added [ERROR] flag if command aborts

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 02b30e3c1b172281fff8661146013ede04a41f31..baf449e34d8bac9e67ab424ba02539fb053033e6 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -64,8 +64,7 @@ vector<string> MatrixOutputCommand::getValidParameters(){
 //**********************************************************************************************************************
 MatrixOutputCommand::MatrixOutputCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
        }
@@ -102,14 +101,14 @@ vector<string> MatrixOutputCommand::getRequiredFiles(){
 MatrixOutputCommand::MatrixOutputCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                Groups.clear();
                Estimators.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
@@ -312,7 +311,7 @@ MatrixOutputCommand::~MatrixOutputCommand(){
 int MatrixOutputCommand::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 (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine();  return 0; }