bugs found while testing

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 7c9671bf9a91e02b23cfd40b44804c38e3e4354d..d9b4a9c1e8f4e31475aa5127adb38d339d1a8631 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -92,7 +92,6 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
                m = MothurOut::getInstance();
                
                if (m->runParse == true) {  parseTreeFile();  m->runParse = false;  }
-        //for(int i = 0; i <   globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }  
                numLeaves = m->Treenames.size();
                numNodes = 2*numLeaves - 1;
                
@@ -134,12 +133,11 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
         //build tree from matrix
         //initialize indexes
         map<int, int> indexes;  //maps row in simMatrix to vector index in the tree
-        int numGroups = (tmap->getNamesOfGroups()).size();
-        for (int g = 0; g < numGroups; g++) {  indexes[g] = g; }
+        for (int g = 0; g < numLeaves; g++) {  indexes[g] = g; }
                
                //do merges and create tree structure by setting parents and children
                //there are numGroups - 1 merges to do
-               for (int i = 0; i < (numGroups - 1); i++) {
+               for (int i = 0; i < (numLeaves - 1); i++) {
                        float largest = -1000.0;
                        
                        if (m->control_pressed) { break; }
@@ -154,11 +152,11 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
             
                        //set non-leaf node info and update leaves to know their parents
                        //non-leaf
-                       tree[numGroups + i].setChildren(indexes[row], indexes[column]);
+                       tree[numLeaves + i].setChildren(indexes[row], indexes[column]);
                        
                        //parents
-                       tree[indexes[row]].setParent(numGroups + i);
-                       tree[indexes[column]].setParent(numGroups + i);
+                       tree[indexes[row]].setParent(numLeaves + i);
+                       tree[indexes[column]].setParent(numLeaves + i);
                        
                        //blength = distance / 2;
                        float blength = ((1.0 - largest) / 2);
@@ -168,12 +166,12 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
                        tree[indexes[column]].setBranchLength(blength - tree[indexes[column]].getLengthToLeaves());
                        
                        //set your length to leaves to your childs length plus branchlength
-                       tree[numGroups + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
+                       tree[numLeaves + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
                        
                        
                        //update index 
-                       indexes[row] = numGroups+i;
-                       indexes[column] = numGroups+i;
+                       indexes[row] = numLeaves+i;
+                       indexes[column] = numLeaves+i;
                        
                        //remove highest value that caused the merge.
                        sims[row][column] = -1000.0;