fixed bug with tree reading

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index be64ec273ec8c62fcba9a7cd206955878f7e21ed..1be4697a4f3fde882fa08985a8a1e01072110596 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -125,6 +125,10 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        }
                        
                        m->runParse = true;
+                       m->Groups.clear();
+                       m->namesOfGroups.clear();
+                       m->Treenames.clear();
+                       m->names.clear();
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        
@@ -188,6 +192,9 @@ int ParsimonyCommand::execute() {
                //randomtree will tell us if user had their own treefile or if they just want the random distribution
                //user has entered their own tree
                if (randomtree == "") { 
+                       
+                       m->setTreeFile(treefile);
+                       
                        if (groupfile != "") {
                                //read in group map info.
                                tmap = new TreeMap(groupfile);