//**********************************************************************************************************************
DistanceCommand::DistanceCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
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
int DistanceCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int startTime = time(NULL);
remove(outputFile.c_str()); //temp file is bad because file mismatch above
}
+ return good;
+
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "sanityCheck");