X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=00bb5d6c39eb0894389be1e5fecaba838d4303bd;hb=65b6a38d00b3a72021611211e7c25392022c69ed;hp=29cdf94091cebb65104e1b5691e5691e19a4e495;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 29cdf94..00bb5d6 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -48,7 +48,7 @@ string UnifracWeightedCommand::getHelpString(){
 		helpString += "Example unifrac.weighted(groups=A-B-C, iters=500).\n";
 		helpString += "The default value for groups is all the groups in your groupfile, and iters is 1000.\n";
 		helpString += "The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -80,6 +80,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(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();
@@ -133,6 +134,10 @@ UnifracWeightedCommand::UnifracWeightedCommand(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);
@@ -141,16 +146,18 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 				treefile = m->getTreeFile(); 
 				if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }								
-			}	
+			}else { m->setTreeFile(treefile); }	
 			
 			//check for required parameters
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
 			else if (groupfile == "not found") { groupfile = ""; }
+			else { m->setGroupFile(groupfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
 			
@@ -200,6 +207,8 @@ int UnifracWeightedCommand::execute() {
 	
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
+		m->setTreeFile(treefile);
+		
 		if (groupfile != "") {
 			//read in group map info.
 			tmap = new TreeMap(groupfile);