changed random forest output filename

[mothur.git] / getlistcountcommand.h

diff --git a/getlistcountcommand.h b/getlistcountcommand.h
index 468ea80ca20308115782bfdf757e8cbd276fe5c9..c2645562f1111c4a03be95c4e27c143745311ed5 100644 (file)
--- a/getlistcountcommand.h
+++ b/getlistcountcommand.h
@@ -12,31 +12,40 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readotu.h"
-
-class GlobalData;
 
 /**********************************************************/
 
 class GetListCountCommand : public Command {
        
 public:
-       GetListCountCommand(string);    
-       ~GetListCountCommand();
-       int execute();
-       void help();    
+       GetListCountCommand(string);
+       GetListCountCommand();  
+       ~GetListCountCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.otulist";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
+       string getDescription()         { return "lists each OTU number and the sequence contained in that OTU"; }
+
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
        ListVector* list;
-       ReadOTUFile* read;
        InputData* input;
        
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string label, listfile;
+       string label, listfile, outputDir, sort;
        ofstream out;
-       
+       vector<string> outputNames;
+               
        void process(ListVector*);
 };
 /**********************************************************/