added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index f93b9335749b4e79bb8c3e3c1be58684efc1cf65..e138121661f19f77d1c8603036793f86a95dfe67 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -453,7 +453,22 @@ void Tree::randomTopology() {
                exit(1);
        }               
 }
-
+/*****************************************************************/
+void Tree::print(ostream& out) {
+       try {
+               int root = findRoot();
+               printBranch(root, out);
+               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);
+       }               
+}
 /*****************************************************************/
 // This prints out the tree in Newick form.
 void Tree::createNewickFile(string f) {
@@ -463,7 +478,7 @@ void Tree::createNewickFile(string f) {
                filename = f;
                openOutputFile(filename, out);
                
-               printBranch(root);
+               printBranch(root, out);
                
                // you are at the end of the tree
                out << ";" << endl;
@@ -501,15 +516,15 @@ int Tree::findRoot() {
 }
 
 /*****************************************************************/
-void Tree::printBranch(int node) {
+void Tree::printBranch(int node, ostream& out) {
        try {
                
                // you are not a leaf
                if (tree[node].getLChild() != -1) {
                        out << "(";
-                       printBranch(tree[node].getLChild());
+                       printBranch(tree[node].getLChild(), out);
                        out << ",";
-                       printBranch(tree[node].getRChild());
+                       printBranch(tree[node].getRChild(), out);
                        out << ")";
                        //if there is a branch length then print it
                        if (tree[node].getBranchLength() != -1) {