fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ae59a8dcef9c43927b08759108c65f4c63d6a0cb..e18e6ac1956e3f21f990d6c5b1c45be42dafebf9 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -107,6 +107,15 @@
 #include "shhhercommand.h"
 #include "pcacommand.h"
 #include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
+#include "mantelcommand.h"
+#include "makefastqcommand.h"
+#include "anosimcommand.h"
+#include "getcurrentcommand.h"
+#include "setcurrentcommand.h"
 
 /*******************************************************/
 
@@ -217,6 +226,15 @@ CommandFactory::CommandFactory(){
        commands["corr.axes"]                   = "corr.axes";
        commands["pca"]                                 = "pca";
        commands["nmds"]                                = "nmds";
+       commands["remove.rare"]                 = "remove.rare";
+       commands["amova"]                               = "amova";
+       commands["homova"]                              = "homova";
+       commands["mantel"]                              = "mantel";
+       commands["anosim"]                              = "anosim";
+       commands["make.fastq"]                  = "make.fastq";
+       commands["merge.groups"]                = "merge.groups";
+       commands["get.current"]                 = "get.current";
+       commands["set.current"]                 = "set.current";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -376,6 +394,15 @@ 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 if(commandName == "mantel")                                {       command = new MantelCommand(optionString);                                      }
+               else if(commandName == "make.fastq")                    {       command = new MakeFastQCommand(optionString);                           }
+               else if(commandName == "get.current")                   {       command = new GetCurrentCommand(optionString);                          }
+               else if(commandName == "set.current")                   {       command = new SetCurrentCommand(optionString);                          }
+               else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -501,6 +528,15 @@ 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 if(commandName == "mantel")                                {       pipecommand = new MantelCommand(optionString);                                  }
+               else if(commandName == "anosim")                                {       pipecommand = new AnosimCommand(optionString);                                  }
+               else if(commandName == "make.fastq")                    {       pipecommand = new MakeFastQCommand(optionString);                               }
+               else if(commandName == "get.current")                   {       pipecommand = new GetCurrentCommand(optionString);                              }
+               else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -614,6 +650,15 @@ 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 if(commandName == "mantel")                                {       shellcommand = new MantelCommand();                                     }
+               else if(commandName == "anosim")                                {       shellcommand = new AnosimCommand();                                     }
+               else if(commandName == "make.fastq")                    {       shellcommand = new MakeFastQCommand();                          }
+               else if(commandName == "get.current")                   {       shellcommand = new GetCurrentCommand();                         }
+               else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;