changes to trim.flows command

[mothur.git] / sensspeccommand.cpp

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 78dce1794003457a077fe993958c75909c1020a7..6a22fd686096e83308faf7a68e98e9391d722fe0 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -24,7 +24,7 @@ vector<string> SensSpecCommand::getValidParameters(){
 //**********************************************************************************************************************
 SensSpecCommand::SensSpecCommand(){    
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["sensspec"] = tempOutNames;
        }
@@ -61,10 +61,10 @@ vector<string> SensSpecCommand::getRequiredFiles(){
 SensSpecCommand::SensSpecCommand(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 {
                        string temp;
@@ -207,7 +207,7 @@ SensSpecCommand::~SensSpecCommand(){        /*      do nothing      */      }
 
 int SensSpecCommand::execute(){
        try{
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                setUpOutput();
                outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);