static boolean addElementLenMULT (FILE *fp, tree *tr, nodeptr p, int partitionCounter)
{
nodeptr q, r, s;
int n, ch, fres, rn;
double randomResolution;
int old;
tr->constraintVector[p->number] = partitionCounter;
if ((ch = treeGetCh(fp)) == '(')
{
partCount++;
old = partCount;
n = (tr->nextnode)++;
if (n > 2*(tr->mxtips) - 2)
{
if (tr->rooted || n > 2*(tr->mxtips) - 1)
{
printf("ERROR: Too many internal nodes. Is tree rooted?\n");
printf(" Deepest splitting should be a trifurcation.\n");
return FALSE;
}
else
{
tr->rooted = TRUE;
}
}
q = tr->nodep[n];
tr->constraintVector[q->number] = partCount;
if (! addElementLenMULT(fp, tr, q->next, old)) return FALSE;
if (! treeNeedCh(fp, ',', "in")) return FALSE;
if (! addElementLenMULT(fp, tr, q->next->next, old)) return FALSE;
hookupDefault(p, q, tr->numBranches);
while((ch = treeGetCh(fp)) == ',')
{
n = (tr->nextnode)++;
if (n > 2*(tr->mxtips) - 2)
{
if (tr->rooted || n > 2*(tr->mxtips) - 1)
{
printf("ERROR: Too many internal nodes. Is tree rooted?\n");
printf(" Deepest splitting should be a trifurcation.\n");
return FALSE;
}
else
{
tr->rooted = TRUE;
}
}
r = tr->nodep[n];
tr->constraintVector[r->number] = partCount;
rn = randomInt(10000);
if(rn == 0)
randomResolution = 0;
else
randomResolution = ((double)rn)/10000.0;
if(randomResolution < 0.5)
{
s = q->next->back;
r->back = q->next;
q->next->back = r;
r->next->back = s;
s->back = r->next;
addElementLenMULT(fp, tr, r->next->next, old);
}
else
{
s = q->next->next->back;
r->back = q->next->next;
q->next->next->back = r;
r->next->back = s;
s->back = r->next;
addElementLenMULT(fp, tr, r->next->next, old);
}
}
if(ch != ')')
{
printf("Missing /) in treeReadLenMULT\n");
exit(-1);
}
(void) treeFlushLabel(fp);
}
else
{
ungetc(ch, fp);
if ((n = treeFindTipName(fp, tr)) <= 0) return FALSE;
q = tr->nodep[n];
tr->constraintVector[q->number] = partitionCounter;
if (tr->start->number > n) tr->start = q;
(tr->ntips)++;
hookupDefault(p, q, tr->numBranches);
}
fres = treeFlushLen(fp);
if(!fres) return FALSE;
return TRUE;
}
int treeReadLen (FILE *fp, tree *tr, boolean readBranches, boolean readNodeLabels, boolean topologyOnly, analdef *adef, boolean completeTree)
{
nodeptr
p;
int
i,
ch,
lcount = 0;
for (i = 1; i <= tr->mxtips; i++)
{
tr->nodep[i]->back = (node *) NULL;
if(topologyOnly)
tr->nodep[i]->support = -1;
}
for(i = tr->mxtips + 1; i < 2 * tr->mxtips; i++)
{
tr->nodep[i]->back = (nodeptr)NULL;
tr->nodep[i]->next->back = (nodeptr)NULL;
tr->nodep[i]->next->next->back = (nodeptr)NULL;
tr->nodep[i]->number = i;
tr->nodep[i]->next->number = i;
tr->nodep[i]->next->next->number = i;
if(topologyOnly)
{
tr->nodep[i]->support = -2;
tr->nodep[i]->next->support = -2;
tr->nodep[i]->next->next->support = -2;
}
}
if(topologyOnly)
tr->start = tr->nodep[tr->mxtips];
else
tr->start = tr->nodep[1];
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = FALSE;
tr->rooted = FALSE;
p = tr->nodep[(tr->nextnode)++];
while((ch = treeGetCh(fp)) != '(');
if(!topologyOnly)
assert(readBranches == FALSE && readNodeLabels == FALSE);
if (! addElementLen(fp, tr, p, readBranches, readNodeLabels, &lcount))
assert(0);
if (! treeNeedCh(fp, ',', "in"))
assert(0);
if (! addElementLen(fp, tr, p->next, readBranches, readNodeLabels, &lcount))
assert(0);
if (! tr->rooted)
{
if ((ch = treeGetCh(fp)) == ',')
{
if (! addElementLen(fp, tr, p->next->next, readBranches, readNodeLabels, &lcount))
assert(0);
}
else
{ /* A rooted format */
tr->rooted = TRUE;
if (ch != EOF) (void) ungetc(ch, fp);
}
}
else
{
p->next->next->back = (nodeptr) NULL;
}
if (! treeNeedCh(fp, ')', "in"))
assert(0);
if(topologyOnly)
assert(!(tr->rooted && readNodeLabels));
(void) treeFlushLabel(fp);
if (! treeFlushLen(fp))
assert(0);
if (! treeNeedCh(fp, ';', "at end of"))
assert(0);
if (tr->rooted)
{
assert(!readNodeLabels);
p->next->next->back = (nodeptr) NULL;
tr->start = uprootTree(tr, p->next->next, FALSE, FALSE);
if (! tr->start)
{
printf("FATAL ERROR UPROOTING TREE\n");
assert(0);
}
}
else
tr->start = findAnyTip(p, tr->rdta->numsp);
if(!topologyOnly)
{
setupPointerMesh(tr);
assert(tr->ntips <= tr->mxtips);
if(tr->ntips < tr->mxtips)
{
if(completeTree)
{
printBothOpen("Hello this is your friendly RAxML tree parsing routine\n");
printBothOpen("The RAxML option you are uisng requires to read in only complete trees\n");
printBothOpen("with %d taxa, there is at least one tree with %d taxa though ... exiting\n", tr->mxtips, tr->ntips);
exit(-1);
}
else
{
if(adef->computeDistance)
{
printBothOpen("Error: pairwise distance computation only allows for complete, i.e., containing all taxa\n");
printBothOpen("bifurcating starting trees\n");
exit(-1);
}
if(adef->mode == CLASSIFY_ML)
{
printBothOpen("RAxML classifier Algo: You provided a reference tree with %d taxa; alignmnet has %d taxa\n", tr->ntips, tr->mxtips);
printBothOpen("%d query taxa will be classifed under ML\n", tr->mxtips - tr->ntips);
classifyML(tr, adef);
}
else
{
printBothOpen("You provided an incomplete starting tree %d alignmnet has %d taxa\n", tr->ntips, tr->mxtips);
makeParsimonyTreeIncomplete(tr, adef);
}
}
}
else
{
if(adef->mode == PARSIMONY_ADDITION)
{
printBothOpen("Error you want to add sequences to a trees via MP stepwise addition, but \n");
printBothOpen("you have provided an input tree that already contains all taxa\n");
exit(-1);
}
if(adef->mode == CLASSIFY_ML)
{
printBothOpen("Error you want to classify query sequences into a tree via ML, but \n");
printBothOpen("you have provided an input tree that already contains all taxa\n");
exit(-1);
}
}
onlyInitrav(tr, tr->start);
}
return lcount;
}
static boolean addElementLen (FILE *fp, tree *tr, nodeptr p, boolean readBranchLengths, boolean readNodeLabels, int *lcount)
{
nodeptr q;
int n, ch, fres;
if ((ch = treeGetCh(fp)) == '(')
{
n = (tr->nextnode)++;
if (n > 2*(tr->mxtips) - 2)
{
if (tr->rooted || n > 2*(tr->mxtips) - 1)
{
printf("ERROR: Too many internal nodes. Is tree rooted?\n");
printf(" Deepest splitting should be a trifurcation.\n");
return FALSE;
}
else
{
assert(!readNodeLabels);
tr->rooted = TRUE;
}
}
q = tr->nodep[n];
if (! addElementLen(fp, tr, q->next, readBranchLengths, readNodeLabels, lcount)) return FALSE;
if (! treeNeedCh(fp, ',', "in")) return FALSE;
if (! addElementLen(fp, tr, q->next->next, readBranchLengths, readNodeLabels, lcount)) return FALSE;
if (! treeNeedCh(fp, ')', "in")) return FALSE;
if(readNodeLabels)
{
char label[64];
int support;
if(treeGetLabel (fp, label, 10))
{
int val = sscanf(label, "%d", &support);
assert(val == 1);
/*printf("LABEL %s Number %d\n", label, support);*/
/*p->support = q->support = support;*/
/*printf("%d %d %d %d\n", p->support, q->support, p->number, q->number);*/
assert(p->number > tr->mxtips && q->number > tr->mxtips);
*lcount = *lcount + 1;
}
}
else
(void) treeFlushLabel(fp);
}
else
{
ungetc(ch, fp);
if ((n = treeFindTipName(fp, tr)) <= 0) return FALSE;
q = tr->nodep[n];
if (tr->start->number > n) tr->start = q;
(tr->ntips)++;
}
if(readBranchLengths)
{
double branch;
if (! treeNeedCh(fp, ':', "in")) return FALSE;
if (! treeProcessLength(fp, &branch)) return FALSE;
/*printf("Branch %8.20f %d\n", branch, tr->numBranches);*/
hookup(p, q, &branch, tr->numBranches);
}
else
{
fres = treeFlushLen(fp);
if(!fres) return FALSE;
hookupDefault(p, q, tr->numBranches);
}
return TRUE;
}
int treeReadLen (FILE *fp, tree *tr, boolean readBranches, boolean readNodeLabels, boolean topologyOnly)
{
nodeptr
p;
int
i,
ch,
lcount = 0;
for (i = 1; i <= tr->mxtips; i++)
{
tr->nodep[i]->back = (node *) NULL;
/*if(topologyOnly)
tr->nodep[i]->support = -1;*/
}
for(i = tr->mxtips + 1; i < 2 * tr->mxtips; i++)
{
tr->nodep[i]->back = (nodeptr)NULL;
tr->nodep[i]->next->back = (nodeptr)NULL;
tr->nodep[i]->next->next->back = (nodeptr)NULL;
tr->nodep[i]->number = i;
tr->nodep[i]->next->number = i;
tr->nodep[i]->next->next->number = i;
/*if(topologyOnly)
{
tr->nodep[i]->support = -2;
tr->nodep[i]->next->support = -2;
tr->nodep[i]->next->next->support = -2;
}*/
}
if(topologyOnly)
tr->start = tr->nodep[tr->mxtips];
else
tr->start = tr->nodep[1];
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = FALSE;
tr->rooted = FALSE;
p = tr->nodep[(tr->nextnode)++];
while((ch = treeGetCh(fp)) != '(');
if(!topologyOnly)
assert(readBranches == FALSE && readNodeLabels == FALSE);
if (! addElementLen(fp, tr, p, readBranches, readNodeLabels, &lcount))
assert(0);
if (! treeNeedCh(fp, ',', "in"))
assert(0);
if (! addElementLen(fp, tr, p->next, readBranches, readNodeLabels, &lcount))
assert(0);
if (! tr->rooted)
{
if ((ch = treeGetCh(fp)) == ',')
{
if (! addElementLen(fp, tr, p->next->next, readBranches, readNodeLabels, &lcount))
assert(0);
}
else
{ /* A rooted format */
tr->rooted = TRUE;
if (ch != EOF) (void) ungetc(ch, fp);
}
}
else
{
p->next->next->back = (nodeptr) NULL;
}
if (! treeNeedCh(fp, ')', "in"))
assert(0);
if(topologyOnly)
assert(!(tr->rooted && readNodeLabels));
(void) treeFlushLabel(fp);
if (! treeFlushLen(fp))
assert(0);
if (! treeNeedCh(fp, ';', "at end of"))
assert(0);
if (tr->rooted)
{
assert(!readNodeLabels);
p->next->next->back = (nodeptr) NULL;
tr->start = uprootTree(tr, p->next->next, FALSE);
if (! tr->start)
{
printf("FATAL ERROR UPROOTING TREE\n");
assert(0);
}
}
else
tr->start = findAnyTip(p, tr->mxtips);
assert(tr->ntips == tr->mxtips);
return lcount;
}
boolean treeReadLenMULT (FILE *fp, tree *tr, int *partCount)
{
nodeptr p, r, s;
int i, ch, n, rn;
int partitionCounter = 0;
double randomResolution;
srand(tr->randomSeed);
for(i = 0; i < 2 * tr->mxtips; i++)
tr->constraintVector[i] = -1;
for (i = 1; i <= tr->mxtips; i++)
tr->nodep[i]->back = (node *) NULL;
for(i = tr->mxtips + 1; i < 2 * tr->mxtips; i++)
{
tr->nodep[i]->back = (nodeptr)NULL;
tr->nodep[i]->next->back = (nodeptr)NULL;
tr->nodep[i]->next->next->back = (nodeptr)NULL;
tr->nodep[i]->number = i;
tr->nodep[i]->next->number = i;
tr->nodep[i]->next->next->number = i;
}
tr->start = tr->nodep[tr->mxtips];
tr->ntips = 0;
tr->nextnode = tr->mxtips + 1;
for(i = 0; i < tr->numBranches; i++)
tr->partitionSmoothed[i] = FALSE;
tr->rooted = FALSE;
p = tr->nodep[(tr->nextnode)++];
while((ch = treeGetCh(fp)) != '(');
if (! addElementLenMULT(fp, tr, p, partitionCounter, partCount)) return FALSE;
if (! treeNeedCh(fp, ',', "in")) return FALSE;
if (! addElementLenMULT(fp, tr, p->next, partitionCounter, partCount)) return FALSE;
if (! tr->rooted)
{
if ((ch = treeGetCh(fp)) == ',')
{
if (! addElementLenMULT(fp, tr, p->next->next, partitionCounter, partCount)) return FALSE;
while((ch = treeGetCh(fp)) == ',')
{
n = (tr->nextnode)++;
assert(n <= 2*(tr->mxtips) - 2);
r = tr->nodep[n];
tr->constraintVector[r->number] = partitionCounter;
rn = randomInt(10000);
if(rn == 0)
randomResolution = 0;
else
randomResolution = ((double)rn)/10000.0;
if(randomResolution < 0.5)
{
s = p->next->next->back;
r->back = p->next->next;
p->next->next->back = r;
r->next->back = s;
s->back = r->next;
addElementLenMULT(fp, tr, r->next->next, partitionCounter, partCount);
}
else
{
s = p->next->back;
r->back = p->next;
p->next->back = r;
r->next->back = s;
s->back = r->next;
addElementLenMULT(fp, tr, r->next->next, partitionCounter, partCount);
}
}
if(ch != ')')
{
printf("Missing /) in treeReadLenMULT\n");
exit(-1);
}
else
ungetc(ch, fp);
}
else
{
tr->rooted = TRUE;
if (ch != EOF) (void) ungetc(ch, fp);
}
}
else
{
p->next->next->back = (nodeptr) NULL;
}
if (! treeNeedCh(fp, ')', "in")) return FALSE;
(void) treeFlushLabel(fp);
if (! treeFlushLen(fp)) return FALSE;
if (! treeNeedCh(fp, ';', "at end of")) return FALSE;
if (tr->rooted)
{
p->next->next->back = (nodeptr) NULL;
tr->start = uprootTree(tr, p->next->next, FALSE);
if (! tr->start) return FALSE;
}
else
{
tr->start = findAnyTip(p, tr->mxtips);
}
assert(tr->ntips == tr->mxtips);
return TRUE;
}
