bug fixes

[mothur.git] / getgroupcommand.h

diff --git a/getgroupcommand.h b/getgroupcommand.h
index b29673529cca9387ed4a5916166180e0a9966ead..fb3e810666320ea2cd1c32d4b14b0c2cac08c995 100644 (file)
--- a/getgroupcommand.h
+++ b/getgroupcommand.h
@@ -6,24 +6,35 @@
  *  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 "command.hpp"
-#include "readmatrix.hpp"
-
-class GlobalData;
+#include "globaldata.hpp"
 
 class GetgroupCommand : public Command {
 public:
+       GetgroupCommand(string);
        GetgroupCommand();
        ~GetgroupCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
        GroupMap* groupMap;
+       string outputFile, sharedfile;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       ofstream out;
+       ifstream in;
+       bool abort;
+
 };
 
 #endif