changed unifrac.weighted()

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index bd52fa6a74b66a0700316ebb069519582d0b8733..ba30d4016886123c1d8b33967899d699619b30b4 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -28,10 +28,11 @@ class ParsimonyCommand : public Command {
                GlobalData* globaldata;
                vector<Tree*> T;           //user trees
                Tree* randT;  //random tree
+               Tree* copyUserTree; 
                TreeMap* tmap; 
                TreeMap* savetmap;
                Parsimony* pars;
-               string parsFile, sumFile, distFile, randomtree;
+               string parsFile, sumFile, randomtree;
                int iters, numGroups;
                vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
                vector<float> userTreeScores; //scores for users trees
@@ -46,11 +47,12 @@ class ParsimonyCommand : public Command {
                map<int, float>::iterator it;
                map<int, float>::iterator it2;
                
-               ofstream out, outSum, outDist;
+               ofstream out, outSum;
                
                void printParsimonyFile();  
                void printUSummaryFile();
                void getUserInput();
+               void setGroups();
                
 };