Revert to previous commit

[mothur.git] / setcurrentcommand.h

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
+
+