filterseqscommand added

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5155095526d1a3d08f4b72ec5236c882400ba5ec..e357e6cd70c45ec8c0fdeaa4100d8473b7fcebda 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -11,6 +11,7 @@
 #include "readdistcommand.h"
 #include "readtreecommand.h"
 #include "readotucommand.h"
+#include "readseqscommand.h"
 #include "clustercommand.h"
 #include "parselistcommand.h"
 #include "collectcommand.h"
@@ -31,11 +32,15 @@
 #include "unifracweightedcommand.h"
 #include "libshuffcommand.h"
 #include "heatmapcommand.h"
-#include "venncommand.h"
+#include "filterseqscommand.h"
 #include "mothur.h"
+#include "venncommand.h"
 #include "nocommands.h"
 #include "binsequencecommand.h"
 #include "getoturepcommand.h"
+#include "treegroupscommand.h"
+#include "bootstrapsharedcommand.h"
+#include "concensuscommand.h"
 
 
 /***********************************************************/
@@ -61,6 +66,7 @@ Command* CommandFactory::getCommand(string commandName){
 
                         if(commandName == "read.dist")                         {       command = new ReadDistCommand();                        }
                else if(commandName == "read.otu")                              {       command = new ReadOtuCommand();                         }
+               else if(commandName == "read.seqs")                             {       command = new ReadSeqsCommand();                        }
                else if(commandName == "read.tree")                             {       command = new ReadTreeCommand();                        }
                else if(commandName == "cluster")                               {       command = new ClusterCommand();                         }
                else if(commandName == "deconvolute")                   {       command = new DeconvoluteCommand();                     }
@@ -80,9 +86,13 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "get.line")              {   command = new GetlineCommand();                             }
                else if(commandName == "libshuff")              {   command = new LibShuffCommand();                    }
                else if(commandName == "heatmap")                               {   command = new HeatMapCommand();                             }
+               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.oturep")                    {   command = new GetOTURepCommand();                   }
+               else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand();                   }
+               else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand();                  }
+               else if(commandName == "concensus")                             {   command = new ConcensusCommand();                   }
                else                                                                                    {       command = new NoCommand();                                      }
 
                return command;