X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.h;fp=getrabundcommand.h;h=cb9e270d170e0ab9dde910fdb7d24ef6c293828f;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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
+