//**********************************************************************************************************************
NMDSCommand::NMDSCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["nmds"] = tempOutNames;
outputTypes["stress"] = tempOutNames;
NMDSCommand::NMDSCommand(string option) {
try {
- 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
m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon."); m->mothurOutEndLine();
m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
- m->mothurOut("The maxdim parameter allows you to select how maximum dimensions to use. Default=2"); m->mothurOutEndLine();
- m->mothurOut("The mindim parameter allows you to select how minimum dimensions to use. Default=2"); m->mothurOutEndLine();
+ m->mothurOut("The maxdim parameter allows you to select the maximum dimensions to use. Default=2"); m->mothurOutEndLine();
+ m->mothurOut("The mindim parameter allows you to select the minimum dimensions to use. Default=2"); m->mothurOutEndLine();
m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine();
m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine();
m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine();
int NMDSCommand::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);