X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=c078f4f0728f0f35a9f2bc75f6174fb3eef38979;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=f93b9335749b4e79bb8c3e3c1be58684efc1cf65;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/tree.cpp b/tree.cpp
index f93b933..c078f4f 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -15,6 +15,8 @@ Tree::Tree() {
 	try {
 		globaldata = GlobalData::getInstance();
 		
+		if (globaldata->runParse == true) {  parseTreeFile();  globaldata->runParse = false;  }
+		
 		numLeaves = globaldata->Treenames.size();
 		numNodes = 2*numLeaves - 1;
 		
@@ -453,6 +455,38 @@ void Tree::randomTopology() {
 		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.
@@ -461,9 +495,10 @@ void Tree::createNewickFile(string f) {
 		int root = findRoot();
 		//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;
@@ -486,7 +521,9 @@ 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; }
+			//cout << "i = " << i << endl;
+			//cout << "i's parent = " << tree[i].getParent() << endl;  
 		}
 		return -1;
 	}
@@ -501,25 +538,39 @@ 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 there is a branch length then print it
-			if (tree[node].getBranchLength() != -1) {
-				out << ":" << tree[node].getBranchLength();
+			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
 			out << tree[node].getGroup(); 
-			//if there is a branch length then print it
-			if (tree[node].getBranchLength() != -1) {
-				out << ":" << tree[node].getBranchLength();
+			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();
+				}
 			}
 		}
 		
@@ -547,4 +598,142 @@ void Tree::printTree() {
 
 /*****************************************************************/
 
+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;
+		
+		//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();
+				}
+
+				readTreeString(filehandle); 
+			}
+		//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; 
+	
+				//ifthere 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.
+					readTreeString(filehandle);	
+					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
+			}
+		}
+		
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}		
+}
+/*******************************************************/
+
+/*******************************************************/
+void Tree::readTreeString(ifstream& filehandle)	{
+	try {
+		int c;
+		string name; //k
+		
+		while((c = filehandle.peek()) != ';') { 
+				//ifyou 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();
+			if(c == ';') { break; }
+		//	k = c;
+//cout << k << endl;
+
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Tree class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}		
+}	
+
+/*******************************************************/
+
+/*******************************************************/