X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=createdatabasecommand.h;fp=createdatabasecommand.h;h=9fc84d7740ebfa4098dce2ee33dc6fb902c1c003;hb=a33a385cc5b7481488f92f794425f01fbf40a543;hp=0000000000000000000000000000000000000000;hpb=36cea83f926066127bf856e7eae1a70ce7e796d0;p=mothur.git

diff --git a/createdatabasecommand.h b/createdatabasecommand.h
new file mode 100644
index 0000000..9fc84d7
--- /dev/null
+++ b/createdatabasecommand.h
@@ -0,0 +1,49 @@
+#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"
+
+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, constaxonomyfile, label, outputDir;
+	
+	vector<string> outputNames;
+		
+	int readFasta();
+	int readNames();
+    int readTax();
+	int processList(ListVector*&);
+	
+};
+
+
+
+
+#endif