worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa...

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 2b7232db4dd050a663c3a5b9514b59ae058e5c4c..66a43976c8c5b6ca61090f78a216acfae99d694f 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -34,7 +34,7 @@ vector<string> BootSharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 BootSharedCommand::BootSharedCommand(){        
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;
        }
@@ -70,14 +70,14 @@ vector<string> BootSharedCommand::getRequiredFiles(){
 BootSharedCommand::BootSharedCommand(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") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -234,7 +234,7 @@ BootSharedCommand::~BootSharedCommand(){
 int BootSharedCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
        
                util = new SharedUtil();