char *Tree2String(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames, boolean printLikelihood,
boolean rellTree, boolean finalPrint, int perGene, boolean branchLabelSupport, boolean printSHSupport)
{
if(rellTree)
assert(!branchLabelSupport && !printSHSupport);
if(branchLabelSupport)
assert(!rellTree && !printSHSupport);
if(printSHSupport)
assert(!branchLabelSupport && !rellTree);
Tree2StringREC(treestr, tr, p, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
while (*treestr) treestr++;
return treestr;
}
char *Tree2String(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames, boolean printLikelihood,
boolean rellTree,
boolean finalPrint, analdef *adef, int perGene, boolean branchLabelSupport, boolean printSHSupport, boolean printIC, boolean printSHSupports)
{
if(rellTree)
assert(!branchLabelSupport && !printSHSupport);
if(branchLabelSupport)
assert(!rellTree && !printSHSupport);
if(printSHSupport)
assert(!branchLabelSupport && !rellTree);
if(finalPrint && adef->outgroup)
{
nodeptr startNode = tr->start;
if(tr->numberOfOutgroups > 1)
{
nodeptr root;
nodeptr *subtrees = (nodeptr *)rax_malloc(sizeof(nodeptr) * tr->mxtips);
int i, k, count = 0;
int *nodeNumbers = (int*)rax_malloc(sizeof(int) * tr->numberOfOutgroups);
int *foundVector = (int*)rax_malloc(sizeof(int) * tr->numberOfOutgroups);
boolean monophyletic = FALSE;
collectSubtrees(tr, subtrees, &count, tr->numberOfOutgroups);
/*printf("Found %d subtrees of size %d\n", count, tr->numberOfOutgroups);*/
for(i = 0; (i < count) && (!monophyletic); i++)
{
int l, sum, nc = 0;
for(k = 0; k < tr->numberOfOutgroups; k++)
{
nodeNumbers[k] = -1;
foundVector[k] = 0;
}
checkOM(subtrees[i], nodeNumbers, &nc, tr);
for(l = 0; l < tr->numberOfOutgroups; l++)
for(k = 0; k < tr->numberOfOutgroups; k++)
{
if(nodeNumbers[l] == tr->outgroupNums[k])
foundVector[l] = 1;
}
sum = 0;
for(l = 0; l < tr->numberOfOutgroups; l++)
sum += foundVector[l];
if(sum == tr->numberOfOutgroups)
{
root = subtrees[i];
tr->start = root;
/*printf("outgroups are monphyletic!\n");*/
monophyletic = TRUE;
}
else
{
if(sum > 0)
{
/*printf("outgroups are NOT monophyletic!\n");*/
monophyletic = FALSE;
}
}
}
if(!monophyletic)
{
printf("WARNING, outgroups are not monophyletic, using first outgroup \"%s\"\n", tr->nameList[tr->outgroupNums[0]]);
printf("from the list to root the tree!\n");
{
FILE *infoFile = myfopen(infoFileName, "ab");
fprintf(infoFile, "\nWARNING, outgroups are not monophyletic, using first outgroup \"%s\"\n", tr->nameList[tr->outgroupNums[0]]);
fprintf(infoFile, "from the list to root the tree!\n");
fclose(infoFile);
}
tr->start = tr->nodep[tr->outgroupNums[0]];
rootedTree(treestr, tr, tr->start->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
}
else
{
if(isTip(tr->start->number, tr->rdta->numsp))
{
printf("Outgroup-Monophyly ERROR; tr->start is a tip \n");
errorExit(-1);
}
if(isTip(tr->start->back->number, tr->rdta->numsp))
{
printf("Outgroup-Monophyly ERROR; tr->start is a tip \n");
errorExit(-1);
}
rootedTree(treestr, tr, tr->start->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
}
rax_free(foundVector);
rax_free(nodeNumbers);
rax_free(subtrees);
}
else
{
tr->start = tr->nodep[tr->outgroupNums[0]];
rootedTree(treestr, tr, tr->start->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, adef, perGene, branchLabelSupport, printSHSupports);
}
tr->start = startNode;
}
else
Tree2StringREC(treestr, tr, p, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport, printIC, printSHSupports);
while (*treestr) treestr++;
return treestr;
}
static char *Tree2StringREC(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames,
boolean printLikelihood, boolean rellTree, boolean finalPrint, int perGene, boolean branchLabelSupport, boolean printSHSupport)
{
char *nameptr;
if(isTip(p->number, tr->mxtips))
{
if(printNames)
{
nameptr = tr->nameList[p->number];
sprintf(treestr, "%s", nameptr);
}
else
sprintf(treestr, "%d", p->number);
while (*treestr) treestr++;
}
else
{
*treestr++ = '(';
treestr = Tree2StringREC(treestr, tr, p->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
*treestr++ = ',';
treestr = Tree2StringREC(treestr, tr, p->next->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
if(p == tr->start->back)
{
*treestr++ = ',';
treestr = Tree2StringREC(treestr, tr, p->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
}
*treestr++ = ')';
}
if(p == tr->start->back)
{
if(printBranchLengths && !rellTree)
sprintf(treestr, ":0.0;\n");
else
sprintf(treestr, ";\n");
}
else
{
if(rellTree || branchLabelSupport || printSHSupport)
{
if(( !isTip(p->number, tr->mxtips)) &&
( !isTip(p->back->number, tr->mxtips)))
{
assert(p->bInf != (branchInfo *)NULL);
if(rellTree)
sprintf(treestr, "%d:%8.20f", p->bInf->support, p->z[0]);
if(branchLabelSupport)
sprintf(treestr, ":%8.20f[%d]", p->z[0], p->bInf->support);
if(printSHSupport)
sprintf(treestr, ":%8.20f[%d]", getBranchLength(tr, perGene, p), p->bInf->support);
}
else
{
if(rellTree || branchLabelSupport)
sprintf(treestr, ":%8.20f", p->z[0]);
if(printSHSupport)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
}
}
else
{
if(printBranchLengths)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
else
sprintf(treestr, "%s", "\0");
}
}
while (*treestr) treestr++;
return treestr;
}
static char *Tree2StringREC(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames,
boolean printLikelihood, boolean rellTree, boolean finalPrint, int perGene, boolean branchLabelSupport, boolean printSHSupport, boolean printIC, boolean printSHSupports)
{
char *nameptr;
if(isTip(p->number, tr->rdta->numsp))
{
if(printNames)
{
nameptr = tr->nameList[p->number];
sprintf(treestr, "%s", nameptr);
}
else
sprintf(treestr, "%d", p->number);
while (*treestr) treestr++;
}
else
{
*treestr++ = '(';
treestr = Tree2StringREC(treestr, tr, p->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport, printIC, printSHSupports);
*treestr++ = ',';
treestr = Tree2StringREC(treestr, tr, p->next->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport, printIC, printSHSupports);
if(p == tr->start->back)
{
*treestr++ = ',';
treestr = Tree2StringREC(treestr, tr, p->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport, printIC, printSHSupports);
}
*treestr++ = ')';
}
if(p == tr->start->back)
{
if(printBranchLengths && !rellTree)
sprintf(treestr, ":0.0;\n");
else
sprintf(treestr, ";\n");
}
else
{
if(rellTree || branchLabelSupport || printSHSupport || printIC || printSHSupports)
{
if(( !isTip(p->number, tr->rdta->numsp)) &&
( !isTip(p->back->number, tr->rdta->numsp)))
{
assert(p->bInf != (branchInfo *)NULL);
assert(rellTree + branchLabelSupport + printSHSupport + printSHSupports == 1);
if(rellTree)
{
if(printIC)
sprintf(treestr, "%1.2f:%8.20f", p->bInf->ic, p->z[0]);
else
sprintf(treestr, "%d:%8.20f", p->bInf->support, p->z[0]);
}
if(branchLabelSupport)
{
if(printIC)
sprintf(treestr, ":%8.20f[%1.2f,%1.2f]", p->z[0], p->bInf->ic, p->bInf->icAll);
else
sprintf(treestr, ":%8.20f[%d]", p->z[0], p->bInf->support);
}
if(printSHSupport)
sprintf(treestr, ":%8.20f[%d]", getBranchLength(tr, perGene, p), p->bInf->support);
if(printSHSupports)
{
int
model;
sprintf(treestr, ":%8.20f[", getBranchLength(tr, perGene, p));
while(*treestr)
treestr++;
for(model = 0; model < tr->NumberOfModels - 1; model++)
{
sprintf(treestr, "%d,", p->bInf->supports[model]);
while(*treestr)
treestr++;
}
sprintf(treestr, "%d]", p->bInf->supports[model]);
}
}
else
{
if(rellTree || branchLabelSupport)
sprintf(treestr, ":%8.20f", p->z[0]);
if(printSHSupport || printSHSupports)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
}
}
else
{
if(printBranchLengths)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
else
sprintf(treestr, "%s", "\0");
}
}
while (*treestr) treestr++;
return treestr;
}
