modified mpi code to save ram by writing out every 10 seqs.

[mothur.git] / commandfactory.hpp

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 70e263078eee32ad8e706816f15be03a2fb6d369..6f96e90b4813e961222c60f9bb7390188d19c3e5 100644 (file)
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -11,6 +11,7 @@
  */
 
 #include "mothur.h"
+#include "mothurout.h";
 
 class Command;
 
@@ -21,11 +22,17 @@ public:
        Command* getCommand();
        bool isValidCommand(string);
        void printCommands(ostream&);
+       void setOutputDirectory(string o)       {       outputDir = o;          }
+       void setInputDirectory(string i)        {       inputDir = i;           }
+       string getOutputDir()                           {       return outputDir;       }
+       bool MPIEnabled(string);
 
 private:
        Command* command;
+       MothurOut* m;
        map<string, string> commands;
        map<string, string>::iterator it;
+       string outputDir, inputDir;
        
        static CommandFactory* _uniqueInstance;
        CommandFactory( const CommandFactory& ); // Disable copy constructor