added split.abund comand

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e2d114a3ba25e41474af369a8d41752be7616ccd..f358797f7d94bf557c8bf986dd16faaed03743f3 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -74,6 +74,10 @@
 #include "setlogfilecommand.h"
 #include "phylodiversitycommand.h"
 #include "makegroupcommand.h"
+#include "chopseqscommand.h"
+#include "clearcutcommand.h"
+#include "catchallcommand.h"
+#include "splitabundcommand.h"
 
 /*******************************************************/
 
@@ -155,6 +159,10 @@ CommandFactory::CommandFactory(){
        commands["set.logfile"]                 = "set.logfile";
        commands["phylo.diversity"]             = "phylo.diversity";
        commands["make.group"]                  = "make.group";
+       commands["chop.seqs"]                   = "chop.seqs";
+       commands["clearcut"]                    = "clearcut";
+       commands["catchall"]                    = "catchall";
+       commands["split.abund"]                 = "split.abund";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
        commands["filter.seqs"]                 = "MPIEnabled";
@@ -273,6 +281,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
                else if(commandName == "phylo.diversity")               {       command = new PhyloDiversityCommand(optionString);                      }
                else if(commandName == "make.group")                    {       command = new MakeGroupCommand(optionString);                           }
+               else if(commandName == "chop.seqs")                             {       command = new ChopSeqsCommand(optionString);                            }
+               else if(commandName == "clearcut")                              {       command = new ClearcutCommand(optionString);                            }
+               else if(commandName == "catchall")                              {       command = new CatchAllCommand(optionString);                            }
+               else if(commandName == "split.abund")                   {       command = new SplitAbundCommand(optionString);                          }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;