added amova command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 26b8c8620e96b545fbeed8a47be96130ebe1e615..42567e4a36c429cc39c859277af0a3948816ea9d 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -108,6 +108,8 @@
 #include "pcacommand.h"
 #include "nmdscommand.h"
 #include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
 
 /*******************************************************/
 
@@ -219,6 +221,8 @@ CommandFactory::CommandFactory(){
        commands["pca"]                                 = "pca";
        commands["nmds"]                                = "nmds";
        commands["remove.rare"]                 = "remove.rare";
+       commands["amova"]                               = "amova";
+       commands["merge.groups"]                = "merge.groups";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -379,6 +383,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
                else if(commandName == "corr.axes")                             {       command = new CorrAxesCommand(optionString);                            }
                else if(commandName == "remove.rare")                   {       command = new RemoveRareCommand(optionString);                          }
+               else if(commandName == "merge.groups")                  {       command = new MergeGroupsCommand(optionString);                         }
+               else if(commandName == "amova")                                 {       command = new AmovaCommand(optionString);                                       }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -505,6 +511,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
                else if(commandName == "corr.axes")                             {       pipecommand = new CorrAxesCommand(optionString);                                }
                else if(commandName == "remove.rare")                   {       pipecommand = new RemoveRareCommand(optionString);                              }
+               else if(commandName == "merge.groups")                  {       pipecommand = new MergeGroupsCommand(optionString);                             }
+               else if(commandName == "amova")                                 {       pipecommand = new AmovaCommand(optionString);                                   }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -619,6 +627,8 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
                else if(commandName == "corr.axes")                             {       shellcommand = new CorrAxesCommand();                           }
                else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
+               else if(commandName == "merge.groups")                  {       shellcommand = new MergeGroupsCommand();                        }
+               else if(commandName == "amova")                                 {       shellcommand = new AmovaCommand();                                      }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;