+//**********************************************************************************************************************
+vector<string> RareFactCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); 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 pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+ 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, "RareFactCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RareFactCommand::getHelpString(){
+ try {
+ ValidCalculators validCalculator;
+ string helpString = "";
+ helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors, groupmode and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n";
+ helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "The rarefaction.single command should be in the following format: \n";
+ helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
+ helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
+ helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
+ validCalculator.printCalc("rarefaction");
+ helpString += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RareFactCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+ if (type == "rarefaction") { pattern = "[filename],rarefaction"; }
+ else if (type == "r_chao") { pattern = "[filename],r_chao"; }
+ else if (type == "r_ace") { pattern = "[filename],r_ace"; }
+ else if (type == "r_jack") { pattern = "[filename],r_jack"; }
+ else if (type == "r_shannon") { pattern = "[filename],r_shannon"; }
+ else if (type == "r_shannoneven") { pattern = "[filename],r_shannoneven"; }
+ else if (type == "r_smithwilson") { pattern = "[filename],r_smithwilson"; }
+ else if (type == "r_npshannon") { pattern = "[filename],r_npshannon"; }
+ else if (type == "r_simpson") { pattern = "[filename],r_simpson"; }
+ else if (type == "r_simpsoneven") { pattern = "[filename],r_simpsoneven"; }
+ else if (type == "r_invsimpson") { pattern = "[filename],r_invsimpson"; }
+ else if (type == "r_bootstrap") { pattern = "[filename],r_bootstrap"; }
+ else if (type == "r_coverage") { pattern = "[filename],r_coverage"; }
+ else if (type == "r_nseqs") { pattern = "[filename],r_nseqs"; }
+ else if (type == "r_heip") { pattern = "[filename],r_heip"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RareFactCommand::RareFactCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["rarefaction"] = tempOutNames;
+ outputTypes["r_chao"] = tempOutNames;
+ outputTypes["r_ace"] = tempOutNames;
+ outputTypes["r_jack"] = tempOutNames;
+ outputTypes["r_shannon"] = tempOutNames;
+ outputTypes["r_shannoneven"] = tempOutNames;
+ outputTypes["r_heip"] = tempOutNames;
+ outputTypes["r_smithwilson"] = tempOutNames;
+ outputTypes["r_npshannon"] = tempOutNames;
+ outputTypes["r_simpson"] = tempOutNames;
+ outputTypes["r_simpsoneven"] = tempOutNames;
+ outputTypes["r_invsimpson"] = tempOutNames;
+ outputTypes["r_bootstrap"] = tempOutNames;
+ outputTypes["r_coverage"] = tempOutNames;
+ outputTypes["r_nseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "RareFactCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************