//**********************************************************************************************************************
vector<string> GetlabelCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
//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();
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
- else { format = "sabund"; inputfile = sabundfile; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
- else { format = "rabund"; inputfile = rabundfile; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
//is there are current file available for any of these?