added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 8653643a0e5f89058f95842bfdb134b711ab4de5..6d87a68c49c6d9154572adcbc51ebc3b4555a35f 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -135,6 +135,7 @@
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
 #include "sffmultiplecommand.h"
+#include "classifysharedcommand.h"
 
 /*******************************************************/
 
@@ -293,6 +294,8 @@ CommandFactory::CommandFactory(){
     commands["make.table"]          = "make.table";
     commands["sff.multiple"]        = "sff.multiple";
        commands["quit"]                                = "MPIEnabled"; 
+    commands["classify.shared"]                = "classify.shared"; 
+    
 
 }
 /***********************************************************/
@@ -506,6 +509,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "make.contigs")          {      command = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {      command = new LoadLogfileCommand(optionString);             }
         else if(commandName == "sff.multiple")          {      command = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {      command = new ClassifySharedCommand(optionString);          }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -661,6 +665,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "make.contigs")          {      pipecommand = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {      pipecommand = new LoadLogfileCommand(optionString);             }
         else if(commandName == "sff.multiple")          {      pipecommand = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.shared")       {      pipecommand = new ClassifySharedCommand(optionString);          }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -802,6 +807,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "make.contigs")          {      shellcommand = new MakeContigsCommand();            }
         else if(commandName == "load.logfile")          {      shellcommand = new LoadLogfileCommand();            }
         else if(commandName == "sff.multiple")          {      shellcommand = new SffMultipleCommand();            }
+        else if(commandName == "classify.shared")       {      shellcommand = new ClassifySharedCommand();         }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;