align.check command added

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index fce55bbe9e856634a25b8141a3715965e88251b0..dd5b36317deae9007ccf8951f8133f573e75e316 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -54,6 +54,7 @@
 #include "getseqscommand.h"
 #include "removeseqscommand.h"
 #include "systemcommand.h"
+#include "secondarystructurecommand.h"
 
 /***********************************************************/
 
@@ -106,6 +107,7 @@ CommandFactory::CommandFactory(){
        commands["get.seqs"]                    = "get.seqs";
        commands["remove.seqs"]                 = "get.seqs";
        commands["system"]                              = "system";
+       commands["align.check"]                 = "align.check";
        commands["quit"]                                = "quit"; 
 
 }
@@ -168,6 +170,7 @@ Command* CommandFactory::getCommand(string commandName, string 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;