working on slayer bug

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index a8c2d156be775455c729d9341386ecfb952323e4..1be4697a4f3fde882fa08985a8a1e01072110596 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -43,7 +43,7 @@ string ParsimonyCommand::getHelpString(){
                helpString += "Example parsimony(random=out, iters=500).\n";
                helpString += "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n";
                helpString += "and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -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);