                  _ = self.update_file_format(*os.path.split(legacy_filename))
                  break
              logger.debug("Legacy alignments file does not exist: '%s'", legacy_filename)
  
      def update_file_format(self, folder, filename):
          """ Convert old style alignments format to new style format """
          logger.info("Reformatting legacy alignments file...")
          old_location = os.path.join(str(folder), filename)
          new_location = "{}.{}".format(os.path.splitext(old_location)[0],
                                        self.serializer.file_extension)
          if os.path.exists(old_location):
 
</s> remove                 _ = self.update_file_format(*os.path.split(legacy_filename))
 </s> add                 _ = self._update_file_format(*os.path.split(legacy_filename)) </s> remove                                       self.serializer.file_extension)
 </s> add                                       self._serializer.file_extension) </s> remove             filename = "{}.{}".format(noext_name, self.serializer.file_extension)
 </s> add             filename = "{}.{}".format(noext_name, self._serializer.file_extension) </s> remove     def get_location(self, folder, filename):
        """ Return the path to alignments file """
 </s> add     def _get_location(self, folder, filename):
        """ Obtains the location of an alignments file.

        If a legacy alignments file is provided/discovered, then the alignments file will be
        updated to the custom ``.fsa`` format and saved.

        Parameters
        ----------
        folder: str
            The folder that the alignments file is located in
        filename: str
            The filename of the alignments file

        Returns
        -------
        str
            The full path to the alignments file
        """ </s> remove                          self.serializer.file_extension)
 </s> add                          self._serializer.file_extension)
    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
        """
                  _ = self.update_file_format(*os.path.split(legacy_filename))
                  break
              logger.debug("Legacy alignments file does not exist: '%s'", legacy_filename)
  
    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
        """
    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
        """
          logger.info("Reformatting legacy alignments file...")
          old_location = os.path.join(str(folder), filename)
          new_location = "{}.{}".format(os.path.splitext(old_location)[0],
                                        self.serializer.file_extension)
          if os.path.exists(old_location):
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