added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / commandfactory.hpp

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 9bbba573057e23c820e24a5c1d6d8c62e7fc5d5b..d84be62a074dde5dc29b8006a636bd7b67b9607d 100644 (file)
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -10,15 +10,32 @@
  *
  */
 
+#include "mothur.h"
+
 class Command;
 
 class CommandFactory {
 public:
-       CommandFactory();
-       ~CommandFactory();
-       Command* getCommand(string);
+       static CommandFactory* getInstance();
+       Command* getCommand(string, string);
+       Command* getCommand();
+       bool isValidCommand(string);
+       void printCommands(ostream&);
+       void setOutputDirectory(string o)       {       outputDir = o;          }
+       void setInputDirectory(string i)        {       inputDir = i;           }
+       string getOutputDir()                           {       return outputDir;       }
+
 private:
        Command* command;
+       map<string, string> commands;
+       map<string, string>::iterator it;
+       string outputDir, inputDir;
+       
+       static CommandFactory* _uniqueInstance;
+       CommandFactory( const CommandFactory& ); // Disable copy constructor
+       void operator=( const CommandFactory& ); // Disable assignment operator
+       CommandFactory();
+       ~CommandFactory();
 
 };