added citation function to commands

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 66a3211296edc7f2105af0ba2bfc10f85b7ae109..81a5d910b53c84db70c560255ce2b508c4361f33 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -13,25 +13,38 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "listvector.hpp"
 
-class GlobalData;
 
 class GetRAbundCommand : public Command {
 public:
+       GetRAbundCommand(string);
        GetRAbundCommand();
-       ~GetRAbundCommand();
-       int execute();
+       ~GetRAbundCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.rabund";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       string filename;
+       
+       string filename, listfile, sabundfile, inputfile, format, outputDir;
        ofstream out;
-       ReadOTUFile* read;
        InputData* input;
-       ListVector* list;
        RAbundVector* rabund;
+       vector<string> outputNames;
+
+       bool abort, allLines, sorted;
+       set<string> labels; //holds labels to be used
+       string label;
+
+       
 };
 
 #endif