  
      def save(self):
          """ Write the serialized alignments file """
          logger.debug("Saving alignments")
          logger.info("Writing alignments to: '%s'", self.file)
          self.serializer.save(self.file, self.data)
          logger.debug("Saved alignments")
  
      def backup(self):
          """ Backup copy of old alignments """
          logger.debug("Backing up alignments")
 
</s> remove         """ Write the serialized alignments file """
 </s> add         """ Write the contents of :attr:`data` to a serialized ``.fsa`` file at the location
        :attr:`file`. """ </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         """ 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         if not os.path.isfile(self.file):
 </s> add         if not os.path.isfile(self._file): </s> remove         logger.info("Reading alignments from: '%s'", self.file)
        data = self.serializer.load(self.file)
 </s> add         logger.info("Reading alignments from: '%s'", self._file)
        data = self._serializer.load(self._file)
        logger.info("Writing alignments to: '%s'", self._file)
        self._serializer.save(self._file, self._data)
  
      def save(self):
          """ Write the serialized alignments file """
          logger.debug("Saving alignments")
        logger.info("Writing alignments to: '%s'", self._file)
        self._serializer.save(self._file, self._data)
        logger.info("Writing alignments to: '%s'", self._file)
        self._serializer.save(self._file, self._data)
          logger.debug("Saved alignments")
  
      def backup(self):
          """ Backup copy of old alignments """
          logger.debug("Backing up alignments")
keep keep keep keep replace 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