  
      def backup(self):
          """ Backup copy of old alignments """
          logger.debug("Backing up alignments")
          if not os.path.isfile(self.file):
              logger.debug("No alignments to back up")
              return
          now = datetime.now().strftime("%Y%m%d_%H%M%S")
          src = self.file
          split = os.path.splitext(src)
 
</s> remove         src = self.file
 </s> add         src = self._file </s> remove         """ Backup copy of old alignments """
 </s> add         """ Create a backup copy of the alignments :attr:`file`.

        Creates a copy of the serialized alignments :attr:`file` appending a
        timestamp onto the end of the file name and storing in the same folder as
        the original :attr:`file`.
        """ </s> remove         logger.info("Writing alignments to: '%s'", self.file)
        self.serializer.save(self.file, self.data)
 </s> add         logger.info("Writing alignments to: '%s'", self._file)
        self._serializer.save(self._file, self._data) </s> remove     def reload(self):
        """ Read the alignments data from the correct format """
        logger.debug("Re-loading alignments")
        self.data = self.load()
        logger.debug("Re-loaded alignments")

 </s> add  </s> remove     def update_file_format(self, folder, filename):
        """ Convert old style alignments format to new style format """
 </s> add     def _update_file_format(self, folder, filename):
        """ Convert old style serialized alignments to new ``.fsa`` format.

        Parameters
        ----------
        folder: str
            The folder that the legacy alignments exist in
        filename: str
            The file name of the legacy alignments

        Returns
        -------
        str
            The full path to the newly created ``.fsa`` alignments file
        """
        if not os.path.isfile(self._file):
  
      def backup(self):
          """ Backup copy of old alignments """
          logger.debug("Backing up alignments")
        if not os.path.isfile(self._file):
              logger.debug("No alignments to back up")
              return
          now = datetime.now().strftime("%Y%m%d_%H%M%S")
          src = self.file
          split = os.path.splitext(src)
keep keep keep keep replace keep keep keep keep keep
 lib.alignments - Slight update (#978)

* lib.alignments update:
  - Minor structure change (faces to nested dictionary)
  - Refactor internal and external methods
  - Documentation 
lib/alignments.py