          self.args = arguments
          set_system_verbosity(self.args.loglevel)
  
          dest_format = self.get_dest_format()
          self.alignments = AlignmentData(self.args.alignments_file, dest_format)
  
      def get_dest_format(self):
          """ Set the destination format for Alignments """
          dest_format = None
          if hasattr(self.args, 'alignment_format') and self.args.alignment_format:
 
</s> remove         orig, ext = os.path.splitext(self.alignments.file)
        filename = "{}_merged{}".format(orig, ext)
 </s> add         folder = os.path.split(self.final_alignments.file)[0]
        ext = os.path.splitext(self.final_alignments.file)[1]
        now = datetime.now().strftime("%Y%m%d_%H%M%S")
        filename = os.path.join(folder, "alignments_merged_{}{}".format(now, ext)) </s> remove         self.alignments = alignments
        self.alignments2 = AlignmentData(arguments.alignments_file2, "json")
 </s> add         self.final_alignments = alignments[0]
        self.process_alignments = alignments[1:]
        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
          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:
            retval = [AlignmentData(a_file, dest_format) for a_file in self.args.alignments_file]
        logger.debug("Alignments: %s", retval)
        return retval
  
      def get_dest_format(self):
          """ Set the destination format for Alignments """
          dest_format = None
          if hasattr(self.args, 'alignment_format') and self.args.alignment_format:
keep keep keep keep replace 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