sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ce51d7228b415228da4c6c15121001989d03b75a..193c53c4d610111cf369084f1a153400bfbe38e5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -138,6 +138,9 @@
 #include "classifysharedcommand.h"
 #include "filtersharedcommand.h"
 #include "primerdesigncommand.h"
+#include "getdistscommand.h"
+#include "removedistscommand.h"
+#include "mergetaxsummarycommand.h"
 
 /*******************************************************/
 
@@ -298,7 +301,10 @@ CommandFactory::CommandFactory(){
        commands["quit"]                                = "MPIEnabled"; 
     commands["classify.shared"]                = "classify.shared"; 
     commands["filter.shared"]          = "filter.shared"; 
-    commands["primer.design"]          = "primer.design"; 
+    commands["primer.design"]          = "primer.design";
+    commands["get.dists"]           = "get.dists";
+    commands["remove.dists"]        = "remove.dists";
+    commands["merge.taxsummary"]    = "merge.taxsummary";
     
 
 }
@@ -516,6 +522,9 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "get.dists")             {      command = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {      command = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {      command = new MergeTaxSummaryCommand(optionString);         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -674,6 +683,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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 if(commandName == "get.dists")             {      pipecommand = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {      pipecommand = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {      pipecommand = new MergeTaxSummaryCommand(optionString);         }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -818,6 +830,9 @@ Command* CommandFactory::getCommand(string commandName){
         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 if(commandName == "get.dists")             {      shellcommand = new GetDistsCommand();               }
+        else if(commandName == "remove.dists")          {      shellcommand = new RemoveDistsCommand();            }
+        else if(commandName == "merge.taxsummary")      {      shellcommand = new MergeTaxSummaryCommand();        }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;