added check to cluster.classic to make sure file type is phylip. added mapping funct...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e73d60b3683acb5b8b3d25ea583be045354adce7..1241a04e998537fe33446a1c9ba3d933e690e557 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -133,6 +133,7 @@
 #include "makebiomcommand.h"
 #include "getcoremicrobiomecommand.h"
 #include "listotulabelscommand.h"
+#include "makecontigscommand.h"
 
 /*******************************************************/
 
@@ -287,6 +288,7 @@ CommandFactory::CommandFactory(){
     commands["make.biom"]           = "make.biom";
     commands["get.coremicrobiome"]  = "get.coremicrobiome";
     commands["list.otulabels"]      = "list.otulabels";
+    commands["make.contigs"]        = "make.contigs";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -499,6 +501,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "make.biom")             {      command = new MakeBiomCommand(optionString);                }
         else if(commandName == "get.coremicrobiome")    {      command = new GetCoreMicroBiomeCommand(optionString);       }
         else if(commandName == "list.otulabels")        {      command = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "make.contigs")          {      command = new MakeContigsCommand(optionString);             }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -652,6 +655,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "make.biom")             {      pipecommand = new MakeBiomCommand(optionString);                }
         else if(commandName == "get.coremicrobiome")    {      pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
         else if(commandName == "list.otulabels")        {      pipecommand = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "make.contigs")          {      pipecommand = new MakeContigsCommand(optionString);             }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -791,6 +795,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "make.biom")             {      shellcommand = new MakeBiomCommand();               }
         else if(commandName == "get.coremicrobiome")    {      shellcommand = new GetCoreMicroBiomeCommand();      }
         else if(commandName == "list.otulabels")        {      shellcommand = new ListOtuLabelsCommand();          }
+        else if(commandName == "make.contigs")          {      shellcommand = new MakeContigsCommand();            }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;