X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=ea460c026e4c4ea77684893920b328288d3f9f63;hb=943d3038553f82378567d3b651969146716e5862;hp=0be8141636a1fffaacce16f2592e6bf8738ad400;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 0be8141..ea460c0 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -26,7 +26,7 @@ vector<string> RareFactSharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 RareFactSharedCommand::RareFactSharedCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["sharedrarefaction"] = tempOutNames;
 		outputTypes["sharedr_nseqs"] = tempOutNames;
@@ -65,14 +65,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
 		
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		labels.clear();
 		Estimators.clear();
 		Groups.clear();
 				
 		//allow user to run help
-		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -216,7 +216,7 @@ RareFactSharedCommand::~RareFactSharedCommand(){
 int RareFactSharedCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//if the users entered no valid calculators don't execute command
 		if (rDisplays.size() == 0) { return 0; }