added degap.seqs command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index bd519eebfd6eaa24134dad9ac08f2193004e6386..7de4d06f25ddbb1414aaea8e7f4b8d7f72d25590 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -80,6 +80,7 @@
 #include "splitabundcommand.h"
 #include "clustersplitcommand.h"
 #include "classifyotucommand.h"
+#include "degapseqscommand.h"
 
 /*******************************************************/
 
@@ -167,6 +168,7 @@ CommandFactory::CommandFactory(){
        commands["split.abund"]                 = "split.abund";
        commands["cluster.split"]               = "cluster.split";
        commands["classify.otu"]                = "classify.otu";
+       commands["degap.seqs"]                  = "degap.seqs";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -291,6 +293,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
                else if(commandName == "cluster.split")                 {       command = new ClusterSplitCommand(optionString);                        }
                else if(commandName == "classify.otu")                  {       command = new ClassifyOtuCommand(optionString);                         }
+               else if(commandName == "degap.seqs")                    {       command = new DegapSeqsCommand(optionString);                           }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;