added primer.design command. fixed bug with linux unifrac subsampling, metastats...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index c8421d29c513f65bfe8684fe10a09e8c439d7915..ce51d7228b415228da4c6c15121001989d03b75a 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -137,6 +137,7 @@
 #include "sffmultiplecommand.h"
 #include "classifysharedcommand.h"
 #include "filtersharedcommand.h"
+#include "primerdesigncommand.h"
 
 /*******************************************************/
 
@@ -297,6 +298,7 @@ CommandFactory::CommandFactory(){
        commands["quit"]                                = "MPIEnabled"; 
     commands["classify.shared"]                = "classify.shared"; 
     commands["filter.shared"]          = "filter.shared"; 
+    commands["primer.design"]          = "primer.design"; 
     
 
 }
@@ -513,6 +515,7 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "primer.design")         {      command = new PrimerDesignCommand(optionString);            }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -670,6 +673,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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 if(commandName == "primer.design")         {      pipecommand = new PrimerDesignCommand(optionString);            }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -813,6 +817,7 @@ Command* CommandFactory::getCommand(string commandName){
         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 if(commandName == "primer.design")         {      shellcommand = new PrimerDesignCommand();           }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;