moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
deleted file mode 100644 (file)
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
-