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 53a438aebd41ba1c86b1f42f84169e20c8ab9083..1241a04e998537fe33446a1c9ba3d933e690e557 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -131,7 +131,9 @@
 #include "pcrseqscommand.h"
 #include "createdatabasecommand.h"
 #include "makebiomcommand.h"
-#include "GetCoreMicroBiomeCommand.h"
+#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "makecontigscommand.h"
 
 /*******************************************************/
 
@@ -284,7 +286,9 @@ CommandFactory::CommandFactory(){
     commands["pcr.seqs"]            = "pcr.seqs";
     commands["create.database"]     = "create.database";
     commands["make.biom"]           = "make.biom";
-    commands["get.coremicrobiome"]   = "get.coremicrobiome";
+    commands["get.coremicrobiome"]  = "get.coremicrobiome";
+    commands["list.otulabels"]      = "list.otulabels";
+    commands["make.contigs"]        = "make.contigs";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -496,6 +500,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "create.database")       {      command = new CreateDatabaseCommand(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;
@@ -648,6 +654,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "create.database")       {      pipecommand = new CreateDatabaseCommand(optionString);          }
         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;
@@ -786,6 +794,8 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "create.database")       {      shellcommand = new CreateDatabaseCommand();         }
         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;