added get.otus and remove.otus commands

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 1f77b71bfb63b0519527bac53cfbf51511fdbb68..8d038e0c08e6010d21188808b3ff3ad40087a7f7 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -99,7 +99,8 @@
 #include "subsamplecommand.h"
 #include "removegroupscommand.h"
 #include "getgroupscommand.h"
-
+#include "getotuscommand.h"
+#include "removeotuscommand.h"
 
 /*******************************************************/
 
@@ -203,6 +204,8 @@ CommandFactory::CommandFactory(){
        commands["sub.sample"]                  = "sub.sample";
        commands["remove.groups"]               = "remove.groups";
        commands["get.groups"]                  = "get.groups";
+       commands["get.otus"]                    = "get.otus";
+       commands["remove.otus"]                 = "remove.otus";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -347,6 +350,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "remove.lineage")                {       command = new RemoveLineageCommand(optionString);                       }
                else if(commandName == "get.groups")                    {       command = new GetGroupsCommand(optionString);                           }
                else if(commandName == "remove.groups")                 {       command = new RemoveGroupsCommand(optionString);                        }
+               else if(commandName == "get.otus")                              {       command = new GetOtusCommand(optionString);                                     }
+               else if(commandName == "remove.otus")                   {       command = new RemoveOtusCommand(optionString);                          }
                else if(commandName == "fastq.info")                    {       command = new ParseFastaQCommand(optionString);                         }
                else if(commandName == "pipeline.pds")                  {       command = new PipelineCommand(optionString);                            }
                else if(commandName == "deunique.seqs")                 {       command = new DeUniqueSeqsCommand(optionString);                        }
@@ -465,6 +470,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "get.groups")                    {       pipecommand = new GetGroupsCommand(optionString);                               }
                else if(commandName == "remove.lineage")                {       pipecommand = new RemoveLineageCommand(optionString);                   }
                else if(commandName == "remove.groups")                 {       pipecommand = new RemoveGroupsCommand(optionString);                    }
+               else if(commandName == "get.otus")                              {       pipecommand = new GetOtusCommand(optionString);                                 }
+               else if(commandName == "remove.otus")                   {       pipecommand = new RemoveOtusCommand(optionString);                              }
                else if(commandName == "fastq.info")                    {       pipecommand = new ParseFastaQCommand(optionString);                             }
                else if(commandName == "deunique.seqs")                 {       pipecommand = new DeUniqueSeqsCommand(optionString);                    }
                else if(commandName == "pairwise.seqs")                 {       pipecommand = new PairwiseSeqsCommand(optionString);                    }
@@ -570,6 +577,8 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "remove.lineage")                {       shellcommand = new RemoveLineageCommand();                      }
                else if(commandName == "get.groups")                    {       shellcommand = new GetGroupsCommand();                          }
                else if(commandName == "remove.groups")                 {       shellcommand = new RemoveGroupsCommand();                       }
+               else if(commandName == "get.otus")                              {       shellcommand = new GetOtusCommand();                            }
+               else if(commandName == "remove.otus")                   {       shellcommand = new RemoveOtusCommand();                         }
                else if(commandName == "fastq.info")                    {       shellcommand = new ParseFastaQCommand();                        }
                else if(commandName == "deunique.seqs")                 {       shellcommand = new DeUniqueSeqsCommand();                       }
                else if(commandName == "pairwise.seqs")                 {       shellcommand = new PairwiseSeqsCommand();                       }