added indicator command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 1f77b71bfb63b0519527bac53cfbf51511fdbb68..25d6cfe14e183ce072cb656322676babfdaa094f 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -99,7 +99,9 @@
 #include "subsamplecommand.h"
 #include "removegroupscommand.h"
 #include "getgroupscommand.h"
-
+#include "getotuscommand.h"
+#include "removeotuscommand.h"
+#include "indicatorcommand.h"
 
 /*******************************************************/
 
@@ -203,6 +205,9 @@ 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["indicator"]                   = "indicator";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -347,12 +352,15 @@ 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);                        }
                else if(commandName == "pairwise.seqs")                 {       command = new PairwiseSeqsCommand(optionString);                        }
                else if(commandName == "cluster.classic")               {       command = new ClusterDoturCommand(optionString);                        }
                else if(commandName == "sub.sample")                    {       command = new SubSampleCommand(optionString);                           }
+               else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -465,11 +473,14 @@ 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);                    }
                else if(commandName == "cluster.classic")               {       pipecommand = new ClusterDoturCommand(optionString);                    }
                else if(commandName == "sub.sample")                    {       pipecommand = new SubSampleCommand(optionString);                               }
+               else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -570,11 +581,14 @@ 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();                       }
                else if(commandName == "cluster.classic")               {       shellcommand = new ClusterDoturCommand();                       }
                else if(commandName == "sub.sample")                    {       shellcommand = new SubSampleCommand();                          }
+               else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;