  
  class Alignments():
      """ Perform tasks relating to alignments file """
      def __init__(self, arguments):
          self.args = arguments
          set_system_verbosity(self.args.loglevel)
          self.alignments = self.load_alignments()
          logger.debug("Initialized %s", self.__class__.__name__)
  
 
</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         self.alignments = alignments
        self.alignments2 = AlignmentData(arguments.alignments_file2, "json")
 </s> add         self.final_alignments = alignments[0]
        self.process_alignments = alignments[1:]
        logger.debug("Initializing %s: (arguments: '%s'", self.__class__.__name__, arguments)
  
  class Alignments():
      """ Perform tasks relating to alignments file """
      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__)
  
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