fixes while testing 1.33.0

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5a32ac1a526450b8d9408a88e0e57cc31e946720..e8e9c2754677ee639fce944fbc533d3bd9eb98db 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -149,6 +149,7 @@
 #include "lefsecommand.h"
 #include "kruskalwalliscommand.h"
 #include "sracommand.h"
+#include "mergesfffilecommand.h"
 
 /*******************************************************/
 
@@ -321,6 +322,7 @@ CommandFactory::CommandFactory(){
     commands["lefse"]               = "lefse";
     commands["kruskal.wallis"]      = "kruskal.wallis";
     commands["sra"]                 = "sra";
+    commands["merge.sfffiles"]      = "merge.sfffiles";
     
 
 }
@@ -549,6 +551,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "lefse")                 {      command = new LefseCommand(optionString);                   }
         else if(commandName == "kruskal.wallis")        {      command = new KruskalWallisCommand(optionString);           }
         else if(commandName == "sra")                   {      command = new SRACommand(optionString);                     }
+        else if(commandName == "merge.sfffiles")        {      command = new MergeSfffilesCommand(optionString);           }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -718,6 +721,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "lefse")                 {      pipecommand = new LefseCommand(optionString);                   }
         else if(commandName == "kruskal.wallis")        {      pipecommand = new KruskalWallisCommand(optionString);           }
         else if(commandName == "sra")                   {      pipecommand = new SRACommand(optionString);                     }
+        else if(commandName == "merge.sfffiles")        {      pipecommand = new MergeSfffilesCommand(optionString);           }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -873,6 +877,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "lefse")                 {      shellcommand = new LefseCommand();                  }
         else if(commandName == "kruskal.wallis")        {      shellcommand = new KruskalWallisCommand();          }
         else if(commandName == "sra")                   {      shellcommand = new SRACommand();                    }
+        else if(commandName == "merge.sfffiles")        {      shellcommand = new MergeSfffilesCommand();          }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;