added cooccurence command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 303bf084c15b6d2f525ed70152348374b00f03b0..bdcfbbab528a785abce1330a3bb6b19d8212fdd6 100644 (file)
--- 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;