changes while testing

[mothur.git] / getgroupcommand.h

diff --git a/getgroupcommand.h b/getgroupcommand.h
index 00c1b51936009de1fb24d5fa227cc40c3c5325dd..fb438dfd91caf9a8213e780db8c7b626768873d3 100644 (file)
--- a/getgroupcommand.h
+++ b/getgroupcommand.h
@@ -6,26 +6,39 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 2/2/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
-
-class GlobalData;
 
 class GetgroupCommand : public Command {
 public:
+       GetgroupCommand(string);
        GetgroupCommand();
-       ~GetgroupCommand();
-       int execute();
+       ~GetgroupCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.group";                           }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+    string getOutputPattern(string)    { return "";  }
+       string getCitation() { return "http://www.mothur.org/wiki/Get.group"; }
+       string getDescription()         { return "outputs group names"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       GroupMap* groupMap;
+       
+       string outputFile, sharedfile, outputDir;
+       vector<string> outputNames;
+       ofstream out;
+       ifstream in;
+       bool abort;
+
 };
 
 #endif