fixed summary.shared bug and set jumble default to 1.

[mothur.git] / treenode.cpp

diff --git a/treenode.cpp b/treenode.cpp
new file mode 100644 (file)
index 0000000..6cd99f9
--- /dev/null
+++ b/treenode.cpp
@@ -0,0 +1,71 @@
+/*
+ *  treenode.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/23/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treenode.h"
+
+
+/****************************************************************/     
+Node::Node() {
+       //initialize node
+       name = "";
+       branchLength = -1;
+       parent = -1;
+       lchild = -1;
+       rchild = -1;
+       
+}
+/****************************************************************/
+void Node::setName(string Name) {  name = Name; }
+/****************************************************************/
+//non leaf nodes will belong to multiple groups, leaf nodes will only belong to one.
+void Node::setGroup(string groups)  { group.push_back(groups); }
+/****************************************************************/
+void Node::setBranchLength(float l) { branchLength = l; }
+/****************************************************************/
+void Node::setParent(int p)  { parent = p; }
+/****************************************************************/
+void Node::setIndex(int i)  { vectorIndex = i; }
+/****************************************************************/
+void Node::setChildren(int lc, int rc) { lchild = lc; rchild = rc; }   //leftchild, rightchild
+/****************************************************************/
+string Node::getName() { return name; }
+/****************************************************************/
+vector<string> Node::getGroup() { return group; }
+/****************************************************************/
+float Node::getBranchLength() { return branchLength; }
+/****************************************************************/
+int Node::getParent() { return parent; }
+/****************************************************************/
+int Node::getLChild() { return lchild; }
+/****************************************************************/
+int Node::getRChild() { return rchild; }
+/****************************************************************/
+int Node::getIndex() { return vectorIndex; }
+/****************************************************************/
+//to be used by printTree in the Tree class to print the leaf info                     
+void Node::printNode(ostream& out) {
+       try{
+               out << name;
+               
+               //there is a branch length
+               if (branchLength != -1) { 
+                       out << ":" << setprecision(4) << branchLength; 
+               }
+               
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Node class Function printNode. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Node class function printNode. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+/****************************************************************/     
\ No newline at end of file