X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setcurrentcommand.h;fp=setcurrentcommand.h;h=3949519e9ec3f04392d555539fd5409dcab59dea;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
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+#ifndef SETCURRENTCOMMAND_H
+#define SETCURRENTCOMMAND_H
+
+/*
+ *  setcurrentcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 3/16/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+
+class SetCurrentCommand : public Command {
+	
+public:
+	SetCurrentCommand(string);
+	SetCurrentCommand();
+	~SetCurrentCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "set.current";	}
+	string getCommandCategory()		{ return "General";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
+	string getDescription()		{ return "set current files for mothur"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	
+	vector<string> outputNames;
+	bool abort;
+	
+	string clearTypes;
+	vector<string> types;
+	
+	string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
+	string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
+
+	
+};
+
+#endif
+
+