added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 4a77211d2bd5e8d90585a9f19e6383db6e5f16fc..3eeeae292e674dbc7823522ce8e35d8d531ab70e 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -484,74 +484,13 @@ Tree* TreeGroupCommand::createTree(vector< vector<double> >& simMatrix){
                //create tree
                t = new Tree(tmap, simMatrix);
         
-       /* //initialize index
-        map<int, int> index;  //maps row in simMatrix to vector index in the tree
-        for (int g = 0; g < numGroups; g++) {  index[g] = g;   }
+        if (m->control_pressed) { delete t; t = NULL; return t; }
                
-               //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++) {
-                       float largest = -1000.0;
-                       
-                       if (m->control_pressed) { delete t; t = NULL; return t; }
-                       
-                       int row, column;
-                       //find largest value in sims matrix by searching lower triangle
-                       for (int j = 1; j < simMatrix.size(); j++) {
-                               for (int k = 0; k < j; k++) {
-                                       if (simMatrix[j][k] > largest) {  largest = simMatrix[j][k]; row = j; column = k;  }
-                               }
-                       }
+        //assemble tree
+        map<string, string> empty;
+               t->assembleTree(empty);
 
-                       //set non-leaf node info and update leaves to know their parents
-                       //non-leaf
-                       t->tree[numGroups + i].setChildren(index[row], index[column]);
-                       
-                       //parents
-                       t->tree[index[row]].setParent(numGroups + i);
-                       t->tree[index[column]].setParent(numGroups + i);
-                       
-                       //blength = distance / 2;
-                       float blength = ((1.0 - largest) / 2);
-                       
-                       //branchlengths
-                       t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
-                       t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
-                       
-                       //set your length to leaves to your childs length plus branchlength
-                       t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
-                       
-                       
-                       //update index 
-                       index[row] = numGroups+i;
-                       index[column] = numGroups+i;
-                       
-                       //remove highest value that caused the merge.
-                       simMatrix[row][column] = -1000.0;
-                       simMatrix[column][row] = -1000.0;
-                       
-                       //merge values in simsMatrix
-                       for (int n = 0; n < simMatrix.size(); n++)      {
-                               //row becomes merge of 2 groups
-                               simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
-                               simMatrix[n][row] = simMatrix[row][n];
-                               //delete column
-                               simMatrix[column][n] = -1000.0;
-                               simMatrix[n][column] = -1000.0;
-                       }
-               }
-               
-               //adjust tree to make sure root to tip length is .5
-               int root = t->findRoot();
-               t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
-               */
-               //assemble tree
-               t->assembleTree();
-               
-               if (m->control_pressed) { delete t; t = NULL; return t; }
-               
                return t;
-       
        }
        catch(exception& e) {
                m->errorOut(e, "TreeGroupCommand", "createTree");
@@ -1006,7 +945,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 Consensus consensus;
                 //clear old tree names if any
                 m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
-                Tree* conTree = consensus.getTree(trees, tmap);
+                Tree* conTree = consensus.getTree(trees);
                 
                 //create a new filename
                 string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons.tre";