added chimera.uchime

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 63e0690f40cebb2b1ac0bf1b481a6848261c71bd..681e3e59f7e987a792b934d4ade36e182ed984ca 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -69,6 +69,7 @@
 #include "chimeraslayercommand.h"
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
+#include "chimerauchimecommand.h"
 #include "setlogfilecommand.h"
 #include "phylodiversitycommand.h"
 #include "makegroupcommand.h"
@@ -247,6 +248,7 @@ CommandFactory::CommandFactory(){
        commands["chimera.ccode"]               = "MPIEnabled";
        commands["chimera.check"]               = "MPIEnabled";
        commands["chimera.slayer"]              = "MPIEnabled";
+       commands["chimera.uchime"]              = "MPIEnabled";
        commands["chimera.pintail"]             = "MPIEnabled";
        commands["chimera.bellerophon"] = "MPIEnabled";
        commands["screen.seqs"]                 = "MPIEnabled";
@@ -351,6 +353,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
                else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
                else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
+               else if(commandName == "chimera.uchime")                {       command = new ChimeraUchimeCommand(optionString);                       }
                else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
                else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
                else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
@@ -486,6 +489,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "classify.seqs")                 {       pipecommand = new ClassifySeqsCommand(optionString);                    }
                else if(commandName == "chimera.ccode")                 {       pipecommand = new ChimeraCcodeCommand(optionString);                    }
                else if(commandName == "chimera.check")                 {       pipecommand = new ChimeraCheckCommand(optionString);                    }
+               else if(commandName == "chimera.uchime")                {       pipecommand = new ChimeraUchimeCommand(optionString);                   }
                else if(commandName == "chimera.slayer")                {       pipecommand = new ChimeraSlayerCommand(optionString);                   }
                else if(commandName == "chimera.pintail")               {       pipecommand = new ChimeraPintailCommand(optionString);                  }
                else if(commandName == "chimera.bellerophon")   {       pipecommand = new ChimeraBellerophonCommand(optionString);              }
@@ -610,6 +614,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "chimera.ccode")                 {       shellcommand = new ChimeraCcodeCommand();                       }
                else if(commandName == "chimera.check")                 {       shellcommand = new ChimeraCheckCommand();                       }
                else if(commandName == "chimera.slayer")                {       shellcommand = new ChimeraSlayerCommand();                      }
+               else if(commandName == "chimera.uchime")                {       shellcommand = new ChimeraUchimeCommand();                      }
                else if(commandName == "chimera.pintail")               {       shellcommand = new ChimeraPintailCommand();                     }
                else if(commandName == "chimera.bellerophon")   {       shellcommand = new ChimeraBellerophonCommand();         }
                else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }