X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=7da3cef3718502640d61377bccbaae0d8e4213d3;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=03eb17127d5ebc174c8c3018452eb36290fb9346;hpb=60fdefb3a300b59c3bbeffdca8a5f1f30c6a43af;p=mothur.git

diff --git a/tree.cpp b/tree.cpp
index 03eb171..7da3cef 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -14,44 +14,132 @@
 Tree::Tree() {
 	try {
 		globaldata = GlobalData::getInstance();
-
-		numLeaves = globaldata->gTreemap->getNumSeqs();
+		m = MothurOut::getInstance();
+		
+		if (globaldata->runParse == true) {  parseTreeFile();  globaldata->runParse = false;  }
+//for(int i = 0; i < 	globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }	
+		numLeaves = globaldata->Treenames.size();
 		numNodes = 2*numLeaves - 1;
 		
 		tree.resize(numNodes);
 
 		//initialize tree with correct number of nodes, name and group info.
 		for (int i = 0; i < numNodes; i++) {
-
 			//initialize leaf nodes
 			if (i <= (numLeaves-1)) {
-				tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
-				tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
-				//the node knows its index
-				tree[i].setIndex(i);
+				tree[i].setName(globaldata->Treenames[i]);
+				vector<string> tempGroups; tempGroups.push_back(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+				tree[i].setGroup(tempGroups);
+				//set pcount and pGroup for groupname to 1.
+				tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
+				tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
 				//Treemap knows name, group and index to speed up search
-				globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+				globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
+	
 			//intialize non leaf nodes
 			}else if (i > (numLeaves-1)) {
 				tree[i].setName("");
-				tree[i].setGroup("");
-				//the node knows its index
-				tree[i].setIndex(i);
+				vector<string> tempGroups;
+				tree[i].setGroup(tempGroups);
 			}
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Tree", "Tree");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Tree class function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /*****************************************************************/
+Tree::~Tree() {}
+/*****************************************************************/
+void Tree::addNamesToCounts() {
+	try {
+		//ex. seq1	seq2,seq3,se4
+		//		seq1 = pasture
+		//		seq2 = forest
+		//		seq4 = pasture
+		//		seq3 = ocean
+		
+		//before this function seq1.pcount = pasture -> 1
+		//after				   seq1.pcount = pasture -> 2, forest -> 1, ocean -> 1
+		
+		//before this function seq1.pgroups = pasture -> 1
+		//after				   seq1.pgroups = pasture -> 1 since that is the dominant group
 
+				
+		//go through each leaf and update its pcounts and pgroups
+		for (int i = 0; i < numLeaves; i++) {
+			string name = tree[i].getName();
+			
+			map<string, string>::iterator itNames = globaldata->names.find(name);
+			
+			if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
+			else {
+				vector<string> dupNames;
+				splitAtComma(globaldata->names[name], dupNames);
+				
+				map<string, int>::iterator itCounts;
+				int maxPars = 1;
+				for (int j = 0; j < dupNames.size(); j++) {
+				
+					if (dupNames[j] != name) {//you already added yourself in the constructor
+						string group = globaldata->gTreemap->getGroup(dupNames[j]);
+						
+						//update pcounts
+						itCounts = tree[i].pcount.find(group);
+						if (itCounts == tree[i].pcount.end()) { //new group, add it
+							tree[i].pcount[group] = 1;
+						}else {
+							tree[i].pcount[group]++;
+						}
+							
+						//update pgroups
+						itCounts = tree[i].pGroups.find(group);
+						if (itCounts == tree[i].pGroups.end()) { //new group, add it
+							tree[i].pGroups[group] = 1;
+						}else {
+							tree[i].pGroups[group]++;
+						}
+						
+						//keep highest group
+						if(tree[i].pGroups[group] > maxPars){
+							maxPars = tree[i].pGroups[group];
+						}
+					}//end if
+				}//end for
+				
+				if (maxPars > 1) { //then we have some more dominant groups
+					//erase all the groups that are less than maxPars because you found a more dominant group.
+					for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+						if(it->second < maxPars){
+							tree[i].pGroups.erase(it++);
+						}else { it++; }
+					}
+					//set one remaining groups to 1
+					for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+						tree[i].pGroups[it->first] = 1;
+					}
+				}//end if
+				
+				//update groups to reflect all the groups this node represents
+				vector<string> nodeGroups;
+				map<string, int>::iterator itGroups;
+				for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
+					nodeGroups.push_back(itGroups->first);
+				}
+				tree[i].setGroup(nodeGroups);
+				
+			}//end else
+		}//end for
+				
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "addNamesToCounts");
+		exit(1);
+	}
+}
+/*****************************************************************/
 int Tree::getIndex(string searchName) {
 	try {
 		//Treemap knows name, group and index to speed up search
@@ -61,13 +149,9 @@ int Tree::getIndex(string searchName) {
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Tree", "getIndex");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Tree class function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 /*****************************************************************/
 
@@ -77,37 +161,402 @@ void Tree::setIndex(string searchName, int index) {
 		globaldata->gTreemap->setIndex(searchName, index);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Tree", "setIndex");
+		exit(1);
+	}
+}
+/*****************************************************************/
+int Tree::assembleTree() {
+	try {
+	
+		//if user has given a names file we want to include that info in the pgroups and pcount info.
+		if(globaldata->names.size() != 0) {  addNamesToCounts();  }
+		
+		//build the pGroups in non leaf nodes to be used in the parsimony calcs.
+		for (int i = numLeaves; i < numNodes; i++) {
+			if (m->control_pressed) { return 1; }
+
+			tree[i].pGroups = (mergeGroups(i));
+			tree[i].pcount = (mergeGcounts(i));
+		}
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "assembleTree");
+		exit(1);
+	}
+}
+/*****************************************************************/
+void Tree::getCopy(Tree* copy) {
+	try {
+	
+		//for each node in the tree copy its info
+		for (int i = 0; i < numNodes; i++) {
+			//copy name
+			tree[i].setName(copy->tree[i].getName());
+		
+			//copy group
+			tree[i].setGroup(copy->tree[i].getGroup());
+			
+			//copy branch length
+			tree[i].setBranchLength(copy->tree[i].getBranchLength());
+		
+			//copy parent
+			tree[i].setParent(copy->tree[i].getParent());
+		
+			//copy children
+			tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
+		
+			//copy index in node and tmap
+			tree[i].setIndex(copy->tree[i].getIndex());
+			setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
+			
+			//copy pGroups
+			tree[i].pGroups = copy->tree[i].pGroups;
+		
+			//copy pcount
+			tree[i].pcount = copy->tree[i].pcount;
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "getCopy");
+		exit(1);
+	}
+}
+/*****************************************************************/
+//returns a map with a groupname and the number of times that group was seen in the children
+//for instance if your children are white and black then it would return a map with 2 entries
+// p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
+//and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
+
+map<string, int> Tree::mergeGroups(int i) {
+	try {
+		int lc = tree[i].getLChild();
+		int rc = tree[i].getRChild();
+
+		//set parsimony groups to left child
+		map<string,int> parsimony = tree[lc].pGroups;
+		
+		int maxPars = 1;
+
+		//look at right child groups and update maxPars if right child has something higher for that group.
+		for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
+			it2 = parsimony.find(it->first);
+			if (it2 != parsimony.end()) {
+				parsimony[it->first]++;
+			}else {
+				parsimony[it->first] = 1;
+			}
+			
+			if(parsimony[it->first] > maxPars){
+				maxPars = parsimony[it->first];
+			}
+		}
+	
+		// this is true if right child had a greater parsimony for a certain group
+		if(maxPars > 1){
+			//erase all the groups that are only 1 because you found something with 2.
+			for(it=parsimony.begin();it!=parsimony.end();){
+				if(it->second == 1){
+					parsimony.erase(it++);
+				}else { it++; }
+			}
+			//set one remaining groups to 1
+			//so with our above example p[white] = 2 would be left and it would become p[white] = 1
+			for(it=parsimony.begin();it!=parsimony.end();it++){
+				parsimony[it->first] = 1;
+			}
+		
+		}
+	
+		return parsimony;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "mergeGroups");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Tree class function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/*****************************************************************/
+//returns a map with a groupname and the number of times that group was seen in the children
+//for instance if your children are white and black then it would return a map with 2 entries
+// p[white] = 1 and p[black] = 1.  Now go up a level and merge that with a node who has p[white] = 1
+//and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
+
+map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
+	try {
+	
+		int lc = tree[i].getLChild();
+		int rc = tree[i].getRChild();
+		
+		//loop through nodes groups removing the ones the user doesn't want
+		for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
+				if (inUsersGroups(it->first, g) != true) {
+					tree[lc].pGroups.erase(it++);
+				}else { it++; }
+		}
+
+		//loop through nodes groups removing the ones the user doesn't want
+		for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
+				if (inUsersGroups(it->first, g) != true) {
+					tree[rc].pGroups.erase(it++);
+				}else { it++; }
+		}
+
+		//set parsimony groups to left child
+		map<string,int> parsimony = tree[lc].pGroups;
+		
+		int maxPars = 1;
+
+		//look at right child groups and update maxPars if right child has something higher for that group.
+		for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
+			it2 = parsimony.find(it->first);
+			if (it2 != parsimony.end()) {
+				parsimony[it->first]++;
+			}else {
+				parsimony[it->first] = 1;
+			}
+			
+			if(parsimony[it->first] > maxPars){
+				maxPars = parsimony[it->first];
+			}
+		}
+			
+		// this is true if right child had a greater parsimony for a certain group
+		if(maxPars > 1){
+			//erase all the groups that are only 1 because you found something with 2.
+			for(it=parsimony.begin();it!=parsimony.end();){
+				if(it->second == 1){
+					parsimony.erase(it++);
+				}else { it++; }
+			}
+
+			for(it=parsimony.begin();it!=parsimony.end();it++){
+				parsimony[it->first] = 1;
+			}
+		}		
+		
+		return parsimony;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "mergeUserGroups");
+		exit(1);
+	}
+}
+
+
+/**************************************************************************************************/
+
+map<string,int> Tree::mergeGcounts(int position) {
+	try{
+		map<string,int>::iterator pos;
+	
+		int lc = tree[position].getLChild();
+		int rc = tree[position].getRChild();
+	
+		map<string,int> sum = tree[lc].pcount;
+    
+		for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
+			sum[it->first] += it->second;
+		}
+		return sum;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "mergeGcounts");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+
+void Tree::randomLabels(vector<string> g) {
+	try {
+		
+		for(int i = 0; i < numLeaves; i++){
+			int z;
+			//get random index to switch with
+			z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));	
+			
+			//you only want to randomize the nodes that are from a group the user wants analyzed, so
+			//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.
+			bool treez, treei;
+		
+			treez = inUsersGroups(tree[z].getGroup(), g);
+			treei = inUsersGroups(tree[i].getGroup(), g);
+			
+			if ((treez == true) && (treei == true)) {
+				//switches node i and node z's info.
+				map<string,int> lib_hold = tree[z].pGroups;
+				tree[z].pGroups = (tree[i].pGroups);
+				tree[i].pGroups = (lib_hold);
+				
+				vector<string> zgroup = tree[z].getGroup();
+				tree[z].setGroup(tree[i].getGroup());
+				tree[i].setGroup(zgroup);
+				
+				string zname = tree[z].getName();
+				tree[z].setName(tree[i].getName());
+				tree[i].setName(zname);
+				
+				map<string,int> gcount_hold = tree[z].pcount;
+				tree[z].pcount = (tree[i].pcount);
+				tree[i].pcount = (gcount_hold);
+			}
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "randomLabels");
 		exit(1);
+	}
+}
+/**************************************************************************************************
+
+void Tree::randomLabels(string groupA, string groupB) {
+	try {
+		int numSeqsA = globaldata->gTreemap->seqsPerGroup[groupA];
+		int numSeqsB = globaldata->gTreemap->seqsPerGroup[groupB];
+
+		vector<string> randomGroups(numSeqsA+numSeqsB, groupA);
+		for(int i=numSeqsA;i<randomGroups.size();i++){
+			randomGroups[i] = groupB;
+		}
+		random_shuffle(randomGroups.begin(), randomGroups.end());
+				
+		int randomCounter = 0;				
+		for(int i=0;i<numLeaves;i++){
+			if(tree[i].getGroup() == groupA || tree[i].getGroup() == groupB){
+				tree[i].setGroup(randomGroups[randomCounter]);
+				tree[i].pcount.clear();
+				tree[i].pcount[randomGroups[randomCounter]] = 1;
+				tree[i].pGroups.clear();
+				tree[i].pGroups[randomGroups[randomCounter]] = 1;
+				randomCounter++;
+			}
+		}
 	}		
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "randomLabels");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+void Tree::randomBlengths()  {
+	try {
+		for(int i=numNodes-1;i>=0;i--){
+			int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));	
+		
+			float bl_hold = tree[z].getBranchLength();
+			tree[z].setBranchLength(tree[i].getBranchLength());
+			tree[i].setBranchLength(bl_hold);
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "randomBlengths");
+		exit(1);
+	}
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(vector<string> g) {
+	randomLabels(g);
+	assembleTree();
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
+
+	vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
+	randomLabels(temp);
+	assembleTree();
 }
 
+/*************************************************************************************************/
+//for now it's just random topology but may become random labels as well later that why this is such a simple function now...
+void Tree::assembleRandomTree() {
+	randomTopology();
+	assembleTree();
+}
+/**************************************************************************************************/
+
+void Tree::randomTopology() {
+	try {
+		for(int i=0;i<numNodes;i++){
+			tree[i].setParent(-1);
+		}
+		for(int i=numLeaves;i<numNodes;i++){
+			tree[i].setChildren(-1, -1); 
+		}
+    
+		for(int i=numLeaves;i<numNodes;i++){
+			int escape =0;
+			int rnd_index1, rnd_index2;
+			while(escape == 0){
+				rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
+				if(tree[rnd_index1].getParent() == -1){escape = 1;}
+			}
+		
+			escape = 0;
+			while(escape == 0){
+				rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
+				if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
+					escape = 1;
+				}		
+			}
+	
+			tree[i].setChildren(rnd_index1,rnd_index2);
+			tree[i].setParent(-1);
+			tree[rnd_index1].setParent(i);
+			tree[rnd_index2].setParent(i);
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "randomTopology");
+		exit(1);
+	}
+}
+/*****************************************************************/
+void Tree::print(ostream& out) {
+	try {
+		int root = findRoot();
+		printBranch(root, out, "branch");
+		out << ";" << endl;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "print");
+		exit(1);
+	}
+}
+/*****************************************************************/
+void Tree::printForBoot(ostream& out) {
+	try {
+		int root = findRoot();
+		printBranch(root, out, "boot");
+		out << ";" << endl;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "printForBoot");
+		exit(1);
+	}
+}
 
 /*****************************************************************/
 // This prints out the tree in Newick form.
-void Tree::createNewickFile() {
+void Tree::createNewickFile(string f) {
 	try {
 		int root = findRoot();
-		filename = getRootName(globaldata->getTreeFile()) + "newick";
+		//filename = getRootName(globaldata->getTreeFile()) + "newick";
+		filename = f;
+
 		openOutputFile(filename, out);
 		
-		printBranch(root);
+		printBranch(root, out, "branch");
 		
 		// you are at the end of the tree
 		out << ";" << endl;
+		out.close();
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Tree", "createNewickFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Tree class function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /*****************************************************************/
@@ -118,46 +567,224 @@ int Tree::findRoot() {
 		for (int i = 0; i < numNodes; i++) {
 			//you found the root
 			if (tree[i].getParent() == -1) { return i; }
+			//cout << "i = " << i << endl;
+			//cout << "i's parent = " << tree[i].getParent() << endl;  
 		}
 		return -1;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Tree", "findRoot");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Tree class function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /*****************************************************************/
-void Tree::printBranch(int node) {
+void Tree::printBranch(int node, ostream& out, string mode) {
 	try {
 		
 		// you are not a leaf
 		if (tree[node].getLChild() != -1) {
 			out << "(";
-			printBranch(tree[node].getLChild());
+			printBranch(tree[node].getLChild(), out, mode);
 			out << ",";
-			printBranch(tree[node].getRChild());
+			printBranch(tree[node].getRChild(), out, mode);
 			out << ")";
+			if (mode == "branch") {
+				//if there is a branch length then print it
+				if (tree[node].getBranchLength() != -1) {
+					out << ":" << tree[node].getBranchLength();
+				}
+			}else if (mode == "boot") {
+				//if there is a label then print it
+				if (tree[node].getLabel() != -1) {
+					out << tree[node].getLabel();
+				}
+			}
 		}else { //you are a leaf
-			tree[node].printNode(out);  //prints out name and branch length
+			string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
+			
+			out << leafGroup; 
+			if (mode == "branch") {
+				//if there is a branch length then print it
+				if (tree[node].getBranchLength() != -1) {
+					out << ":" << tree[node].getBranchLength();
+				}
+			}else if (mode == "boot") {
+				//if there is a label then print it
+				if (tree[node].getLabel() != -1) {
+					out << tree[node].getLabel();
+				}
+			}
 		}
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Tree", "printBranch");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
 
 /*****************************************************************/
 
+void Tree::printTree() {
+	
+	for(int i=0;i<numNodes;i++){
+		cout << i << '\t';
+		tree[i].printNode();
+	}
+	
+}
+
+/*****************************************************************/
+//this code is a mess and should be rethought...-slw
+void Tree::parseTreeFile() {
+	
+	//only takes names from the first tree and assumes that all trees use the same names.
+	try {
+		string filename = globaldata->getTreeFile();
+		ifstream filehandle;
+		openInputFile(filename, filehandle);
+		int c, comment;
+		comment = 0;
+		int done = 1;
+		
+		//ifyou are not a nexus file 
+		if((c = filehandle.peek()) != '#') {  
+			while((c = filehandle.peek()) != ';') { 
+				while ((c = filehandle.peek()) != ';') {
+					// get past comments
+					if(c == '[') {
+						comment = 1;
+					}
+					if(c == ']'){
+						comment = 0;
+					}
+					if((c == '(') && (comment != 1)){ break; }
+					filehandle.get();
+				}
+
+				done = readTreeString(filehandle); 
+				if (done == 0) { break; }
+			}
+		//ifyou are a nexus file
+		}else if((c = filehandle.peek()) == '#') {
+			string holder = "";
+					
+			// get past comments
+			while(holder != "translate" && holder != "Translate"){	
+				if(holder == "[" || holder == "[!"){
+					comment = 1;
+				}
+				if(holder == "]"){
+					comment = 0;
+				}
+				filehandle >> holder; 
+
+				//if there is no translate then you must read tree string otherwise use translate to get names
+				if((holder == "tree") && (comment != 1)){	
+					//pass over the "tree rep.6878900 = "
+					while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
+
+					if(c == EOF) { break; }
+					filehandle.putback(c);  //put back first ( of tree.
+					done = readTreeString(filehandle);
+	
+					break;
+				}
+			
+				if (done == 0) { break;  }
+			}
+			
+			//use nexus translation rather than parsing tree to save time
+			if((holder == "translate") || (holder == "Translate")) {
+
+				string number, name, h;
+				h = ""; // so it enters the loop the first time
+				while((h != ";") && (number != ";")) { 
+					filehandle >> number;
+					filehandle >> name;
+	
+					//c = , until done with translation then c = ;
+					h = name.substr(name.length()-1, name.length()); 
+					name.erase(name.end()-1);  //erase the comma
+					globaldata->Treenames.push_back(number);
+				}
+				if(number == ";") { globaldata->Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
+			}
+		}
+		filehandle.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "parseTreeFile");
+		exit(1);
+	}
+}
+/*******************************************************/
+
+/*******************************************************/
+int Tree::readTreeString(ifstream& filehandle)	{
+	try {
+		int c;
+		string name;  //, k
+		
+		while((c = filehandle.peek()) != ';') { 
+//k = c;
+//cout << " at beginning of while " <<  k << endl;			
+			if(c == ')')  {    
+				//to pass over labels in trees
+				c=filehandle.get();
+				while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+				filehandle.putback(c);
+			}
+			if(c == ';') { return 0; }
+			if(c == -1) { return 0; }
+			//if you are a name
+			if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
+				name = "";
+				c = filehandle.get();
+			//k = c;
+//cout << k << endl;
+				while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {			
+					name += c;
+					c = filehandle.get();
+			//k = c;
+//cout << " in name while " << k << endl;
+				}
+				
+//cout << "name = " << name << endl;
+				globaldata->Treenames.push_back(name);
+				filehandle.putback(c);
+//k = c;
+//cout << " after putback" <<  k << endl;
+			} 
+			
+			if(c  == ':') { //read until you reach the end of the branch length
+				while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+					c = filehandle.get();
+	//k = c;
+	//cout << " in branch while " << k << endl;
+				}
+				filehandle.putback(c);
+			}
+		
+			c = filehandle.get();
+//k = c;
+	//cout << " here after get " << k << endl;
+			if(c == ';') { return 0; }
+			if(c == ')') { filehandle.putback(c); }
+	//k = c;
+//cout << k << endl;
+
+		}
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "readTreeString");
+		exit(1);
+	}
+}	
+
+/*******************************************************/
 
+/*******************************************************/