeprint, false, false);
summarize(numtrees);
which++;
}
FClose(intree);
} else {
if (jumb == 1) {
inputdata(replicates, printdata, lower, upper, x, reps);
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, nextsp);
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) {
nums = nextsp;
buildnewtip(enterorder[nextsp - 1], &curtree, nextsp);
copy_(&curtree, &priortree);
bestree.likelihood = -99999.0;
addtraverse(curtree.nodep[enterorder[nextsp - 1] - 1]->back,
curtree.start, true, &numtrees,&succeeded);
copy_(&bestree, &curtree);
if (progress) {
writename(nextsp - 1, 1, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
if (global && nextsp == spp) {
if (progress) {
printf("Doing global rearrangements\n");
printf(" !");
for (j = 1; j <= (spp - 2); j++)
putchar('-');
printf("!\n");
printf(" ");
}
}
succeeded = true;
while (succeeded) {
succeeded = false;
rearrange(curtree.start,
&numtrees,&nextsp,&succeeded);
if (global && ((nextsp) == spp) && progress)
printf("\n ");
}
if (global && nextsp == spp) {
putc('\n', outfile);
if (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(&curtree, curtree.start, treeprint, true, false);
summarize(numtrees);
}
nextsp++;
}
}
if (jumb == njumble && progress) {
printf("\nOutput written to output file\n\n");
if (trout) {
printf("Tree also written onto file\n");
putchar('\n');
}
}
} /* maketree */
