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_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,)
