              logger.debug("Valid Alignments filename provided: '%s'", filename)
          else:
              filename = "{}.{}".format(noext_name, self.serializer.file_extension)
              logger.debug("File extension set from serializer: '%s'",
                           self.serializer.file_extension)
          location = os.path.join(str(folder), filename)
          if not os.path.exists(location):
              # Test for old format alignments files and reformat if they exist
              # This will be executed if an alignments file has not been explicitly provided
              # therefore it will not have been picked up in the extension test
 
</s> remove             # Test for old format alignments files and reformat if they exist
            # This will be executed if an alignments file has not been explicitly provided
            # therefore it will not have been picked up in the extension test
            self.test_for_legacy(location)
 </s> add             # Test for old format alignments files and reformat if they exist. This will be
            # executed if an alignments file has not been explicitly provided therefore it will not
            # have been picked up in the extension test
            self._test_for_legacy(location) </s> remove             filename = "{}.{}".format(noext_name, self.serializer.file_extension)
 </s> add             filename = "{}.{}".format(noext_name, self._serializer.file_extension) </s> remove         if extension[1:] == self.serializer.file_extension:
 </s> add         if extension[1:] == self._serializer.file_extension: </s> remove             filename = self.update_file_format(folder, filename)
 </s> add             filename = self._update_file_format(folder, filename) </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
        """
                         self._serializer.file_extension)
              logger.debug("Valid Alignments filename provided: '%s'", filename)
          else:
              filename = "{}.{}".format(noext_name, self.serializer.file_extension)
              logger.debug("File extension set from serializer: '%s'",
                         self._serializer.file_extension)
          location = os.path.join(str(folder), filename)
          if not os.path.exists(location):
              # Test for old format alignments files and reformat if they exist
              # This will be executed if an alignments file has not been explicitly provided
              # therefore it will not have been picked up in the extension test
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