def verify_dataset(self, ds): self.assertEqual(len(ds.taxon_namespaces), 1) tns = ds.taxon_namespaces[0] checkers = ( standard_file_test_chars.RnaTestChecker, standard_file_test_chars.ProteinTestChecker, standard_file_test_chars.Standard01234TestChecker, standard_file_test_chars.DnaTestChecker, ) self.assertEqual(len(ds.char_matrices), len(checkers)) for idx, (char_matrix, checker) in enumerate(zip(ds.char_matrices, checkers)): self.assertIs(char_matrix.taxon_namespace, tns) if checker.matrix_type is dendropy.StandardCharacterMatrix: checker.create_class_fixtures_label_sequence_map_based_on_state_alphabet( checker, char_matrix.default_state_alphabet) standard_file_test_chars.general_char_matrix_checker( self, char_matrix, checker, check_taxon_annotations=self.check_taxon_annotations, check_matrix_annotations=self.check_matrix_annotations, check_sequence_annotations=self.check_sequence_annotations, check_column_annotations=self.check_column_annotations, check_cell_annotations=self.check_cell_annotations, )
def verify_char_matrix(self, char_matrix, src_matrix_checker_type): self.assertEqual(type(char_matrix), src_matrix_checker_type.matrix_type) if src_matrix_checker_type.matrix_type is dendropy.StandardCharacterMatrix: src_matrix_checker_type.create_class_fixtures_label_sequence_map_based_on_state_alphabet(src_matrix_checker_type, char_matrix.default_state_alphabet) standard_file_test_chars.general_char_matrix_checker( self, char_matrix, src_matrix_checker_type, check_taxon_annotations=self.check_taxon_annotations, check_matrix_annotations=self.check_matrix_annotations, check_sequence_annotations=self.check_sequence_annotations, check_column_annotations=self.check_column_annotations, check_cell_annotations=self.check_cell_annotations,)
def verify_chars(self, ds): self.assertEqual(len(ds.taxon_namespaces), 1) tns = ds.taxon_namespaces[0] checkers = ( standard_file_test_chars.RnaTestChecker, standard_file_test_chars.ProteinTestChecker, standard_file_test_chars.Standard01234TestChecker, standard_file_test_chars.DnaTestChecker, ) self.assertEqual(len(ds.char_matrices), len(checkers)) for idx, (char_matrix, checker) in enumerate(zip(ds.char_matrices, checkers)): self.assertIs(char_matrix.taxon_namespace, tns) if checker.matrix_type is dendropy.StandardCharacterMatrix: checker.create_class_fixtures_label_sequence_map_based_on_state_alphabet(checker, char_matrix.default_state_alphabet) standard_file_test_chars.general_char_matrix_checker( self, char_matrix, checker, check_taxon_annotations=self.check_taxon_annotations, check_matrix_annotations=self.check_matrix_annotations, check_sequence_annotations=self.check_sequence_annotations, check_column_annotations=self.check_column_annotations, check_cell_annotations=self.check_cell_annotations,)