Revert to previous commit

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
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+#ifndef GETRABUNDCOMMAND_H
+#define GETRABUNDCOMMAND_H
+
+/*
+ *  getrabundcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "listvector.hpp"
+
+
+class GetRAbundCommand : public Command {
+public:
+       GetRAbundCommand(string);
+       GetRAbundCommand();
+       ~GetRAbundCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.rabund";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+       string getDescription()         { return "creates a rabund file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       
+       string filename, listfile, sabundfile, inputfile, format, outputDir;
+       ofstream out;
+       InputData* input;
+       RAbundVector* rabund;
+       vector<string> outputNames;
+
+       bool abort, allLines, sorted;
+       set<string> labels; //holds labels to be used
+       string label;
+
+       
+};
+
+#endif
+