added get.lineage and remove.lineage commands

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 45f89060e62307a463a6637ec89913577f450b72..94da28fdd112dcd7347768088f58164d3973ca05 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -88,6 +88,9 @@
 #include "normalizesharedcommand.h"
 #include "metastatscommand.h"
 #include "splitgroupscommand.h"
+#include "clusterfragmentscommand.h"
+#include "getlineagecommand.h"
+#include "removelineagecommand.h"
 
 /*******************************************************/
 
@@ -180,6 +183,9 @@ CommandFactory::CommandFactory(){
        commands["normalize.shared"]    = "normalize.shared";
        commands["metastats"]                   = "metastats";
        commands["split.groups"]                = "split.groups";
+       commands["cluster.fragments"]   = "cluster.fragments";
+       commands["get.lineage"]                 = "get.lineage";
+       commands["remove.lineage"]              = "remove.lineage";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -315,6 +321,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "normalize.shared")              {       command = new NormalizeSharedCommand(optionString);                     }
                else if(commandName == "metastats")                             {       command = new MetaStatsCommand(optionString);                           }
                else if(commandName == "split.groups")                  {       command = new SplitGroupCommand(optionString);                          }
+               else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
+               else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(optionString);                          }
+               else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;