X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=bdcfbbab528a785abce1330a3bb6b19d8212fdd6;hb=597560b3c23f03d0069082cf096ce65e0c087519;hp=303bf084c15b6d2f525ed70152348374b00f03b0;hpb=6b2ac07f3e9ee57594d2358a3a25f9f700bd7362;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 303bf08..bdcfbba 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -129,6 +129,7 @@
 #include "otuassociationcommand.h"
 #include "sortseqscommand.h"
 #include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
 
 /*******************************************************/
 
@@ -279,6 +280,7 @@ CommandFactory::CommandFactory(){
 	commands["otu.association"]		= "otu.association";
     commands["sort.seqs"]           = "sort.seqs";
     commands["classify.tree"]       = "classify.tree";
+    commands["cooccurrence"]        = "cooccurrence";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -442,6 +444,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "otu.association")		{	command = new OTUAssociationCommand(optionString);			}
         else if(commandName == "sort.seqs")             {	command = new SortSeqsCommand(optionString);                }
         else if(commandName == "classify.tree")         {	command = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {	command = new CooccurrenceCommand(optionString);            }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -589,6 +592,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "otu.association")		{	pipecommand = new OTUAssociationCommand(optionString);			}
         else if(commandName == "sort.seqs")             {	pipecommand = new SortSeqsCommand(optionString);                }
         else if(commandName == "classify.tree")         {	pipecommand = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {	pipecommand = new CooccurrenceCommand(optionString);            }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -724,6 +728,7 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "otu.association")		{	shellcommand = new OTUAssociationCommand();			}
         else if(commandName == "sort.seqs")             {	shellcommand = new SortSeqsCommand();               }
         else if(commandName == "classify.tree")         {	shellcommand = new ClassifyTreeCommand();           }
+        else if(commandName == "cooccurrence")          {	shellcommand = new CooccurrenceCommand();           }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;