added get.groups and remove.groups commands

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a4d6506df3128579158f2f1ff5ee99f67bfc9bc2..1f77b71bfb63b0519527bac53cfbf51511fdbb68 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -94,6 +94,11 @@
 #include "parsefastaqcommand.h"
 #include "pipelinepdscommand.h"
 #include "deuniqueseqscommand.h"
+#include "pairwiseseqscommand.h"
+#include "clusterdoturcommand.h"
+#include "subsamplecommand.h"
+#include "removegroupscommand.h"
+#include "getgroupscommand.h"
 
 
 /*******************************************************/
@@ -194,6 +199,11 @@ CommandFactory::CommandFactory(){
        commands["remove.lineage"]              = "remove.lineage";
        commands["fastq.info"]                  = "fastq.info";
        commands["deunique.seqs"]               = "deunique.seqs";
+       commands["cluster.classic"]             = "cluster.classic";
+       commands["sub.sample"]                  = "sub.sample";
+       commands["remove.groups"]               = "remove.groups";
+       commands["get.groups"]                  = "get.groups";
+       commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
        commands["dist.seqs"]                   = "MPIEnabled";
@@ -335,9 +345,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "cluster.fragments")             {       command = new ClusterFragmentsCommand(optionString);            }
                else if(commandName == "get.lineage")                   {       command = new GetLineageCommand(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 == "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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -447,9 +462,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "split.groups")                  {       pipecommand = new SplitGroupCommand(optionString);                              }
                else if(commandName == "cluster.fragments")             {       pipecommand = new ClusterFragmentsCommand(optionString);                }
                else if(commandName == "get.lineage")                   {       pipecommand = new GetLineageCommand(optionString);                              }
+               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 == "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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -548,8 +568,13 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "cluster.fragments")             {       shellcommand = new ClusterFragmentsCommand();           }
                else if(commandName == "get.lineage")                   {       shellcommand = new GetLineageCommand();                         }
                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 == "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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;