added merge.groups command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5a7b23712c3c3503c44e31e2276123fb7b5c3c56..250e4f6e3176ee10c7674778f365f9785a4df855 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -61,7 +61,7 @@
 #include "phylotypecommand.h"
 #include "mgclustercommand.h"
 #include "preclustercommand.h"
-#include "pcacommand.h"
+#include "pcoacommand.h"
 #include "otuhierarchycommand.h"
 #include "setdircommand.h"
 #include "parselistscommand.h"
@@ -105,6 +105,10 @@
 #include "trimflowscommand.h"
 #include "corraxescommand.h"
 #include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
 
 /*******************************************************/
 
@@ -213,6 +217,10 @@ CommandFactory::CommandFactory(){
        commands["indicator"]                   = "indicator";
        commands["consensus.seqs"]              = "consensus.seqs";
        commands["corr.axes"]                   = "corr.axes";
+       commands["pca"]                                 = "pca";
+       commands["nmds"]                                = "nmds";
+       commands["remove.rare"]                 = "remove.rare";
+       commands["merge.groups"]                = "merge.groups";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -333,7 +341,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
                else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                           }
                else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                          }
-               else if(commandName == "pcoa")                                  {       command = new PCACommand(optionString);                                         }
+               else if(commandName == "pcoa")                                  {       command = new PCOACommand(optionString);                                        }
+               else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                         }
+               else if(commandName == "nmds")                                  {       command = new NMDSCommand(optionString);                                        }
                else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
                else if(commandName == "set.logfile")                   {       command = new SetLogFileCommand(optionString);                          }
@@ -370,6 +380,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "indicator")                             {       command = new IndicatorCommand(optionString);                           }
                else if(commandName == "consensus.seqs")                {       command = new ConsensusSeqsCommand(optionString);                       }
                else if(commandName == "corr.axes")                             {       command = new CorrAxesCommand(optionString);                            }
+               else if(commandName == "remove.rare")                   {       command = new RemoveRareCommand(optionString);                          }
+               else if(commandName == "merge.groups")                  {       command = new MergeGroupsCommand(optionString);                         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -457,7 +469,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "phylotype")                             {       pipecommand = new PhylotypeCommand(optionString);                               }
                else if(commandName == "mgcluster")                             {       pipecommand = new MGClusterCommand(optionString);                               }
                else if(commandName == "pre.cluster")                   {       pipecommand = new PreClusterCommand(optionString);                              }
-               else if(commandName == "pcoa")                                  {       pipecommand = new PCACommand(optionString);                                             }
+               else if(commandName == "pcoa")                                  {       pipecommand = new PCOACommand(optionString);                                    }
+               else if(commandName == "pca")                                   {       pipecommand = new PCACommand(optionString);                                             }
+               else if(commandName == "nmds")                                  {       pipecommand = new NMDSCommand(optionString);                                    }
                else if(commandName == "otu.hierarchy")                 {       pipecommand = new OtuHierarchyCommand(optionString);                    }
                else if(commandName == "set.dir")                               {       pipecommand = new SetDirectoryCommand(optionString);                    }
                else if(commandName == "set.logfile")                   {       pipecommand = new SetLogFileCommand(optionString);                              }
@@ -493,6 +507,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "indicator")                             {       pipecommand = new IndicatorCommand(optionString);                               }
                else if(commandName == "consensus.seqs")                {       pipecommand = new ConsensusSeqsCommand(optionString);                   }
                else if(commandName == "corr.axes")                             {       pipecommand = new CorrAxesCommand(optionString);                                }
+               else if(commandName == "remove.rare")                   {       pipecommand = new RemoveRareCommand(optionString);                              }
+               else if(commandName == "merge.groups")                  {       pipecommand = new MergeGroupsCommand(optionString);                             }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -568,7 +584,9 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
                else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
                else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
-               else if(commandName == "pcoa")                                  {       shellcommand = new PCACommand();                                        }
+               else if(commandName == "pcoa")                                  {       shellcommand = new PCOACommand();                                       }
+               else if(commandName == "pca")                                   {       shellcommand = new PCACommand();                                        }
+               else if(commandName == "nmds")                                  {       shellcommand = new NMDSCommand();                                       }
                else if(commandName == "otu.hierarchy")                 {       shellcommand = new OtuHierarchyCommand();                       }
                else if(commandName == "set.dir")                               {       shellcommand = new SetDirectoryCommand();                       }
                else if(commandName == "set.logfile")                   {       shellcommand = new SetLogFileCommand();                         }
@@ -604,6 +622,8 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "indicator")                             {       shellcommand = new IndicatorCommand();                          }
                else if(commandName == "consensus.seqs")                {       shellcommand = new ConsensusSeqsCommand();                      }
                else if(commandName == "corr.axes")                             {       shellcommand = new CorrAxesCommand();                           }
+               else if(commandName == "remove.rare")                   {       shellcommand = new RemoveRareCommand();                         }
+               else if(commandName == "merge.groups")                  {       shellcommand = new MergeGroupsCommand();                        }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;