X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=2822d0b9920a0f5cc5005cf01ce653b38b9ede6d;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=527f7bfe4fddf6ecf1ddce45ab7c93a161f52ad1;hpb=aa23898d895a8c04cc4582a8809343df0aef6622;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 527f7bf..2822d0b 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -131,6 +131,11 @@
 #include "pcrseqscommand.h"
 #include "createdatabasecommand.h"
 #include "makebiomcommand.h"
+#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
+#include "makecontigscommand.h"
 
 /*******************************************************/
 
@@ -283,6 +288,11 @@ CommandFactory::CommandFactory(){
     commands["pcr.seqs"]            = "pcr.seqs";
     commands["create.database"]     = "create.database";
     commands["make.biom"]           = "make.biom";
+    commands["get.coremicrobiome"]  = "get.coremicrobiome";
+    commands["list.otulabels"]      = "list.otulabels";
+    commands["get.otulabels"]       = "get.otulabels";
+    commands["remove.otulabels"]    = "remove.otulabels";
+    commands["make.contigs"]        = "make.contigs";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -493,6 +503,11 @@ 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.coremicrobiome")    {	command = new GetCoreMicroBiomeCommand(optionString);       }
+        else if(commandName == "list.otulabels")        {	command = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {	command = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {	command = new RemoveOtuLabelsCommand(optionString);         }
+        else if(commandName == "make.contigs")          {	command = new MakeContigsCommand(optionString);             }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -644,6 +659,11 @@ 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.coremicrobiome")    {	pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
+        else if(commandName == "list.otulabels")        {	pipecommand = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {	pipecommand = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {	pipecommand = new RemoveOtuLabelsCommand(optionString);         }
+        else if(commandName == "make.contigs")          {	pipecommand = new MakeContigsCommand(optionString);             }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -781,6 +801,11 @@ 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.coremicrobiome")    {	shellcommand = new GetCoreMicroBiomeCommand();      }
+        else if(commandName == "list.otulabels")        {	shellcommand = new ListOtuLabelsCommand();          }
+        else if(commandName == "get.otulabels")         {	shellcommand = new GetOtuLabelsCommand();           }
+        else if(commandName == "remove.otulabels")      {	shellcommand = new RemoveOtuLabelsCommand();        }
+        else if(commandName == "make.contigs")          {	shellcommand = new MakeContigsCommand();            }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;