X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mgclustercommand.cpp;h=23f359eae8ab7fe84e9b86faf96d54d33ac8dcd3;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=3ed9bf2131a45ac7a4b0ac44d959b16bfe28cd36;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 3ed9bf2..23f359e 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -25,8 +25,7 @@ vector<string> MGClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 MGClusterCommand::MGClusterCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["list"] = tempOutNames;
 		outputTypes["rabund"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> MGClusterCommand::getRequiredFiles(){
 MGClusterCommand::MGClusterCommand(string option) {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -202,7 +201,7 @@ MGClusterCommand::~MGClusterCommand(){}
 int MGClusterCommand::execute(){
 	try {
 		
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//read names file
 		if (namefile != "") {
@@ -508,6 +507,26 @@ int MGClusterCommand::execute(){
 		m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine();	outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
 		m->mothurOutEndLine();
 		
+		//set list file as new current listfile
+		string current = "";
+		itTypes = outputTypes.find("list");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+		}
+		
+		//set rabund file as new current rabundfile
+		itTypes = outputTypes.find("rabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+		}
+		
+		//set sabund file as new current sabundfile
+		itTypes = outputTypes.find("sabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+		}
+		
+		
 		m->mothurOut("It took " + toString(time(NULL) - start) + " seconds to cluster."); m->mothurOutEndLine();
 			
 		return 0;