changes while testing 1.26

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index d9b4a9c1e8f4e31475aa5127adb38d339d1a8631..44ecadd534b60d60b602d9e052259ac69709f9d3 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -588,6 +588,37 @@ int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
        }
 }
 /*****************************************************************/
+void Tree::getCopy(Tree* copy, map<string, string> nameMap) {
+       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());
+        }
+               
+        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) { 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 {