X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=secondarystructurecommand.cpp;h=c9002cab4a458c1ef9fbb3a2acb85706e01513dc;hp=26bd35444d866132fd37c34fc3e0d8fd4cf84c40;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 26bd354..c9002ca 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -25,8 +25,7 @@ vector<string> AlignCheckCommand::getValidParameters(){
 //**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["aligncheck"] = tempOutNames;
 	}
@@ -62,11 +61,11 @@ vector<string> AlignCheckCommand::getRequiredFiles(){
 
 AlignCheckCommand::AlignCheckCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		haderror = 0;
 			
 		//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
@@ -155,7 +154,7 @@ void AlignCheckCommand::help(){
 int AlignCheckCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get secondary structure info.
 		readMap();