added [ERROR] flag if command aborts

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 2018170648761a91b5b9026fada7079b0b4e73e1..4b524dd09af79b7d9cc2653caec6eb9d4dfb36ad 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -28,8 +28,7 @@ vector<string> PhylotypeCommand::getValidParameters(){
 //**********************************************************************************************************************
 PhylotypeCommand::PhylotypeCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;
                outputTypes["sabund"] = tempOutNames;
@@ -66,10 +65,10 @@ vector<string> PhylotypeCommand::getRequiredFiles(){
 /**********************************************************************************************************************/
 PhylotypeCommand::PhylotypeCommand(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 {
                        
@@ -181,7 +180,7 @@ PhylotypeCommand::~PhylotypeCommand(){}
 int PhylotypeCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //reads in taxonomy file and makes all the taxonomies the same length 
                //by appending the last taxon to a given taxonomy as many times as needed to