5 * Created by Sarah Westcott on 1/22/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 /*****************************************************************/
15 globaldata = GlobalData::getInstance();
16 m = MothurOut::getInstance();
19 numNodes = 2*numLeaves - 1;
21 tree.resize(numNodes);
24 m->errorOut(e, "Tree", "Tree - numNodes");
28 /*****************************************************************/
29 Tree::Tree(string g) {
31 globaldata = GlobalData::getInstance();
32 m = MothurOut::getInstance();
34 parseTreeFile(); globaldata->runParse = false;
37 m->errorOut(e, "Tree", "Tree - just parse");
41 /*****************************************************************/
44 globaldata = GlobalData::getInstance();
45 m = MothurOut::getInstance();
47 if (globaldata->runParse == true) { parseTreeFile(); globaldata->runParse = false; }
48 //for(int i = 0; i < globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl; }
49 numLeaves = globaldata->Treenames.size();
50 numNodes = 2*numLeaves - 1;
52 tree.resize(numNodes);
54 //initialize groupNodeInfo
55 for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
56 groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
59 //initialize tree with correct number of nodes, name and group info.
60 for (int i = 0; i < numNodes; i++) {
61 //initialize leaf nodes
62 if (i <= (numLeaves-1)) {
63 tree[i].setName(globaldata->Treenames[i]);
66 string group = globaldata->gTreemap->getGroup(globaldata->Treenames[i]);
67 vector<string> tempGroups; tempGroups.push_back(group);
68 tree[i].setGroup(tempGroups);
69 groupNodeInfo[group].push_back(i);
71 //set pcount and pGroup for groupname to 1.
72 tree[i].pcount[group] = 1;
73 tree[i].pGroups[group] = 1;
75 //Treemap knows name, group and index to speed up search
76 globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
78 //intialize non leaf nodes
79 }else if (i > (numLeaves-1)) {
81 vector<string> tempGroups;
82 tree[i].setGroup(tempGroups);
87 m->errorOut(e, "Tree", "Tree");
92 /*****************************************************************/
94 /*****************************************************************/
95 void Tree::addNamesToCounts() {
97 //ex. seq1 seq2,seq3,se4
103 //before this function seq1.pcount = pasture -> 1
104 //after seq1.pcount = pasture -> 2, forest -> 1, ocean -> 1
106 //before this function seq1.pgroups = pasture -> 1
107 //after seq1.pgroups = pasture -> 1 since that is the dominant group
110 //go through each leaf and update its pcounts and pgroups
114 for (int i = 0; i < numLeaves; i++) {
116 string name = tree[i].getName();
118 map<string, string>::iterator itNames = globaldata->names.find(name);
120 if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
122 vector<string> dupNames;
123 m->splitAtComma(globaldata->names[name], dupNames);
125 map<string, int>::iterator itCounts;
127 set<string> groupsAddedForThisNode;
128 for (int j = 0; j < dupNames.size(); j++) {
130 string group = globaldata->gTreemap->getGroup(dupNames[j]);
132 if (dupNames[j] != name) {//you already added yourself in the constructor
134 if (groupsAddedForThisNode.count(group) == 0) { groupNodeInfo[group].push_back(i); groupsAddedForThisNode.insert(group); } //if you have not already added this node for this group, then add it
137 itCounts = tree[i].pcount.find(group);
138 if (itCounts == tree[i].pcount.end()) { //new group, add it
139 tree[i].pcount[group] = 1;
141 tree[i].pcount[group]++;
145 itCounts = tree[i].pGroups.find(group);
146 if (itCounts == tree[i].pGroups.end()) { //new group, add it
147 tree[i].pGroups[group] = 1;
149 tree[i].pGroups[group]++;
153 if(tree[i].pGroups[group] > maxPars){
154 maxPars = tree[i].pGroups[group];
156 }else { groupsAddedForThisNode.insert(group); } //add it so you don't add it to groupNodeInfo again
159 if (maxPars > 1) { //then we have some more dominant groups
160 //erase all the groups that are less than maxPars because you found a more dominant group.
161 for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
162 if(it->second < maxPars){
163 tree[i].pGroups.erase(it++);
166 //set one remaining groups to 1
167 for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
168 tree[i].pGroups[it->first] = 1;
172 //update groups to reflect all the groups this node represents
173 vector<string> nodeGroups;
174 map<string, int>::iterator itGroups;
175 for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
176 nodeGroups.push_back(itGroups->first);
178 tree[i].setGroup(nodeGroups);
184 //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;
187 catch(exception& e) {
188 m->errorOut(e, "Tree", "addNamesToCounts");
192 /*****************************************************************/
193 int Tree::getIndex(string searchName) {
195 //Treemap knows name, group and index to speed up search
196 // getIndex function will return the vector index or -1 if seq is not found.
197 int index = globaldata->gTreemap->getIndex(searchName);
201 catch(exception& e) {
202 m->errorOut(e, "Tree", "getIndex");
206 /*****************************************************************/
208 void Tree::setIndex(string searchName, int index) {
210 //set index in treemap
211 globaldata->gTreemap->setIndex(searchName, index);
213 catch(exception& e) {
214 m->errorOut(e, "Tree", "setIndex");
218 /*****************************************************************/
219 int Tree::assembleTree() {
223 //if user has given a names file we want to include that info in the pgroups and pcount info.
224 if(globaldata->names.size() != 0) { addNamesToCounts(); }
226 //build the pGroups in non leaf nodes to be used in the parsimony calcs.
227 for (int i = numLeaves; i < numNodes; i++) {
228 if (m->control_pressed) { return 1; }
230 tree[i].pGroups = (mergeGroups(i));
231 tree[i].pcount = (mergeGcounts(i));
234 //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
237 catch(exception& e) {
238 m->errorOut(e, "Tree", "assembleTree");
242 /*****************************************************************/
243 int Tree::assembleTree(string n) {
246 //build the pGroups in non leaf nodes to be used in the parsimony calcs.
247 for (int i = numLeaves; i < numNodes; i++) {
248 if (m->control_pressed) { return 1; }
250 tree[i].pGroups = (mergeGroups(i));
251 tree[i].pcount = (mergeGcounts(i));
254 //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
257 catch(exception& e) {
258 m->errorOut(e, "Tree", "assembleTree");
262 /*****************************************************************/
263 void Tree::getSubTree(Tree* copy, vector<string> Groups) {
266 //we want to select some of the leaf nodes to create the output tree
267 //go through the input Tree starting at parents of leaves
268 for (int i = 0; i < numNodes; i++) {
270 //initialize leaf nodes
271 if (i <= (numLeaves-1)) {
272 tree[i].setName(Groups[i]);
275 string group = globaldata->gTreemap->getGroup(Groups[i]);
276 vector<string> tempGroups; tempGroups.push_back(group);
277 tree[i].setGroup(tempGroups);
278 groupNodeInfo[group].push_back(i);
280 //set pcount and pGroup for groupname to 1.
281 tree[i].pcount[group] = 1;
282 tree[i].pGroups[group] = 1;
284 //Treemap knows name, group and index to speed up search
285 globaldata->gTreemap->setIndex(Groups[i], i);
287 //intialize non leaf nodes
288 }else if (i > (numLeaves-1)) {
290 vector<string> tempGroups;
291 tree[i].setGroup(tempGroups);
295 set<int> removedLeaves;
296 for (int i = 0; i < copy->getNumLeaves(); i++) {
298 if (removedLeaves.count(i) == 0) {
301 int parent = copy->tree[i].getParent();
304 if (m->inUsersGroups(copy->tree[i].getName(), Groups)) {
305 //find my siblings name
306 int parentRC = copy->tree[parent].getRChild();
307 int parentLC = copy->tree[parent].getLChild();
309 //if I am the right child, then my sib is the left child
310 int sibIndex = parentRC;
311 if (parentRC == i) { sibIndex = parentLC; }
313 string sibsName = copy->tree[sibIndex].getName();
315 //if yes, is my sibling
316 if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
317 //we both are okay no trimming required
319 //i am, my sib is not, so remove sib by setting my parent to my grandparent
320 int grandparent = copy->tree[parent].getParent();
321 int grandparentLC = copy->tree[grandparent].getLChild();
322 int grandparentRC = copy->tree[grandparent].getRChild();
324 //whichever of my granparents children was my parent now equals me
325 if (grandparentLC == parent) { grandparentLC = i; }
326 else { grandparentRC = i; }
328 copy->tree[i].setParent(grandparent);
329 copy->tree[i].setBranchLength((copy->tree[i].getBranchLength()+copy->tree[parent].getBranchLength()));
330 copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
331 removedLeaves.insert(sibIndex);
334 //find my siblings name
335 int parentRC = copy->tree[parent].getRChild();
336 int parentLC = copy->tree[parent].getLChild();
338 //if I am the right child, then my sib is the left child
339 int sibIndex = parentRC;
340 if (parentRC == i) { sibIndex = parentLC; }
342 string sibsName = copy->tree[sibIndex].getName();
344 //if no is my sibling
345 if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
346 //i am not, but my sib is
347 int grandparent = copy->tree[parent].getParent();
348 int grandparentLC = copy->tree[grandparent].getLChild();
349 int grandparentRC = copy->tree[grandparent].getRChild();
351 //whichever of my granparents children was my parent now equals my sib
352 if (grandparentLC == parent) { grandparentLC = sibIndex; }
353 else { grandparentRC = sibIndex; }
355 copy->tree[sibIndex].setParent(grandparent);
356 copy->tree[sibIndex].setBranchLength((copy->tree[sibIndex].getBranchLength()+copy->tree[parent].getBranchLength()));
357 copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
358 removedLeaves.insert(i);
360 //neither of us are, so we want to eliminate ourselves and our parent
361 //so set our parents sib to our great-grandparent
362 int parent = copy->tree[i].getParent();
363 int grandparent = copy->tree[parent].getParent();
365 if (grandparent != -1) {
366 int greatgrandparent = copy->tree[grandparent].getParent();
367 int greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
368 int greatgrandparentRC = copy->tree[greatgrandparent].getRChild();
370 int grandparentLC = copy->tree[grandparent].getLChild();
371 int grandparentRC = copy->tree[grandparent].getRChild();
373 int parentsSibIndex = grandparentLC;
374 if (grandparentRC == parent) { parentsSibIndex = grandparentLC; }
376 //whichever of my greatgrandparents children was my grandparent
377 if (greatgrandparentLC == grandparent) { greatgrandparentLC = parentsSibIndex; }
378 else { greatgrandparentRC = parentsSibIndex; }
380 copy->tree[parentsSibIndex].setParent(greatgrandparent);
381 copy->tree[parentsSibIndex].setBranchLength((copy->tree[parentsSibIndex].getBranchLength()+copy->tree[grandparent].getBranchLength()));
382 copy->tree[greatgrandparent].setChildren(greatgrandparentLC, greatgrandparentRC);
384 copy->tree[parent].setChildren(-1, -1);
385 cout << "issues with making subtree" << endl;
387 removedLeaves.insert(sibIndex);
388 removedLeaves.insert(i);
396 for (int i = 0; i < copy->getNumNodes(); i++) {
398 if (copy->tree[i].getParent() == -1) { root = i; break; }
401 int nextSpot = numLeaves;
402 populateNewTree(copy->tree, root, nextSpot);
406 catch(exception& e) {
407 m->errorOut(e, "Tree", "getCopy");
411 /*****************************************************************/
412 int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
415 if (oldtree[node].getLChild() != -1) {
416 int rc = populateNewTree(oldtree, oldtree[node].getLChild(), index);
417 int lc = populateNewTree(oldtree, oldtree[node].getRChild(), index);
419 tree[index].setChildren(lc, rc);
423 }else { //you are a leaf
424 int indexInNewTree = globaldata->gTreemap->getIndex(oldtree[node].getName());
426 tree[indexInNewTree].setParent(index);
427 return indexInNewTree;
431 catch(exception& e) {
432 m->errorOut(e, "Tree", "populateNewTree");
436 /*****************************************************************/
437 void Tree::getCopy(Tree* copy) {
440 //for each node in the tree copy its info
441 for (int i = 0; i < numNodes; i++) {
443 tree[i].setName(copy->tree[i].getName());
446 tree[i].setGroup(copy->tree[i].getGroup());
449 tree[i].setBranchLength(copy->tree[i].getBranchLength());
452 tree[i].setParent(copy->tree[i].getParent());
455 tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
457 //copy index in node and tmap
458 tree[i].setIndex(copy->tree[i].getIndex());
459 setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
462 tree[i].pGroups = copy->tree[i].pGroups;
465 tree[i].pcount = copy->tree[i].pcount;
468 groupNodeInfo = copy->groupNodeInfo;
471 catch(exception& e) {
472 m->errorOut(e, "Tree", "getCopy");
476 /*****************************************************************/
477 //returns a map with a groupname and the number of times that group was seen in the children
478 //for instance if your children are white and black then it would return a map with 2 entries
479 // p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
480 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
482 map<string, int> Tree::mergeGroups(int i) {
484 int lc = tree[i].getLChild();
485 int rc = tree[i].getRChild();
487 //set parsimony groups to left child
488 map<string,int> parsimony = tree[lc].pGroups;
492 //look at right child groups and update maxPars if right child has something higher for that group.
493 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
494 it2 = parsimony.find(it->first);
495 if (it2 != parsimony.end()) {
496 parsimony[it->first]++;
498 parsimony[it->first] = 1;
501 if(parsimony[it->first] > maxPars){
502 maxPars = parsimony[it->first];
506 // this is true if right child had a greater parsimony for a certain group
508 //erase all the groups that are only 1 because you found something with 2.
509 for(it=parsimony.begin();it!=parsimony.end();){
511 parsimony.erase(it++);
514 //set one remaining groups to 1
515 //so with our above example p[white] = 2 would be left and it would become p[white] = 1
516 for(it=parsimony.begin();it!=parsimony.end();it++){
517 parsimony[it->first] = 1;
524 catch(exception& e) {
525 m->errorOut(e, "Tree", "mergeGroups");
529 /*****************************************************************/
530 //returns a map with a groupname and the number of times that group was seen in the children
531 //for instance if your children are white and black then it would return a map with 2 entries
532 // p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
533 //and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
535 map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
538 int lc = tree[i].getLChild();
539 int rc = tree[i].getRChild();
541 //loop through nodes groups removing the ones the user doesn't want
542 for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
543 if (m->inUsersGroups(it->first, g) != true) {
544 tree[lc].pGroups.erase(it++);
548 //loop through nodes groups removing the ones the user doesn't want
549 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
550 if (m->inUsersGroups(it->first, g) != true) {
551 tree[rc].pGroups.erase(it++);
555 //set parsimony groups to left child
556 map<string,int> parsimony = tree[lc].pGroups;
560 //look at right child groups and update maxPars if right child has something higher for that group.
561 for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
562 it2 = parsimony.find(it->first);
563 if (it2 != parsimony.end()) {
564 parsimony[it->first]++;
566 parsimony[it->first] = 1;
569 if(parsimony[it->first] > maxPars){
570 maxPars = parsimony[it->first];
574 // this is true if right child had a greater parsimony for a certain group
576 //erase all the groups that are only 1 because you found something with 2.
577 for(it=parsimony.begin();it!=parsimony.end();){
579 parsimony.erase(it++);
583 for(it=parsimony.begin();it!=parsimony.end();it++){
584 parsimony[it->first] = 1;
590 catch(exception& e) {
591 m->errorOut(e, "Tree", "mergeUserGroups");
597 /**************************************************************************************************/
599 map<string,int> Tree::mergeGcounts(int position) {
601 map<string,int>::iterator pos;
603 int lc = tree[position].getLChild();
604 int rc = tree[position].getRChild();
606 map<string,int> sum = tree[lc].pcount;
608 for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
609 sum[it->first] += it->second;
613 catch(exception& e) {
614 m->errorOut(e, "Tree", "mergeGcounts");
618 /**************************************************************************************************/
620 void Tree::randomLabels(vector<string> g) {
623 //initialize groupNodeInfo
624 for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
625 groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
628 for(int i = 0; i < numLeaves; i++){
630 //get random index to switch with
631 z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
633 //you only want to randomize the nodes that are from a group the user wants analyzed, so
634 //if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
637 treez = m->inUsersGroups(tree[z].getGroup(), g);
638 treei = m->inUsersGroups(tree[i].getGroup(), g);
640 if ((treez == true) && (treei == true)) {
641 //switches node i and node z's info.
642 map<string,int> lib_hold = tree[z].pGroups;
643 tree[z].pGroups = (tree[i].pGroups);
644 tree[i].pGroups = (lib_hold);
646 vector<string> zgroup = tree[z].getGroup();
647 tree[z].setGroup(tree[i].getGroup());
648 tree[i].setGroup(zgroup);
650 string zname = tree[z].getName();
651 tree[z].setName(tree[i].getName());
652 tree[i].setName(zname);
654 map<string,int> gcount_hold = tree[z].pcount;
655 tree[z].pcount = (tree[i].pcount);
656 tree[i].pcount = (gcount_hold);
659 for (int k = 0; k < (tree[i].getGroup()).size(); k++) { groupNodeInfo[(tree[i].getGroup())[k]].push_back(i); }
660 for (int k = 0; k < (tree[z].getGroup()).size(); k++) { groupNodeInfo[(tree[z].getGroup())[k]].push_back(z); }
663 catch(exception& e) {
664 m->errorOut(e, "Tree", "randomLabels");
668 /**************************************************************************************************
670 void Tree::randomLabels(string groupA, string groupB) {
672 int numSeqsA = globaldata->gTreemap->seqsPerGroup[groupA];
673 int numSeqsB = globaldata->gTreemap->seqsPerGroup[groupB];
675 vector<string> randomGroups(numSeqsA+numSeqsB, groupA);
676 for(int i=numSeqsA;i<randomGroups.size();i++){
677 randomGroups[i] = groupB;
679 random_shuffle(randomGroups.begin(), randomGroups.end());
681 int randomCounter = 0;
682 for(int i=0;i<numLeaves;i++){
683 if(tree[i].getGroup() == groupA || tree[i].getGroup() == groupB){
684 tree[i].setGroup(randomGroups[randomCounter]);
685 tree[i].pcount.clear();
686 tree[i].pcount[randomGroups[randomCounter]] = 1;
687 tree[i].pGroups.clear();
688 tree[i].pGroups[randomGroups[randomCounter]] = 1;
693 catch(exception& e) {
694 m->errorOut(e, "Tree", "randomLabels");
698 /**************************************************************************************************/
699 void Tree::randomBlengths() {
701 for(int i=numNodes-1;i>=0;i--){
702 int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
704 float bl_hold = tree[z].getBranchLength();
705 tree[z].setBranchLength(tree[i].getBranchLength());
706 tree[i].setBranchLength(bl_hold);
709 catch(exception& e) {
710 m->errorOut(e, "Tree", "randomBlengths");
714 /*************************************************************************************************/
715 void Tree::assembleRandomUnifracTree(vector<string> g) {
717 assembleTree("noNameCounts");
719 /*************************************************************************************************/
720 void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
722 vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
724 assembleTree("noNameCounts");
727 /*************************************************************************************************/
728 //for now it's just random topology but may become random labels as well later that why this is such a simple function now...
729 void Tree::assembleRandomTree() {
733 /**************************************************************************************************/
735 void Tree::randomTopology() {
737 for(int i=0;i<numNodes;i++){
738 tree[i].setParent(-1);
740 for(int i=numLeaves;i<numNodes;i++){
741 tree[i].setChildren(-1, -1);
744 for(int i=numLeaves;i<numNodes;i++){
746 int rnd_index1, rnd_index2;
748 rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
749 if(tree[rnd_index1].getParent() == -1){escape = 1;}
754 rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
755 if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
760 tree[i].setChildren(rnd_index1,rnd_index2);
761 tree[i].setParent(-1);
762 tree[rnd_index1].setParent(i);
763 tree[rnd_index2].setParent(i);
766 catch(exception& e) {
767 m->errorOut(e, "Tree", "randomTopology");
771 /*****************************************************************/
772 void Tree::print(ostream& out) {
774 int root = findRoot();
775 printBranch(root, out, "branch");
778 catch(exception& e) {
779 m->errorOut(e, "Tree", "print");
783 /*****************************************************************/
784 void Tree::print(ostream& out, string mode) {
786 int root = findRoot();
787 printBranch(root, out, mode);
790 catch(exception& e) {
791 m->errorOut(e, "Tree", "print");
795 /*****************************************************************/
796 // This prints out the tree in Newick form.
797 void Tree::createNewickFile(string f) {
799 int root = findRoot();
800 //filename = m->getRootName(globaldata->getTreeFile()) + "newick";
803 m->openOutputFile(filename, out);
805 printBranch(root, out, "branch");
807 // you are at the end of the tree
811 catch(exception& e) {
812 m->errorOut(e, "Tree", "createNewickFile");
817 /*****************************************************************/
818 //This function finds the index of the root node.
820 int Tree::findRoot() {
822 for (int i = 0; i < numNodes; i++) {
824 if (tree[i].getParent() == -1) { return i; }
825 //cout << "i = " << i << endl;
826 //cout << "i's parent = " << tree[i].getParent() << endl;
830 catch(exception& e) {
831 m->errorOut(e, "Tree", "findRoot");
835 /*****************************************************************/
836 void Tree::printBranch(int node, ostream& out, string mode) {
839 // you are not a leaf
840 if (tree[node].getLChild() != -1) {
842 printBranch(tree[node].getLChild(), out, mode);
844 printBranch(tree[node].getRChild(), out, mode);
846 if (mode == "branch") {
847 //if there is a branch length then print it
848 if (tree[node].getBranchLength() != -1) {
849 out << ":" << tree[node].getBranchLength();
851 }else if (mode == "boot") {
852 //if there is a label then print it
853 if (tree[node].getLabel() != -1) {
854 out << tree[node].getLabel();
856 }else if (mode == "both") {
857 if (tree[node].getLabel() != -1) {
858 out << tree[node].getLabel();
860 //if there is a branch length then print it
861 if (tree[node].getBranchLength() != -1) {
862 out << ":" << tree[node].getBranchLength();
865 }else { //you are a leaf
866 string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
868 if (mode == "branch") {
870 //if there is a branch length then print it
871 if (tree[node].getBranchLength() != -1) {
872 out << ":" << tree[node].getBranchLength();
874 }else if (mode == "boot") {
876 //if there is a label then print it
877 if (tree[node].getLabel() != -1) {
878 out << tree[node].getLabel();
880 }else if (mode == "both") {
881 out << tree[node].getName();
882 if (tree[node].getLabel() != -1) {
883 out << tree[node].getLabel();
885 //if there is a branch length then print it
886 if (tree[node].getBranchLength() != -1) {
887 out << ":" << tree[node].getBranchLength();
893 catch(exception& e) {
894 m->errorOut(e, "Tree", "printBranch");
899 /*****************************************************************/
901 void Tree::printTree() {
903 for(int i=0;i<numNodes;i++){
910 /*****************************************************************/
911 //this code is a mess and should be rethought...-slw
912 void Tree::parseTreeFile() {
914 //only takes names from the first tree and assumes that all trees use the same names.
916 string filename = globaldata->getTreeFile();
918 m->openInputFile(filename, filehandle);
923 //ifyou are not a nexus file
924 if((c = filehandle.peek()) != '#') {
925 while((c = filehandle.peek()) != ';') {
926 while ((c = filehandle.peek()) != ';') {
934 if((c == '(') && (comment != 1)){ break; }
938 done = readTreeString(filehandle);
939 if (done == 0) { break; }
941 //ifyou are a nexus file
942 }else if((c = filehandle.peek()) == '#') {
946 while(holder != "translate" && holder != "Translate"){
947 if(holder == "[" || holder == "[!"){
953 filehandle >> holder;
955 //if there is no translate then you must read tree string otherwise use translate to get names
956 if((holder == "tree") && (comment != 1)){
957 //pass over the "tree rep.6878900 = "
958 while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
960 if(c == EOF) { break; }
961 filehandle.putback(c); //put back first ( of tree.
962 done = readTreeString(filehandle);
967 if (done == 0) { break; }
970 //use nexus translation rather than parsing tree to save time
971 if((holder == "translate") || (holder == "Translate")) {
973 string number, name, h;
974 h = ""; // so it enters the loop the first time
975 while((h != ";") && (number != ";")) {
976 filehandle >> number;
979 //c = , until done with translation then c = ;
980 h = name.substr(name.length()-1, name.length());
981 name.erase(name.end()-1); //erase the comma
982 globaldata->Treenames.push_back(number);
984 if(number == ";") { globaldata->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
989 //for (int i = 0; i < globaldata->Treenames.size(); i++) {
990 //cout << globaldata->Treenames[i] << endl; }
991 //cout << globaldata->Treenames.size() << endl;
993 catch(exception& e) {
994 m->errorOut(e, "Tree", "parseTreeFile");
998 /*******************************************************/
1000 /*******************************************************/
1001 int Tree::readTreeString(ifstream& filehandle) {
1006 while((c = filehandle.peek()) != ';') {
1008 //cout << " at beginning of while " << k << endl;
1010 //to pass over labels in trees
1012 while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
1013 filehandle.putback(c);
1015 if(c == ';') { return 0; }
1016 if(c == -1) { return 0; }
1018 if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
1020 c = filehandle.get();
1022 //cout << k << endl;
1023 while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
1025 c = filehandle.get();
1027 //cout << " in name while " << k << endl;
1030 //cout << "name = " << name << endl;
1031 globaldata->Treenames.push_back(name);
1032 filehandle.putback(c);
1034 //cout << " after putback" << k << endl;
1037 if(c == ':') { //read until you reach the end of the branch length
1038 while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
1039 c = filehandle.get();
1041 //cout << " in branch while " << k << endl;
1043 filehandle.putback(c);
1046 c = filehandle.get();
1048 //cout << " here after get " << k << endl;
1049 if(c == ';') { return 0; }
1050 if(c == ')') { filehandle.putback(c); }
1052 //cout << k << endl;
1057 catch(exception& e) {
1058 m->errorOut(e, "Tree", "readTreeString");
1063 /*******************************************************/
1065 /*******************************************************/