+//
+// createdatabasecommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 3/28/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "createdatabasecommand.h"
+#include "sequence.hpp"
+#include "inputdata.h"
+
+//**********************************************************************************************************************
+vector<string> CreateDatabaseCommand::setParameters(){
+ try {
+ CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
+ CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcontaxonomy);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); 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, "CreateDatabaseCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string CreateDatabaseCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The create.database command reads a listfile, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, and creates a database file.\n";
+ helpString += "The create.database command parameters are repfasta, list, repname, contaxonomy, group and label. List, repfasta, repnames, and contaxonomy are required. \n";
+
+ helpString += "The create.database command should be in the following format: \n";
+ helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
+ helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, name=final.an.0.03.rep.names, list=fina.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+