X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getrelabundcommand.h;h=dcb4cf71e43a919bc6fce2588b8d7e8e7c2864dd;hp=90d5f9a2ceb9c3164640d8482e88599324557495;hb=615301e57c25e241356a9c2380648d117709458d;hpb=37eac2026d91179acda0494c4dcca22f176551b9

diff --git a/getrelabundcommand.h b/getrelabundcommand.h
index 90d5f9a..dcb4cf7 100644
--- a/getrelabundcommand.h
+++ b/getrelabundcommand.h
@@ -12,35 +12,37 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
 
 class GetRelAbundCommand : public Command {
 
 public:
 	GetRelAbundCommand(string);
 	GetRelAbundCommand();
-	~GetRelAbundCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~GetRelAbundCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.relabund";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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:
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	InputData* input;
 	vector<SharedRAbundVector*> lookup;
 	
 	bool abort, allLines, pickedGroups;
 	set<string> labels; //holds labels to be used
-	string groups, label, outputDir, scale;
+	string groups, label, outputDir, scale, sharedfile;
 	vector<string> Groups, outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);