X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=normalizesharedcommand.h;h=53bcd6b5e4aac7d0a463fa436fc8ed6346f5f069;hp=22158bd6d5ff136d0df81d0304b476ec580b8b7a;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
index 22158bd..53bcd6b 100644
--- a/normalizesharedcommand.h
+++ b/normalizesharedcommand.h
@@ -12,39 +12,44 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
-
 class NormalizeSharedCommand : public Command {
 
 public:
 	NormalizeSharedCommand(string);
 	NormalizeSharedCommand();
-	~NormalizeSharedCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~NormalizeSharedCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "normalize.shared";		}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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:
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	InputData* input;
 	vector<SharedRAbundVector*> lookup;
+	vector<SharedRAbundFloatVector*> lookupFloat;
 	
-	bool abort, allLines, pickedGroups;
+	bool abort, allLines, pickedGroups, makeRelabund;
 	set<string> labels; //holds labels to be used
-	string groups, label, outputDir, method;
+	string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
 	int norm;
 	vector<string> Groups, outputNames;
-	map<string, vector<string> > outputTypes;
-	
-	int normalize(vector<SharedRAbundVector*>&, ofstream&);
-	int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);
+		
+	int normalize(vector<SharedRAbundVector*>&);
+	int normalize(vector<SharedRAbundFloatVector*>&);
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
 
 };