X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=8c5c0faef60a480a189f98994afc250e4c36a8c6;hb=HEAD;hp=5a32ac1a526450b8d9408a88e0e57cc31e946720;hpb=37b23ba7d98eca13d02cde8d3b1ad08ac92fefb9;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5a32ac1..8c5c0fa 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -149,6 +149,8 @@
 #include "lefsecommand.h"
 #include "kruskalwalliscommand.h"
 #include "sracommand.h"
+#include "mergesfffilecommand.h"
+#include "getmimarkspackagecommand.h"
 
 /*******************************************************/
 
@@ -321,6 +323,8 @@ CommandFactory::CommandFactory(){
     commands["lefse"]               = "lefse";
     commands["kruskal.wallis"]      = "kruskal.wallis";
     commands["sra"]                 = "sra";
+    commands["merge.sfffiles"]      = "merge.sfffiles";
+    commands["get.mimarkspackage"]  = "get.mimarkspackage";
     
 
 }
@@ -549,6 +553,8 @@ 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 if(commandName == "get.mimarkspackage")    {	command = new GetMIMarksPackageCommand(optionString);       }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -718,6 +724,8 @@ 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 if(commandName == "get.mimarkspackage")    {	pipecommand = new GetMIMarksPackageCommand(optionString);       }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -873,6 +881,8 @@ 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 if(commandName == "get.mimarkspackage")    {	shellcommand = new GetMIMarksPackageCommand();      }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;