X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=createdatabasecommand.h;fp=createdatabasecommand.h;h=643ff6ec9fc3691c4a9de5f146cbfb1fdcaff354;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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