fixed mpi version compile issue with chimera.slayer

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 42567e4a36c429cc39c859277af0a3948816ea9d..56cca07fd19266820a29e3f529f784581ae00d80 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -110,6 +110,9 @@
 #include "removerarecommand.h"
 #include "mergegroupscommand.h"
 #include "amovacommand.h"
+#include "homovacommand.h"
+#include "mantelcommand.h"
+#include "makefastqcommand.h"
 
 /*******************************************************/
 
@@ -222,6 +225,9 @@ CommandFactory::CommandFactory(){
        commands["nmds"]                                = "nmds";
        commands["remove.rare"]                 = "remove.rare";
        commands["amova"]                               = "amova";
+       commands["homova"]                              = "homova";
+       commands["mantel"]                              = "mantel";
+       commands["make.fastq"]                  = "make.fastq";
        commands["merge.groups"]                = "merge.groups";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
@@ -385,6 +391,9 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "homova")                                {       command = new HomovaCommand(optionString);                                      }
+               else if(commandName == "mantel")                                {       command = new MantelCommand(optionString);                                      }
+               else if(commandName == "make.fastq")                    {       command = new MakeFastQCommand(optionString);                           }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -513,6 +522,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                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 if(commandName == "homova")                                {       pipecommand = new HomovaCommand(optionString);                                  }
+               else if(commandName == "mantel")                                {       pipecommand = new MantelCommand(optionString);                                  }
+               else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -629,6 +641,9 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
                else if(commandName == "merge.groups")                  {       shellcommand = new MergeGroupsCommand();                        }
                else if(commandName == "amova")                                 {       shellcommand = new AmovaCommand();                                      }
+               else if(commandName == "homova")                                {       shellcommand = new HomovaCommand();                                     }
+               else if(commandName == "mantel")                                {       shellcommand = new MantelCommand();                                     }
+               else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;