added [ERROR] flag if command aborts

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index a2d0aaa5331a402a538d253e4d1f00d7800fa77e..767981de36e7c3da3063ea4a9b1df696040c0e4f 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -31,8 +31,7 @@ vector<string> ClearcutCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClearcutCommand::ClearcutCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;
                outputTypes["matrixout"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> ClearcutCommand::getRequiredFiles(){
 /**************************************************************************************/
 ClearcutCommand::ClearcutCommand(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
@@ -231,7 +230,7 @@ void ClearcutCommand::help(){
 int ClearcutCommand::execute() {       
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //prepare filename
                string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";