added filter.shared command. fixed lci and uci for thetayc calc

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 6d87a68c49c6d9154572adcbc51ebc3b4555a35f..a691509ab0ae00e5f19ae52a8bffe6801fc26a31 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -136,6 +136,7 @@
 #include "loadlogfilecommand.h"
 #include "sffmultiplecommand.h"
 #include "classifysharedcommand.h"
+#include "filtersharedcommand.h"
 
 /*******************************************************/
 
@@ -295,6 +296,7 @@ CommandFactory::CommandFactory(){
     commands["sff.multiple"]        = "sff.multiple";
        commands["quit"]                                = "MPIEnabled"; 
     commands["classify.shared"]                = "classify.shared"; 
+    commands["filter.shared"]          = "filter.shared"; 
     
 
 }
@@ -510,6 +512,7 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "filter.shared")         {      command = new FilterSharedCommand(optionString);            }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -666,6 +669,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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 if(commandName == "filter.shared")         {      pipecommand = new FilterSharedCommand(optionString);            }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -808,6 +812,7 @@ Command* CommandFactory::getCommand(string commandName){
         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 if(commandName == "filter.shared")         {      shellcommand = new FilterSharedCommand();           }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;