fixed bug with tree reading

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 01bc2f1d7405093db6a3f5fc4b44a0c17e76fbd3..c25e4fa13b4b7cc8eaf7f320d66b1806a3bf194d 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -90,6 +90,10 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        }
                        
                        m->runParse = true;
+                       m->Groups.clear();
+                       m->namesOfGroups.clear();
+                       m->Treenames.clear();
+                       m->names.clear();
                        
                        vector<string> tempOutNames;
                        outputTypes["tree"] = tempOutNames;
@@ -231,6 +235,7 @@ int IndicatorCommand::execute(){
                //    reading tree info                                                    //
                /***************************************************/
                string groupfile = ""; 
+               m->setTreeFile(treefile);
                Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
                treeMap = new TreeMap();
                bool mismatch = false;