align.check command added

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 3d90269590b3f42e2d140821ba39220ccde9c251..dd5b36317deae9007ccf8951f8133f573e75e316 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -51,6 +51,10 @@
 #include "mergefilecommand.h"
 #include "chimeraseqscommand.h"
 #include "listseqscommand.h"
+#include "getseqscommand.h"
+#include "removeseqscommand.h"
+#include "systemcommand.h"
+#include "secondarystructurecommand.h"
 
 /***********************************************************/
 
@@ -100,6 +104,10 @@ CommandFactory::CommandFactory(){
        commands["trim.seqs"]                   = "trim.seqs";
        commands["chimera.seqs"]                = "chimera.seqs";
        commands["list.seqs"]                   = "list.seqs";
+       commands["get.seqs"]                    = "get.seqs";
+       commands["remove.seqs"]                 = "get.seqs";
+       commands["system"]                              = "system";
+       commands["align.check"]                 = "align.check";
        commands["quit"]                                = "quit"; 
 
 }
@@ -158,7 +166,11 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                             }
+               else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                  }
                else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                   }
+               else if(commandName == "system")                                {       command = new SystemCommand(optionString);                              }
+               else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                  }
                else                                                                                    {       command = new NoCommand(optionString);                                  }
 
                return command;