/*
 *  tree.cpp
 *  Mothur
 *
 *  Created by Sarah Westcott on 1/22/09.
 *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
 *
 */

#include "tree.h"

/*****************************************************************/
Tree::Tree(int num, CountTable* t) : ct(t) {
	try {
		m = MothurOut::getInstance();
		
		numLeaves = num;  
		numNodes = 2*numLeaves - 1;
        
		tree.resize(numNodes);
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "Tree - numNodes");
		exit(1);
	}
}
/*****************************************************************/
Tree::Tree(string g) { //do not use tree generated by this its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
	try {
		m = MothurOut::getInstance();
		parseTreeFile();  m->runParse = false;  
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "Tree - just parse");
		exit(1);
	}
}
/*****************************************************************/
Tree::Tree(CountTable* t) : ct(t) {
	try {
		m = MothurOut::getInstance();
		
		if (m->runParse == true) {  parseTreeFile();  m->runParse = false;  }

		numLeaves = m->Treenames.size();
		numNodes = 2*numLeaves - 1;
		
		tree.resize(numNodes);
			
		//initialize groupNodeInfo
        vector<string> namesOfGroups = ct->getNamesOfGroups();
		for (int i = 0; i < namesOfGroups.size(); i++) {  groupNodeInfo[namesOfGroups[i]].resize(0);  }
		
		//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(m->Treenames[i]);
				
				//save group info
                int maxPars = 1;
				vector<string> group;
                vector<int> counts = ct->getGroupCounts(m->Treenames[i]);
				for (int j = 0; j < namesOfGroups.size(); j++) {  
                    if (counts[j] != 0) { //you have seqs from this group
                        groupNodeInfo[namesOfGroups[j]].push_back(i);
                        group.push_back(namesOfGroups[j]);
                        tree[i].pGroups[namesOfGroups[j]] = counts[j];
                        tree[i].pcount[namesOfGroups[j]] = counts[j];
                        //keep highest group
						if(counts[j] > maxPars){ maxPars = counts[j]; }
                    }  
                }
				tree[i].setGroup(group);
				setIndex(m->Treenames[i], i);
                
                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
                
			//intialize non leaf nodes
			}else if (i > (numLeaves-1)) {
				tree[i].setName("");
				vector<string> tempGroups;
				tree[i].setGroup(tempGroups);
			}
		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "Tree");
		exit(1);
	}
}
/*****************************************************************/
Tree::Tree(CountTable* t, vector< vector<double> >& sims) : ct(t) {
	try {
		m = MothurOut::getInstance();
		
		if (m->runParse == true) {  parseTreeFile();  m->runParse = false;  }
		numLeaves = m->Treenames.size();
		numNodes = 2*numLeaves - 1;
		
		tree.resize(numNodes);
        
		//initialize groupNodeInfo
        vector<string> namesOfGroups = ct->getNamesOfGroups();
		for (int i = 0; i < namesOfGroups.size(); i++) {  groupNodeInfo[namesOfGroups[i]].resize(0);  }
		
		//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(m->Treenames[i]);
				
				//save group info
                int maxPars = 1;
				vector<string> group;
                vector<int> counts = ct->getGroupCounts(m->Treenames[i]);
				for (int j = 0; j < namesOfGroups.size(); j++) {  
                    if (counts[j] != 0) { //you have seqs from this group
                        groupNodeInfo[namesOfGroups[j]].push_back(i);
                        group.push_back(namesOfGroups[j]);
                        tree[i].pGroups[namesOfGroups[j]] = counts[j];
                        tree[i].pcount[namesOfGroups[j]] = counts[j];
                        //keep highest group
						if(counts[j] > maxPars){ maxPars = counts[j]; }
                    }  
                }
				tree[i].setGroup(group);
				setIndex(m->Treenames[i], i);
                
                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
                
                //intialize non leaf nodes
			}else if (i > (numLeaves-1)) {
				tree[i].setName("");
				vector<string> tempGroups;
				tree[i].setGroup(tempGroups);
			}
		}

        
        //build tree from matrix
        //initialize indexes
        map<int, int> thisIndexes;  //maps row in simMatrix to vector index in the tree
        for (int g = 0; g < numLeaves; g++) {	thisIndexes[g] = g;	}
		
		//do merges and create tree structure by setting parents and children
		//there are numGroups - 1 merges to do
		for (int i = 0; i < (numLeaves - 1); i++) {
			float largest = -1000.0;
			
			if (m->control_pressed) { break; }
			
			int row, column;
			//find largest value in sims matrix by searching lower triangle
			for (int j = 1; j < sims.size(); j++) {
				for (int k = 0; k < j; k++) {
					if (sims[j][k] > largest) {  largest = sims[j][k]; row = j; column = k;  }
				}
			}
            
			//set non-leaf node info and update leaves to know their parents
			//non-leaf
			tree[numLeaves + i].setChildren(thisIndexes[row], thisIndexes[column]);
			
			//parents
			tree[thisIndexes[row]].setParent(numLeaves + i);
			tree[thisIndexes[column]].setParent(numLeaves + i);
			
			//blength = distance / 2;
			float blength = ((1.0 - largest) / 2);
			
			//branchlengths
			tree[thisIndexes[row]].setBranchLength(blength - tree[thisIndexes[row]].getLengthToLeaves());
			tree[thisIndexes[column]].setBranchLength(blength - tree[thisIndexes[column]].getLengthToLeaves());
			
			//set your length to leaves to your childs length plus branchlength
			tree[numLeaves + i].setLengthToLeaves(tree[thisIndexes[row]].getLengthToLeaves() + tree[thisIndexes[row]].getBranchLength());
			
			
			//update index 
			thisIndexes[row] = numLeaves+i;
			thisIndexes[column] = numLeaves+i;
			
			//remove highest value that caused the merge.
			sims[row][column] = -1000.0;
			sims[column][row] = -1000.0;
			
			//merge values in simsMatrix
			for (int n = 0; n < sims.size(); n++)	{
				//row becomes merge of 2 groups
				sims[row][n] = (sims[row][n] + sims[column][n]) / 2;
				sims[n][row] = sims[row][n];
				//delete column
				sims[column][n] = -1000.0;
				sims[n][column] = -1000.0;
			}
		}
		
		//adjust tree to make sure root to tip length is .5
		int root = findRoot();
		tree[root].setBranchLength((0.5 - tree[root].getLengthToLeaves()));
        
    }
	catch(exception& e) {
		m->errorOut(e, "Tree", "Tree");
		exit(1);
	}
}
/*****************************************************************/
Tree::~Tree() {}
/*****************************************************************
void Tree::addNamesToCounts(map<string, string> nameMap) {
	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
		
		//float A = clock();

		for (int i = 0; i < numLeaves; i++) {

			string name = tree[i].getName();
		
			map<string, string>::iterator itNames = nameMap.find(name);
		
			if (itNames == nameMap.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
			else {
				vector<string> dupNames;
				m->splitAtComma(nameMap[name], dupNames);
				
				map<string, int>::iterator itCounts;
				int maxPars = 1;
				set<string> groupsAddedForThisNode;
				for (int j = 0; j < dupNames.size(); j++) {
					
					string group = tmap->getGroup(dupNames[j]);
					
					if (dupNames[j] != name) {//you already added yourself in the constructor
				
						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
						
						//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];
						}
					}else {	 groupsAddedForThisNode.insert(group);  } //add it so you don't add it to groupNodeInfo again
				}//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		
		
		//float B = clock();
		//cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;	

	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "addNamesToCounts");
		exit(1);
	}
}*/
/*****************************************************************/
int Tree::getIndex(string searchName) {
	try {
        map<string, int>::iterator itIndex = indexes.find(searchName);
        if (itIndex != indexes.end()) {
            return itIndex->second;
        }
		return -1;
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "getIndex");
		exit(1);
	}
}
/*****************************************************************/

void Tree::setIndex(string searchName, int index) {
	try {
		map<string, int>::iterator itIndex = indexes.find(searchName);
        if (itIndex == indexes.end()) {
            indexes[searchName] = index;
        }
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "setIndex");
		exit(1);
	}
}
/*****************************************************************/
int Tree::assembleTree() {
	try {		
		//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);
	}
}
/*****************************************************************/
//assumes leaf node names are in groups and no names file - used by indicator command
void Tree::getSubTree(Tree* Ctree, vector<string> Groups) {
	try {
        
        //copy Tree since we are going to destroy it
        Tree* copy = new Tree(ct);
        copy->getCopy(Ctree);
        copy->assembleTree();
        
		//we want to select some of the leaf nodes to create the output tree
		//go through the input Tree starting at parents of leaves
        //initialize groupNodeInfo
        vector<string> namesOfGroups = ct->getNamesOfGroups();
		for (int i = 0; i < namesOfGroups.size(); i++) {  groupNodeInfo[namesOfGroups[i]].resize(0);  }
		
		//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(Groups[i]);
				
				//save group info
                int maxPars = 1;
				vector<string> group;
                vector<int> counts = ct->getGroupCounts(Groups[i]);
				for (int j = 0; j < namesOfGroups.size(); j++) {  
                    if (counts[j] != 0) { //you have seqs from this group
                        groupNodeInfo[namesOfGroups[j]].push_back(i);
                        group.push_back(namesOfGroups[j]);
                        tree[i].pGroups[namesOfGroups[j]] = counts[j];
                        tree[i].pcount[namesOfGroups[j]] = counts[j];
                        //keep highest group
						if(counts[j] > maxPars){ maxPars = counts[j]; }
                    }  
                }
				tree[i].setGroup(group);
				setIndex(Groups[i], i);
                
                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
                
                //intialize non leaf nodes
			}else if (i > (numLeaves-1)) {
				tree[i].setName("");
				vector<string> tempGroups;
				tree[i].setGroup(tempGroups);
			}
		}

		set<int> removedLeaves;
		for (int i = 0; i < copy->getNumLeaves(); i++) {
			
			if (removedLeaves.count(i) == 0) {
			
			//am I in the group
			int parent = copy->tree[i].getParent();
			
			if (parent != -1) {
				
				if (m->inUsersGroups(copy->tree[i].getName(), Groups)) {
					//find my siblings name
					int parentRC = copy->tree[parent].getRChild();
					int parentLC = copy->tree[parent].getLChild();
					
					//if I am the right child, then my sib is the left child
					int sibIndex = parentRC;
					if (parentRC == i) { sibIndex = parentLC; }
					
					string sibsName = copy->tree[sibIndex].getName();
					
					//if yes, is my sibling
					if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
						//we both are okay no trimming required
					}else{
						//i am, my sib is not, so remove sib by setting my parent to my grandparent
						int grandparent = copy->tree[parent].getParent();
						int grandparentLC = copy->tree[grandparent].getLChild();
						int grandparentRC = copy->tree[grandparent].getRChild();
						
						//whichever of my granparents children was my parent now equals me
						if (grandparentLC == parent) { grandparentLC = i; }
						else { grandparentRC = i; }
						
						copy->tree[i].setParent(grandparent);
						copy->tree[i].setBranchLength((copy->tree[i].getBranchLength()+copy->tree[parent].getBranchLength()));
						if (grandparent != -1) {
							copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
						}
						removedLeaves.insert(sibIndex);
					}
				}else{
					//find my siblings name
					int parentRC = copy->tree[parent].getRChild();
					int parentLC = copy->tree[parent].getLChild();
					
					//if I am the right child, then my sib is the left child
					int sibIndex = parentRC;
					if (parentRC == i) { sibIndex = parentLC; }
					
					string sibsName = copy->tree[sibIndex].getName();
					
					//if no is my sibling
					if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
						//i am not, but my sib is
						int grandparent = copy->tree[parent].getParent();
						int grandparentLC = copy->tree[grandparent].getLChild();
						int grandparentRC = copy->tree[grandparent].getRChild();
						
						//whichever of my granparents children was my parent now equals my sib
						if (grandparentLC == parent) { grandparentLC = sibIndex; }
						else { grandparentRC = sibIndex; }
						
						copy->tree[sibIndex].setParent(grandparent);
						copy->tree[sibIndex].setBranchLength((copy->tree[sibIndex].getBranchLength()+copy->tree[parent].getBranchLength()));
						if (grandparent != -1) {
							copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
						}
						removedLeaves.insert(i);
					}else{
						//neither of us are, so we want to eliminate ourselves and our parent
						//so set our parents sib to our great-grandparent
						int parent = copy->tree[i].getParent();
						int grandparent = copy->tree[parent].getParent();
						int parentsSibIndex;
						if (grandparent != -1) {
							int greatgrandparent = copy->tree[grandparent].getParent();
							int greatgrandparentLC, greatgrandparentRC;
							if (greatgrandparent != -1) {
								greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
								greatgrandparentRC = copy->tree[greatgrandparent].getRChild();
							}
							
							int grandparentLC = copy->tree[grandparent].getLChild();
							int grandparentRC = copy->tree[grandparent].getRChild();
							
							parentsSibIndex = grandparentLC;
							if (grandparentLC == parent) { parentsSibIndex = grandparentRC; }

							//whichever of my greatgrandparents children was my grandparent
							if (greatgrandparentLC == grandparent) { greatgrandparentLC = parentsSibIndex; }
							else { greatgrandparentRC = parentsSibIndex; }
							
							copy->tree[parentsSibIndex].setParent(greatgrandparent);
							copy->tree[parentsSibIndex].setBranchLength((copy->tree[parentsSibIndex].getBranchLength()+copy->tree[grandparent].getBranchLength()));
							if (greatgrandparent != -1) {
								copy->tree[greatgrandparent].setChildren(greatgrandparentLC, greatgrandparentRC);
							}
						}else{
							copy->tree[parent].setParent(-1);
							//cout << "issues with making subtree" << endl;
						}
						removedLeaves.insert(sibIndex);
						removedLeaves.insert(i);
					}
				}
			}
			}
		}
		
		int root = 0;
		for (int i = 0; i < copy->getNumNodes(); i++) {
			//you found the root
			if (copy->tree[i].getParent() == -1) { root = i; break; }
		}
        
		int nextSpot = numLeaves;
		populateNewTree(copy->tree, root, nextSpot);
        
        delete copy;
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "getSubTree");
		exit(1);
	}
}
/*****************************************************************
//assumes nameMap contains unique names as key or is empty. 
//assumes numLeaves defined in tree constructor equals size of seqsToInclude and seqsToInclude only contains unique seqs.
int Tree::getSubTree(Tree* copy, vector<string> seqsToInclude, map<string, string> nameMap) {
	try {
        
        if (numLeaves != seqsToInclude.size()) { m->mothurOut("[ERROR]: numLeaves does not equal numUniques, cannot create subtree.\n"); m->control_pressed = true; return 0; }
        
        getSubTree(copy, seqsToInclude);
        if (nameMap.size() != 0) {  addNamesToCounts(nameMap);  }
        
        //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", "getSubTree");
		exit(1);
	}
}
/*****************************************************************/
int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
	try {
		
		if (oldtree[node].getLChild() != -1) {
			int rc = populateNewTree(oldtree, oldtree[node].getLChild(), index);
			int lc = populateNewTree(oldtree, oldtree[node].getRChild(), index);

			tree[index].setChildren(lc, rc);
			tree[rc].setParent(index);
			tree[lc].setParent(index);
			
			tree[index].setBranchLength(oldtree[node].getBranchLength());
			tree[rc].setBranchLength(oldtree[oldtree[node].getLChild()].getBranchLength());
			tree[lc].setBranchLength(oldtree[oldtree[node].getRChild()].getBranchLength());
			
			return (index++);
		}else { //you are a leaf
			int indexInNewTree = getIndex(oldtree[node].getName());
			return indexInNewTree;
		}
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "populateNewTree");
		exit(1);
	}
}
/*****************************************************************/
void Tree::getCopy(Tree* copy, bool subsample) {
	try {
        
		//for each node in the tree copy its info
		for (int i = 0; i < numNodes; i++) {
			//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());
        }
        
        //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) { break; }
            
			tree[i].pGroups = (mergeGroups(i));
			tree[i].pcount = (mergeGcounts(i));
		}
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "getCopy");
		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
            setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
			tree[i].setIndex(copy->tree[i].getIndex());
			
			//copy pGroups
			tree[i].pGroups = copy->tree[i].pGroups;
		
			//copy pcount
			tree[i].pcount = copy->tree[i].pcount;
		}
		
		groupNodeInfo = copy->groupNodeInfo;
		
	}
	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);
	}
}
/*****************************************************************/
//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 (m->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 (m->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 {
	
		//initialize groupNodeInfo
		for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
			groupNodeInfo[(ct->getNamesOfGroups())[i]].resize(0);
		}
		
		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 = m->inUsersGroups(tree[z].getGroup(), g);
			treei = m->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);
			}
			
			for (int k = 0; k < (tree[i].getGroup()).size(); k++) {  groupNodeInfo[(tree[i].getGroup())[k]].push_back(i); }
			for (int k = 0; k < (tree[z].getGroup()).size(); k++) {  groupNodeInfo[(tree[z].getGroup())[k]].push_back(z); }
		}
	}
	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::print(ostream& out, map<string, string> nameMap) {
	try {
		int root = findRoot();
		printBranch(root, out, nameMap);
		out << ";" << endl;
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "print");
		exit(1);
	}
}
/*****************************************************************/
void Tree::print(ostream& out, string mode) {
	try {
		int root = findRoot();
		printBranch(root, out, mode);
		out << ";" << endl;
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "print");
		exit(1);
	}
}
/*****************************************************************/
// This prints out the tree in Newick form.
void Tree::createNewickFile(string f) {
	try {
		int root = findRoot();
	
		filename = f;

		m->openOutputFile(filename, out);
		
		printBranch(root, out, "branch");
		
		// you are at the end of the tree
		out << ";" << endl;
		out.close();
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "createNewickFile");
		exit(1);
	}
}

/*****************************************************************/
//This function finds the index of the root node.

int Tree::findRoot() {
	try {
		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) {
		m->errorOut(e, "Tree", "findRoot");
		exit(1);
	}
}
/*****************************************************************/
void Tree::printBranch(int node, ostream& out, map<string, string> names) {
try {

// you are not a leaf
		if (tree[node].getLChild() != -1) {
			out << "(";
			printBranch(tree[node].getLChild(), out, names);
			out << ",";
			printBranch(tree[node].getRChild(), out, names);
			out << ")";
			
            //if there is a branch length then print it
            if (tree[node].getBranchLength() != -1) {
                out << ":" << tree[node].getBranchLength();
            }
			
		}else { //you are a leaf
            map<string, string>::iterator itNames = names.find(tree[node].getName());
            
            string outputString = "";
            if (itNames != names.end()) { 
                
                vector<string> dupNames;
                m->splitAtComma((itNames->second), dupNames);
                
                if (dupNames.size() == 1) {
                    outputString += tree[node].getName();
                    if (tree[node].getBranchLength() != -1) {
                        outputString += ":" + toString(tree[node].getBranchLength());
                    }
                }else {
                    outputString += "(";
                    
                    for (int u = 0; u < dupNames.size()-1; u++) {
                        outputString += dupNames[u];
                        
                        if (tree[node].getBranchLength() != -1) {
                            outputString += ":" + toString(0.0);
                        }
                        outputString += ",";
                    }
                    
                    outputString += dupNames[dupNames.size()-1];
                    if (tree[node].getBranchLength() != -1) {
                        outputString += ":" + toString(0.0);
                    }
                    
                    outputString += ")";
                    if (tree[node].getBranchLength() != -1) {
                        outputString += ":" + toString(tree[node].getBranchLength());
                    }
                }
            }else { 
                outputString = tree[node].getName();
                //if there is a branch length then print it
                if (tree[node].getBranchLength() != -1) {
                    outputString += ":" + toString(tree[node].getBranchLength());
                }
                
                m->mothurOut("[ERROR]: " + tree[node].getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); 
            }
                
            out << outputString;
		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "printBranch");
		exit(1);
	}
}
/*****************************************************************/
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(), out, mode);
			out << ",";
			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 if (mode == "both") {
				if (tree[node].getLabel() != -1) {
					out << tree[node].getLabel();
				}
				//if there is a branch length then print it
				if (tree[node].getBranchLength() != -1) {
					out << ":" << tree[node].getBranchLength();
				}
			}
		}else { //you are a leaf
			vector<string> leafGroup = ct->getGroups(tree[node].getName());
			
			if (mode == "branch") {
				out << leafGroup[0]; 
				//if there is a branch length then print it
				if (tree[node].getBranchLength() != -1) {
					out << ":" << tree[node].getBranchLength();
				}
			}else if (mode == "boot") {
				out << leafGroup[0]; 
				//if there is a label then print it
				if (tree[node].getLabel() != -1) {
					out << tree[node].getLabel();
				}
			}else if (mode == "both") {
				out << tree[node].getName();
				if (tree[node].getLabel() != -1) {
					out << tree[node].getLabel();
				}
				//if there is a branch length then print it
				if (tree[node].getBranchLength() != -1) {
					out << ":" << tree[node].getBranchLength();
				}
			}
		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "printBranch");
		exit(1);
	}
}
/*****************************************************************/
void Tree::printBranch(int node, ostream& out, string mode, vector<Node>& theseNodes) {
	try {
		
		// you are not a leaf
		if (theseNodes[node].getLChild() != -1) {
			out << "(";
			printBranch(theseNodes[node].getLChild(), out, mode);
			out << ",";
			printBranch(theseNodes[node].getRChild(), out, mode);
			out << ")";
			if (mode == "branch") {
				//if there is a branch length then print it
				if (theseNodes[node].getBranchLength() != -1) {
					out << ":" << theseNodes[node].getBranchLength();
				}
			}else if (mode == "boot") {
				//if there is a label then print it
				if (theseNodes[node].getLabel() != -1) {
					out << theseNodes[node].getLabel();
				}
			}else if (mode == "both") {
				if (theseNodes[node].getLabel() != -1) {
					out << theseNodes[node].getLabel();
				}
				//if there is a branch length then print it
				if (theseNodes[node].getBranchLength() != -1) {
					out << ":" << theseNodes[node].getBranchLength();
				}
			}
		}else { //you are a leaf
			vector<string> leafGroup = ct->getGroups(theseNodes[node].getName());
			
			if (mode == "branch") {
				out << leafGroup[0]; 
				//if there is a branch length then print it
				if (theseNodes[node].getBranchLength() != -1) {
					out << ":" << theseNodes[node].getBranchLength();
				}
			}else if (mode == "boot") {
				out << leafGroup[0]; 
				//if there is a label then print it
				if (theseNodes[node].getLabel() != -1) {
					out << theseNodes[node].getLabel();
				}
			}else if (mode == "both") {
				out << theseNodes[node].getName();
				if (theseNodes[node].getLabel() != -1) {
					out << theseNodes[node].getLabel();
				}
				//if there is a branch length then print it
				if (theseNodes[node].getBranchLength() != -1) {
					out << ":" << theseNodes[node].getBranchLength();
				}
			}
		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "Tree", "printBranch");
		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
int Tree::parseTreeFile() {
	
	//only takes names from the first tree and assumes that all trees use the same names.
	try {
		string filename = m->getTreeFile();
		ifstream filehandle;
		m->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()) != ';') {
                if (m->control_pressed) {  filehandle.close(); return 0; }
				while ((c = filehandle.peek()) != ';') {
                    if (m->control_pressed) {  filehandle.close(); return 0; }
					// 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 (m->control_pressed) {  filehandle.close(); return 0; }
				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 != ";")) {
                    if (m->control_pressed) {  filehandle.close(); return 0; }
					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
					m->Treenames.push_back(number);
				}
				if(number == ";") { m->Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
			}
		}
		filehandle.close();
		return 0;
		//for (int i = 0; i < globaldata->Treenames.size(); i++) {
//cout << globaldata->Treenames[i] << endl; }
//cout << globaldata->Treenames.size() << endl;
	}
	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()) != ';') {
            if (m->control_pressed) {  return 0; }
//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;
                if (name != "\r" ) {
                    m->Treenames.push_back(name);   } //cout << m->Treenames.size() << '\t' << name << endl;
                
				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);
	}
}	

/*******************************************************/

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