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[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index c03751518e3e9a2ab54da2e38be693e08a3d6c34..06e7e84f06602796d143cdb8d535e46006dc0fb1 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -41,6 +41,8 @@
 #include "bootstrapsharedcommand.h"
 #include "concensuscommand.h"
 #include "distancecommand.h"
+#include "aligncommand.h"
+#include "matrixoutputcommand.h"
 
 
 /***********************************************************/
@@ -90,9 +92,11 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand();                              }
                else if(commandName == "get.oturep")                    {   command = new GetOTURepCommand();                   }
                else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand();                   }
+               else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand();                }
                else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand();                  }
                else if(commandName == "concensus")                             {   command = new ConcensusCommand();                   }
-               else if(commandName == "dist.seq")                              {   command = new DistanceCommand();                    }
+               else if(commandName == "dist.seqs")                             {   command = new DistanceCommand();                    }
+               else if(commandName == "align.seqs")                    {   command = new AlignCommand();                               }
                else                                                                                    {       command = new NoCommand();                                      }
 
                return command;