added homova command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e3eb2b230ebbd11d83311feb3b63336eb928e698..924e3f78479f449d09a6ce6d9bd3985aa846409c 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -105,6 +105,12 @@
 #include "trimflowscommand.h"
 #include "corraxescommand.h"
 #include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
 
 /*******************************************************/
 
@@ -213,6 +219,12 @@ 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["amova"]                               = "amova";
+       commands["homova"]                              = "homova";
+       commands["merge.groups"]                = "merge.groups";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -333,7 +345,9 @@ 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 PCOACommand(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 +384,10 @@ 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 if(commandName == "amova")                                 {       command = new AmovaCommand(optionString);                                       }
+               else if(commandName == "homova")                                {       command = new HomovaCommand(optionString);                                      }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -457,7 +475,9 @@ 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 PCOACommand(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 +513,10 @@ 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 if(commandName == "amova")                                 {       pipecommand = new AmovaCommand(optionString);                                   }
+               else if(commandName == "homova")                                {       pipecommand = new HomovaCommand(optionString);                                  }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -569,6 +593,8 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "mgcluster")                             {       shellcommand = new MGClusterCommand();                          }
                else if(commandName == "pre.cluster")                   {       shellcommand = new PreClusterCommand();                         }
                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 +630,10 @@ 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 if(commandName == "amova")                                 {       shellcommand = new AmovaCommand();                                      }
+               else if(commandName == "homova")                                {       shellcommand = new HomovaCommand();                                     }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;