X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=normalizesharedcommand.h;fp=normalizesharedcommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=4b6f7fd9e93f4912bf648f2c826ab0a09b15910c;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
deleted file mode 100644
index 4b6f7fd..0000000
--- a/normalizesharedcommand.h
+++ /dev/null
@@ -1,55 +0,0 @@
-#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
-