//**********************************************************************************************************************
PhyloDiversityCommand::PhyloDiversityCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylodiv"] = tempOutNames;
outputTypes["rarefy"] = tempOutNames;
PhyloDiversityCommand::PhyloDiversityCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- 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
int PhyloDiversityCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
for (int i = 0; i < globaldata->Groups.size(); i++) { if (globaldata->Groups[i] == "xxx") { globaldata->Groups.erase(globaldata->Groups.begin()+i); break; } }
exit(1);
}
}
-//**********************************************************************************************************************
\ No newline at end of file
+//**********************************************************************************************************************
+
+
+