added name option to trim.seqs

[mothur.git] / setdircommand.h

diff --git a/setdircommand.h b/setdircommand.h
index 663496523e55a9cd2e2a8999043a8eeb743a8b7b..625c83b63d40c6674490fe00b510cd2780449d08 100644 (file)
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -19,14 +19,24 @@ class SetDirectoryCommand : public Command {
        
 public:
        SetDirectoryCommand(string);
-       ~SetDirectoryCommand();
-       int execute();
-       void help();
+       SetDirectoryCommand() { abort = true; calledHelp = true; setParameters(); }
+       ~SetDirectoryCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "set.dir";             }
+       string getCommandCategory()             { return "General";             }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        CommandFactory* commandFactory;
-       string output, input;
+       string output, input, tempdefault;
        bool abort;
+       vector<string> outputNames;
+       
                
 };