minor changes to pcr.seqs. Added filterToPos and filterFromPos to sequence class...

[mothur.git] / createdatabasecommand.cpp

diff --git a/createdatabasecommand.cpp b/createdatabasecommand.cpp
new file mode 100644 (file)
index 0000000..e4a911f
--- /dev/null
+++ b/createdatabasecommand.cpp
@@ -0,0 +1,54 @@
+//
+//  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);
+       }
+}
+//**********************************************************************************************************************
+
+