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[mothur.git] / getrelabundcommand.h

diff --git a/getrelabundcommand.h b/getrelabundcommand.h
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+#ifndef GETRELABUNDCOMMAND_H
+#define GETRELABUNDCOMMAND_H
+
+/*
+ *  getrelabundcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 6/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+
+
+class GetRelAbundCommand : public Command {
+
+public:
+       GetRelAbundCommand(string);
+       GetRelAbundCommand();
+       ~GetRelAbundCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.relabund";                        }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
+       string getDescription()         { return "calculates the relative abundance of each OTU in a sample"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       InputData* input;
+       vector<SharedRAbundVector*> lookup;
+       
+       bool abort, allLines, pickedGroups;
+       set<string> labels; //holds labels to be used
+       string groups, label, outputDir, scale, sharedfile;
+       vector<string> Groups, outputNames;
+       
+       int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
+
+};
+
+#endif
+