added [ERROR] flag if command aborts

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 8fb41213c7f836cb45cb89474ae8c874e96cd42e..2e8f132eefa8a491f1b5e23a2d9650da22ee1c84 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -25,8 +25,7 @@ vector<string> PCACommand::getValidParameters(){
 //**********************************************************************************************************************
 PCACommand::PCACommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["pca"] = tempOutNames;
                outputTypes["loadings"] = tempOutNames;
@@ -63,12 +62,12 @@ vector<string> PCACommand::getRequiredFiles(){
 
 PCACommand::PCACommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                globaldata = GlobalData::getInstance();
                
                //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
@@ -150,7 +149,7 @@ PCACommand::~PCACommand(){}
 int PCACommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                cout.setf(ios::fixed, ios::floatfield);
                cout.setf(ios::showpoint);