changing command name classify.shared to classifyrf.shared

[mothur.git] / getrelabundcommand.h

diff --git a/getrelabundcommand.h b/getrelabundcommand.h
index 90d5f9a2ceb9c3164640d8482e88599324557495..dcb4cf71e43a919bc6fce2588b8d7e8e7c2864dd 100644 (file)
--- 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&);