+vector<string> GetRAbundCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
+ CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psorted);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetRAbundCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.rabund command parameters are list, sabund, label and sorted. list or sabund parameters are required, unless you have valid current files.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n";
+ helpString += "The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n";
+ helpString += "The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n";
+ helpString += "Example get.rabund(sorted=F).\n";
+ helpString += "The default value for label is all labels in your inputfile.\n";
+ helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getHelpString");
+ exit(1);
+ }
+}