added pipeline commands which involved change to command factory and command class...

[mothur.git] / commandfactory.hpp

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 44e78fd66fa290d9664d773f470249f0600a2836..a6dc5b72e0b403df37dd77b7ee593ca5ff19de73 100644 (file)
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -18,11 +18,14 @@ class Command;
 class CommandFactory {\r
 public:\r
        static CommandFactory* getInstance();\r
+       Command* getCommand(string, string, string);\r
        Command* getCommand(string, string);\r
-       Command* getCommand();\r
+       Command* getCommand(string);\r
+       //Command* getCommand();\r
        bool isValidCommand(string);\r
+       bool isValidCommand(string, string);\r
        void printCommands(ostream&);\r
-       void setOutputDirectory(string o)               {       outputDir = o;          }\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
        string getLogfileName()                                 {       return logFileName;     }\r
@@ -32,6 +35,8 @@ public:
 \r
 private:\r
        Command* command;\r
+       Command* shellcommand;\r
+       Command* pipecommand;\r
        MothurOut* m;\r
        map<string, string> commands;\r
        map<string, string>::iterator it;\r