+//**********************************************************************************************************************
+vector<string> ParseListCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
+ 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, "ParseListCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParseListCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n";
+ helpString += "The parse.list command parameters are list, group and label.\n";
+ helpString += "The list and group parameters are required.\n";
+ helpString += "The label parameter is used to read specific labels in your input you want to use.\n";
+ helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n";
+ helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseListCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParseListCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "list") { outputFileName = "list"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseListCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ParseListCommand::ParseListCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseListCommand", "ParseListCommand");
+ exit(1);
+ }
+}