X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;fp=pcoacommand.cpp;h=d8efb2551e2bb6b2f459f14ad041c188f31926da;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=fbcb7e08779d14f28277d8b5e8d0a8ce3b088174;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index fbcb7e0..d8efb25 100644
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -26,8 +26,7 @@ vector<string> PCOACommand::getValidParameters(){
 //**********************************************************************************************************************
 PCOACommand::PCOACommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["pcoa"] = tempOutNames;
 		outputTypes["loadings"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> PCOACommand::getRequiredFiles(){
 
 PCOACommand::PCOACommand(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
@@ -149,7 +148,7 @@ PCOACommand::~PCOACommand(){}
 int PCOACommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		cout.setf(ios::fixed, ios::floatfield);
 		cout.setf(ios::showpoint);