X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setcurrentcommand.h;fp=setcurrentcommand.h;h=98033b7b8d8bb4f1e68c5b62df4ddd97e239a35e;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=0000000000000000000000000000000000000000;hpb=5e031adc86a1fc125c4abb3d4048f209d52f9b6d;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> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute();
+	void help();
+	
+private:
+	
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
+	bool abort;
+	
+	string clearTypes;
+	vector<string> types;
+	
+	string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+	string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
+
+	
+};
+
+#endif
+
+