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[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
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+#ifndef NORMALIZESHAREDCOMMAND_H
+#define NORMALIZESHAREDCOMMAND_H
+
+/*
+ *  normalizesharedcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/15/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+
+class NormalizeSharedCommand : public Command {
+
+public:
+       NormalizeSharedCommand(string);
+       NormalizeSharedCommand();
+       ~NormalizeSharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "normalize.shared";            }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
+       string getDescription()         { return "normalize samples in a shared or relabund file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       InputData* input;
+       vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
+       
+       bool abort, allLines, pickedGroups, makeRelabund;
+       set<string> labels; //holds labels to be used
+       string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
+       int norm;
+       vector<string> Groups, outputNames;
+               
+       int normalize(vector<SharedRAbundVector*>&);
+       int normalize(vector<SharedRAbundFloatVector*>&);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
+
+};
+
+#endif
+