X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.cpp;h=d15899c2f2f853ba9529c9b65f74ce67885c8a63;hb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;hp=48d8555e1285ce854b0a45efbfdb75057bad5a1f;hpb=d4429ccc354708f3c9a13c809ba9b57c22908d2b;p=mothur.git

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 48d8555..d15899c 100644
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -136,6 +136,10 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
 			}
 			
 			m->runParse = true;
+			m->Groups.clear();
+			m->namesOfGroups.clear();
+			m->Treenames.clear();
+			m->names.clear();
 			
 			//check for required parameters
 			treefile = validParameter.validFile(parameters, "tree", true);
@@ -210,6 +214,8 @@ int PhyloDiversityCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
+		m->setTreeFile(treefile);
+		
 		//read in group map info.
 		tmap = new TreeMap(groupfile);
 		tmap->readMap();