fixed parsimony for groups

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 554d24bd93f76c94a223d33ce24159babd0f3e78..59dca88751edfb115cc3c83fcc5c85935b52b9d3 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -62,10 +62,13 @@ int ParsimonyCommand::execute() {
                outDist << "RandomTree#" << '\t' << "ParsScore" << endl;
                
                if (randomtree == "") {
+                       copyUserTree = new Tree();
                        //get pscores for users trees
                        for (int i = 0; i < T.size(); i++) {
+                               //copy users tree so that you can redo pgroups 
+                               copyUserTree->getCopy(T[i]);
                                cout << "Processing tree " << i+1 << endl;
-                               userData = pars->getValues(T[i]);  //userData[0] = pscore
+                               userData = pars->getValues(copyUserTree);  //userData[0] = pscore
                                cout << "Tree " << i+1 << " parsimony score = " << userData[0] << endl;
                                //update uscoreFreq
                                it = uscoreFreq.find(userData[0]);