added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 8c8fe3cb340f0ee56ba8ec7bc9e34ee69c32c021..d813e1b5e22f9184de49151d3183b528c1dfc7cd 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -126,6 +126,7 @@
 #include "chimeraperseuscommand.h"
 #include "shhhseqscommand.h"
 #include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
 
 /*******************************************************/
 
@@ -273,6 +274,7 @@ CommandFactory::CommandFactory(){
        commands["summary.tax"]                 = "summary.tax";
        commands["summary.qual"]                = "summary.qual";
        commands["shhh.seqs"]                   = "shhh.seqs";
+       commands["otu.association"]             = "otu.association";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -433,6 +435,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "summary.qual")                  {       command = new SummaryQualCommand(optionString);                         }
                else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
                else if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
+               else if(commandName == "otu.association")               {       command = new OTUAssociationCommand(optionString);                      }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -577,6 +580,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "summary.qual")                  {       pipecommand = new SummaryQualCommand(optionString);                             }
                else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
                else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
+               else if(commandName == "otu.association")               {       pipecommand = new OTUAssociationCommand(optionString);                  }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -709,6 +713,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "summary.qual")                  {       shellcommand = new SummaryQualCommand();                        }
                else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
                else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
+               else if(commandName == "otu.association")               {       shellcommand = new OTUAssociationCommand();                     }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;