sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 42e99d1331b3694792eed47e94ab9d21b33f9545..193c53c4d610111cf369084f1a153400bfbe38e5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -140,6 +140,7 @@
 #include "primerdesigncommand.h"
 #include "getdistscommand.h"
 #include "removedistscommand.h"
+#include "mergetaxsummarycommand.h"
 
 /*******************************************************/
 
@@ -303,6 +304,7 @@ CommandFactory::CommandFactory(){
     commands["primer.design"]          = "primer.design";
     commands["get.dists"]           = "get.dists";
     commands["remove.dists"]        = "remove.dists";
+    commands["merge.taxsummary"]    = "merge.taxsummary";
     
 
 }
@@ -522,6 +524,7 @@ Command* CommandFactory::getCommand(string commandName, string 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;
@@ -682,6 +685,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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;
@@ -828,6 +832,7 @@ Command* CommandFactory::getCommand(string commandName){
         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;