X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=403b2b86d9addf1f9291e7f87fac63ef1755c002;hb=c6254ca58f680919e7c493e11ae2b029bda43a16;hp=a8c2d156be775455c729d9341386ecfb952323e4;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index a8c2d15..403b2b8 100644
--- 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) {
@@ -74,6 +74,7 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 			
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -125,6 +126,10 @@ 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 +193,9 @@ 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);