added modify names parameter to set.dir

[mothur.git] / commandfactory.hpp

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 8b08c006312240676e1e1466a0470c7f3aa11eae..36e8f462b146fc7846ee6cf9ead1eb42e9757a36 100644 (file)
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -26,6 +26,7 @@ public:
        bool isValidCommand(string);\r
        bool isValidCommand(string, string);\r
        void printCommands(ostream&);\r
+    void printCommandsCategories(ostream&);\r
        void setOutputDirectory(string o)               {       outputDir = o;  m->setOutputDir(o);     }\r
        void setInputDirectory(string i)                {       inputDir = i;           }\r
        void setLogfileName(string n, bool a)   {       logFileName = n;  append = a;           }\r
@@ -33,7 +34,8 @@ 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
@@ -47,6 +49,8 @@ private:
        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