changing command name classify.shared to classifyrf.shared

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
index 38b5ec7643fdd4e79e4d70408c59ba9fe3210be0..fd7a6b07fecf135262e310598a3936221cb98826 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -13,33 +13,41 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "listvector.hpp"
 
-class GlobalData;
 
 class GetRAbundCommand : public Command {
 public:
        GetRAbundCommand(string);
-       ~GetRAbundCommand();
-       int execute();
-       void help();
+       GetRAbundCommand();
+       ~GetRAbundCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.rabund";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+       string getDescription()         { return "creates a rabund file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       string filename;
+       
+       string filename, listfile, sabundfile, inputfile, format, outputDir, countfile;
        ofstream out;
-       ReadOTUFile* read;
-       InputData* input;
-       ListVector* list;
-       RAbundVector* rabund;
+       vector<string> outputNames;
 
-       bool abort, allLines;
-       set<int> lines; //hold lines to be used
+       bool abort, allLines, sorted;
        set<string> labels; //holds labels to be used
-       string line, label;
+       string label;
 
-       
+       int processList(ofstream& out);
+    int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
 };
 
 #endif