X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=a6c9c07a0714fb850498a3d6f4439d4247602468;hb=fb01d5df390a98313ca095a812fc240dc079d084;hp=03eb17127d5ebc174c8c3018452eb36290fb9346;hpb=60fdefb3a300b59c3bbeffdca8a5f1f30c6a43af;p=mothur.git

diff --git a/tree.cpp b/tree.cpp
index 03eb171..a6c9c07 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -14,29 +14,28 @@
 Tree::Tree() {
 	try {
 		globaldata = GlobalData::getInstance();
-
-		numLeaves = globaldata->gTreemap->getNumSeqs();
+		
+		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]);
+				tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+				//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);
 			}
 		}
 	}
@@ -51,7 +50,8 @@ Tree::Tree() {
 }
 
 /*****************************************************************/
-
+Tree::~Tree() {}
+/*****************************************************************/
 int Tree::getIndex(string searchName) {
 	try {
 		//Treemap knows name, group and index to speed up search
@@ -85,20 +85,421 @@ void Tree::setIndex(string searchName, int index) {
 		exit(1);
 	}		
 }
+/*****************************************************************/
+void Tree::assembleTree() {
+	try {
+		//build the pGroups in non leaf nodes to be used in the parsimony calcs.
+		for (int i = numLeaves; i < numNodes; i++) {
+			tree[i].pGroups = (mergeGroups(i));
+			tree[i].pcount = (mergeGcounts(i));
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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();it++){
+				if(it->second == 1){
+					parsimony.erase(it->first);
+//					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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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(); it++) {
+			if (inUsersGroups(it->first, g) != true) { tree[lc].pGroups.erase(it->first); }
+		}
+		
+		//loop through nodes groups removing the ones the user doesn't want
+		for (it = tree[rc].pGroups.begin(); it != tree[rc].pGroups.end(); it++) {
+			if (inUsersGroups(it->first, g) != true) { tree[rc].pGroups.erase(it->first); }
+		}
+
+		//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();it++){
+				if(it->second == 1){
+					parsimony.erase(it->first);
+				}
+			}
+			for(it=parsimony.begin();it!=parsimony.end();it++){
+				parsimony[it->first] = 1;
+			}
+		}		
+		
+		return parsimony;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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);
+				
+				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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}		
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(vector<string> g) {
+	randomLabels(g);
+	assembleTree();
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
+	randomLabels(groupA, groupB);
+	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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}		
+}
+/*****************************************************************/
+void Tree::print(ostream& out) {
+	try {
+		int root = findRoot();
+		printBranch(root, out, "branch");
+		out << ";" << endl;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}		
+}
+/*****************************************************************/
+void Tree::printForBoot(ostream& out) {
+	try {
+		int root = findRoot();
+		printBranch(root, out, "boot");
+		out << ";" << endl;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printForBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function printForBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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";
@@ -117,7 +518,7 @@ int Tree::findRoot() {
 	try {
 		for (int i = 0; i < numNodes; i++) {
 			//you found the root
-			if (tree[i].getParent() == -1) { return i; }
+			if (tree[i].getParent() == -1) { return i; }  
 		}
 		return -1;
 	}
@@ -132,18 +533,40 @@ int Tree::findRoot() {
 }
 
 /*****************************************************************/
-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
+			out << tree[node].getGroup(); 
+			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();
+				}
+			}
 		}
 		
 	}
@@ -159,5 +582,15 @@ void Tree::printBranch(int node) {
 
 /*****************************************************************/
 
+void Tree::printTree() {
+	
+	for(int i=0;i<numNodes;i++){
+		cout << i << '\t';
+		tree[i].printNode();
+	}
+	
+}
+
+/*****************************************************************/