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[mothur.git] / createdatabasecommand.h

diff --git a/createdatabasecommand.h b/createdatabasecommand.h
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+#ifndef Mothur_createdatabasecommand_h
+#define Mothur_createdatabasecommand_h
+
+//
+//  createdatabasecommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 3/28/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "command.hpp"
+#include "listvector.hpp"
+#include "sequence.hpp"
+
+class CreateDatabaseCommand : public Command {
+public:
+       CreateDatabaseCommand(string);
+       CreateDatabaseCommand();
+       ~CreateDatabaseCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "create.database";             }
+       string getCommandCategory()             { return "OTU-Based Approaches"; }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
+       string getDescription()         { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
+    
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       
+       bool abort;
+       string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
+       
+       vector<string> outputNames;
+               
+       vector<int> readFasta(vector<Sequence>&);
+    vector<int> readTax(vector<string>&);
+    int readNames(map<string, string>&); 
+       ListVector* getList();
+       
+};
+
+
+
+
+#endif