X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=1be4697a4f3fde882fa08985a8a1e01072110596;hb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;hp=be64ec273ec8c62fcba9a7cd206955878f7e21ed;hpb=d4429ccc354708f3c9a13c809ba9b57c22908d2b;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index be64ec2..1be4697 100644
--- 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);