changed random forest output filename

[mothur.git] / getlistcountcommand.h

diff --git a/getlistcountcommand.h b/getlistcountcommand.h
index 60d28cc6a351011fdc34af98189025af5d26f487..c2645562f1111c4a03be95c4e27c143745311ed5 100644 (file)
--- a/getlistcountcommand.h
+++ b/getlistcountcommand.h
@@ -12,9 +12,6 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readotu.h"
-
-class GlobalData;
 
 /**********************************************************/
 
@@ -23,18 +20,24 @@ class GetListCountCommand : public Command {
 public:
        GetListCountCommand(string);
        GetListCountCommand();  
-       ~GetListCountCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       ~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;
@@ -42,8 +45,7 @@ private:
        string label, listfile, outputDir, sort;
        ofstream out;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-       
+               
        void process(ListVector*);
 };
 /**********************************************************/