added count file to get.groups and remove.groups. added shortcut parameter to classif...

[mothur.git] / commandfactory.hpp

diff --git a/commandfactory.hpp b/commandfactory.hpp
index a6dc5b72e0b403df37dd77b7ee593ca5ff19de73..e95db8016a4149c9c2defdbb9e7933ff6ee3905a 100644 (file)
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -12,6 +12,7 @@
 \r
 #include "mothur.h"\r
 #include "mothurout.h"\r
+#include "currentfile.h"\r
 \r
 class Command;\r
 \r
@@ -32,17 +33,23 @@ public:
        bool getAppend()                                                {       return append;                  }\r
        string getOutputDir()                                   {       return outputDir;               }\r
        bool MPIEnabled(string);\r
-\r
+       map<string, string> getListCommands()   {       return commands;                }\r
+       \r
 private:\r
        Command* command;\r
        Command* shellcommand;\r
        Command* pipecommand;\r
+       \r
        MothurOut* m;\r
+       CurrentFile* currentFile;\r
+       \r
        map<string, string> commands;\r
        map<string, string>::iterator it;\r
        string outputDir, inputDir, logFileName;\r
        bool append;\r
        \r
+    int checkForRedirects(string);\r
+    \r
        static CommandFactory* _uniqueInstance;\r
        CommandFactory( const CommandFactory& ); // Disable copy constructor\r
        void operator=( const CommandFactory& ); // Disable assignment operator\r