added dist.shared command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index c03751518e3e9a2ab54da2e38be693e08a3d6c34..21e7b54548a370065ab554d3a2b0f7b5c4887146 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -41,6 +41,9 @@
 #include "bootstrapsharedcommand.h"
 #include "concensuscommand.h"
 #include "distancecommand.h"
+#include "aligncommand.h"
+#include "getrepseqscommand.h"
+#include "matrixoutputcommand.h"
 
 
 /***********************************************************/
@@ -88,11 +91,14 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "filter.seqs")                   {   command = new FilterSeqsCommand();          }
                else if(commandName == "venn")                                  {   command = new VennCommand();                                }
                else if(commandName == "bin.seqs")                              {   command = new BinSeqCommand();                              }
+               else if(commandName == "get.repseqs")                   {   command = new GetRepSeqsCommand();                  }
                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;