sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / makegroupcommand.h

diff --git a/makegroupcommand.h b/makegroupcommand.h
index 260deaa5637a580c24d6be89b1c8b822ba262591..f86c707d4516160d0dc9cc99243f54bea34d191a 100644 (file)
--- a/makegroupcommand.h
+++ b/makegroupcommand.h
@@ -17,20 +17,25 @@ class MakeGroupCommand : public Command {
 public:
        MakeGroupCommand(string);
        MakeGroupCommand();     
-       ~MakeGroupCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       ~MakeGroupCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "make.group";  }
+       string getCommandCategory()             { return "General";             }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Make.group"; }
+       string getDescription()         { return "creates a group file"; }
+
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
                
-       string fastaFileName, groups, outputDir, filename;
+       string fastaFileName, groups, outputDir, filename, output;
        vector<string> fastaFileNames;
        vector<string> groupsNames, outputNames;
-       map<string, vector<string> > outputTypes;
        
        bool abort;
 };