X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.cpp;h=5bcfe03416f90700a02a4ff3d58ad312f788bb96;hb=d0954e27635712cdbd8b86e3c4510670803a2665;hp=56fbd5c0d6c2b8e9380959bd6ba97435b28fcd70;hpb=89f19f9c6ab89c2f6c7c6921a328ae87bce6f8e3;p=mothur.git

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 56fbd5c..5bcfe03 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -25,8 +25,7 @@ vector<string> ClusterDoturCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterDoturCommand::ClusterDoturCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["list"] = tempOutNames;
 		outputTypes["rabund"] = tempOutNames;
@@ -65,10 +64,10 @@ vector<string> ClusterDoturCommand::getRequiredFiles(){
 ClusterDoturCommand::ClusterDoturCommand(string option)  {
 	try{
 		
-		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
@@ -189,7 +188,7 @@ ClusterDoturCommand::~ClusterDoturCommand(){}
 int ClusterDoturCommand::execute(){
 	try {
 	
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		if(namefile != ""){	
 			nameMap = new NameAssignment(namefile);
@@ -272,6 +271,25 @@ int ClusterDoturCommand::execute(){
 		//	m->mothurOut("changed cutoff to " + toString(cutoff)); 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->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}