      def __init__(self, arguments):
          logger.debug("Initializing %s: (arguments: '%s'", self.__class__.__name__, arguments)
          self.args = arguments
          set_system_verbosity(self.args.loglevel)
  
          dest_format = self.get_dest_format()
          if len(self.args.alignments_file) == 1:
              retval = AlignmentData(self.args.alignments_file[0], dest_format)
          else:
 
</s> remove         self.alignments = AlignmentData(self.args.alignments_file, dest_format)
 </s> add         if len(self.args.alignments_file) == 1:
            retval = AlignmentData(self.args.alignments_file[0], dest_format)
        else:
            retval = [AlignmentData(a_file, dest_format) for a_file in self.args.alignments_file]
        logger.debug("Alignments: %s", retval)
        return retval </s> remove                     optval = optval.split(" ")
 </s> add                     if "\"" in optval:
                        optval = [arg[1:-1] for arg in re.findall(r"\".+?\"", optval)]
                    else:
                        optval = optval.split(" ")
        self.alignments = self.load_alignments()
        logger.debug("Initialized %s", self.__class__.__name__)

    def load_alignments(self):
        """ Loading alignments """
        logger.debug("Loading alignments")
        if len(self.args.alignments_file) > 1 and self.args.job != "merge":
            logger.error("Multiple alignments files are only permitted for merging")
            exit(0)
        if len(self.args.alignments_file) == 1 and self.args.job == "merge":
            logger.error("More than one alignments file required for merging")
            exit(0)
      def __init__(self, arguments):
          logger.debug("Initializing %s: (arguments: '%s'", self.__class__.__name__, arguments)
          self.args = arguments
          set_system_verbosity(self.args.loglevel)
        self.alignments = self.load_alignments()
        logger.debug("Initialized %s", self.__class__.__name__)

    def load_alignments(self):
        """ Loading alignments """
        logger.debug("Loading alignments")
        if len(self.args.alignments_file) > 1 and self.args.job != "merge":
            logger.error("Multiple alignments files are only permitted for merging")
            exit(0)
        if len(self.args.alignments_file) == 1 and self.args.job == "merge":
            logger.error("More than one alignments file required for merging")
            exit(0)
  
          dest_format = self.get_dest_format()
          if len(self.args.alignments_file) == 1:
              retval = AlignmentData(self.args.alignments_file[0], dest_format)
          else:
keep keep keep add keep keep keep keep keep
 Alignments Tool: Allow merging of many alignments file

Adds multi select functionality to GUI, meaning multiple alignments files can now be selected for merging.

Extract: nFilter, Filter now have a file dialog in gui for selecting 1/multiple files 
tools/alignments.py