added debug flag to mothurOut. added debug parameter to set.dir. added debug code...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 527f7bfe4fddf6ecf1ddce45ab7c93a161f52ad1..c334b095abbc65a5bd9e40cc6f2160f6c37d3e2e 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -131,6 +131,7 @@
 #include "pcrseqscommand.h"
 #include "createdatabasecommand.h"
 #include "makebiomcommand.h"
+#include "getcoremicrobiomcommand.h"
 
 /*******************************************************/
 
@@ -283,6 +284,7 @@ CommandFactory::CommandFactory(){
     commands["pcr.seqs"]            = "pcr.seqs";
     commands["create.database"]     = "create.database";
     commands["make.biom"]           = "make.biom";
+    commands["get.coremicrobiom"]   = "get.coremircrobiom";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -493,6 +495,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "pcr.seqs")              {      command = new PcrSeqsCommand(optionString);                 }
         else if(commandName == "create.database")       {      command = new CreateDatabaseCommand(optionString);          }
         else if(commandName == "make.biom")             {      command = new MakeBiomCommand(optionString);                }
+        else if(commandName == "get.coremicrobiom")     {      command = new GetCoreMicroBiomCommand(optionString);                }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -644,6 +647,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "pcr.seqs")              {      pipecommand = new PcrSeqsCommand(optionString);                 }
         else if(commandName == "create.database")       {      pipecommand = new CreateDatabaseCommand(optionString);          }
         else if(commandName == "make.biom")             {      pipecommand = new MakeBiomCommand(optionString);                }
+        else if(commandName == "get.coremicrobiom")     {      pipecommand = new GetCoreMicroBiomCommand(optionString);                }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -781,6 +785,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "pcr.seqs")              {      shellcommand = new PcrSeqsCommand();                }
         else if(commandName == "create.database")       {      shellcommand = new CreateDatabaseCommand();         }
         else if(commandName == "make.biom")             {      shellcommand = new MakeBiomCommand();               }
+        else if(commandName == "get.coremicrobiom")     {      shellcommand = new GetCoreMicroBiomCommand();       }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;