exit(1);
}
}
-
//**********************************************************************************************************************
AmovaCommand::AmovaCommand(){
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
phylipFileName = m->getPhylipFile();
if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setPhylipFile(phylipFileName); }
//check for required parameters
designFileName = validParameter.validFile(parameters, "design", true);
- if (designFileName == "not open") { abort = true; }
+ if (designFileName == "not open") { designFileName = ""; abort = true; }
else if (designFileName == "not found") {
//if there is a current design file, use it
designFileName = m->getDesignFile();
if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setDesignFile(designFileName); }
string temp = validParameter.validFile(parameters, "iters", false);
if (temp == "not found") { temp = "1000"; }
m->mothurOut("df\t" + toString(dfAmong) + '\t' + toString(dfWithin) + '\t' + toString(dfTotal) + '\n');
AMOVAFile << "MS\t" << MSAmong << '\t' << MSWithin << endl << endl;
- m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n");
+ m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n\n");
AMOVAFile << "Fs:\t" << Fs << endl;
m->mothurOut("Fs:\t" + toString(Fs) + '\n');