//**********************************************************************************************************************
ClassifyOtuCommand::ClassifyOtuCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["constaxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
//**********************************************************************************************************************
ClassifyOtuCommand::ClassifyOtuCommand(string option) {
try{
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
if (option == "help") {
- help(); abort = true;
+ help(); abort = true; calledHelp = true;
} else {
//valid paramters for this command
string Array[] = {"list","label","name","taxonomy","cutoff","probs","basis","reftaxonomy","group","outputdir","inputdir"};
int ClassifyOtuCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if user gave a namesfile then use it
if (namefile != "") { readNamesFile(); }