added list.seqs command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 43f6769f92de125e9b76074e2a2d91cdb9ca3889..3d90269590b3f42e2d140821ba39220ccde9c251 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -49,6 +49,8 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
+#include "chimeraseqscommand.h"
+#include "listseqscommand.h"
 
 /***********************************************************/
 
@@ -96,6 +98,8 @@ CommandFactory::CommandFactory(){
        commands["screen.seqs"]                 = "screen.seqs";
        commands["reverse.seqs"]                = "reverse.seqs";
        commands["trim.seqs"]                   = "trim.seqs";
+       commands["chimera.seqs"]                = "chimera.seqs";
+       commands["list.seqs"]                   = "list.seqs";
        commands["quit"]                                = "quit"; 
 
 }
@@ -145,13 +149,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                       }
                else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);            }
                else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                      }
-               //else if(commandName == "consensus")                           {   command = new ConcensusCommand(optionString);                       }
+               //else if(commandName == "consensus")                   {   command = new ConcensusCommand(optionString);                       }
                else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                        }
                else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                           }
                else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                  }
                else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                  }
                else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                 }
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                    }
+               else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(optionString);                 }
+               else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                    }
                else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                   }
                else                                                                                    {       command = new NoCommand(optionString);                                  }