added set.current and get.current commands and modified existing commands to update...

[mothur.git] / setcurrentcommand.h

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
new file mode 100644 (file)
index 0000000..98033b7
--- /dev/null
+++ b/setcurrentcommand.h
@@ -0,0 +1,46 @@
+#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
+
+