static char *pllTreeToNewickREC(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 = pllTreeToNewickREC(treestr, tr, p->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
*treestr++ = ',';
treestr = pllTreeToNewickREC(treestr, tr, p->next->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
if(p == tr->start->back)
{
*treestr++ = ',';
treestr = pllTreeToNewickREC(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(0);
/*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 *rootedTreeREC(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames,
boolean printLikelihood, boolean rellTree,
boolean finalPrint, analdef *adef, int perGene, boolean branchLabelSupport, boolean printSHSupport)
{
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 = rootedTreeREC(treestr, tr, p->next->back, printBranchLengths, printNames, printLikelihood,
rellTree, finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
*treestr++ = ',';
treestr = rootedTreeREC(treestr, tr, p->next->next->back, printBranchLengths, printNames, printLikelihood,
rellTree, finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
*treestr++ = ')';
}
if(rellTree || branchLabelSupport || printSHSupport)
{
if(( !isTip(p->number, tr->rdta->numsp)) &&
( !isTip(p->back->number, tr->rdta->numsp)))
{
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 *TreeInner2StringREC(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames,
boolean printLikelihood, boolean rellTree, boolean finalPrint, int perGene, boolean branchLabelSupport, boolean printSHSupport, boolean printInnerNodes)
{
/* TODOFER simplify this, should be used just to print inner nodes for testing */
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 = TreeInner2StringREC(treestr, tr, p->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport, printInnerNodes);
*treestr++ = ',';
treestr = TreeInner2StringREC(treestr, tr, p->next->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport, printInnerNodes);
if(p == tr->start->back)
{
*treestr++ = ',';
treestr = TreeInner2StringREC(treestr, tr, p->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport, printInnerNodes);
}
*treestr++ = ')';
}
if(p == tr->start->back)
{
if(printBranchLengths && !rellTree)
sprintf(treestr, ":0.0;\n");
else
sprintf(treestr, ";\n");
}
else
{
if(rellTree || branchLabelSupport || printSHSupport || printInnerNodes)
{
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);
if(printInnerNodes)
sprintf(treestr, "[%d]", p->number);
}
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;
}
