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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Tests for rooting intepretation.
"""
import unittest
import warnings
from dendropy.dataio import newickreader
class RootingInterpreterLegacySupportTestCase(unittest.TestCase):
legacy_kw = (
("as_unrooted", True, "force-unrooted"),
("as_unrooted", False, "force-rooted"),
("as_rooted", True, "force-rooted"),
("as_rooted", False, "force-unrooted"),
("default_as_unrooted", True, "default-unrooted"),
("default_as_unrooted", False, "default-rooted"),
("default_as_rooted", True, "default-rooted"),
("default_as_rooted", False, "default-unrooted"),
)
def test_multiple_keyword_error(self):
with self.assertRaises(ValueError):
nr = newickreader.NewickReader(
as_rooted=True,
as_unrooted=True)
def test_legacy_keywords(self):
for kwset in self.legacy_kw:
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
kwargs = {kwset[0]: kwset[1]}
nr = newickreader.NewickReader(**kwargs)
self.assertEqual(nr.rooting, kwset[2])
class RootingInterpreterForceUnrootedTestCase(unittest.TestCase):
def test_with_no_token(self):
nr = newickreader.NewickReader(rooting="force-unrooted")
self.assertIs(nr._parse_tree_rooting_state(""), False)
def test_with_no_token2(self):
nr = newickreader.NewickReader(rooting="force-unrooted")
self.assertIs(nr._parse_tree_rooting_state(), False)
def test_with_rooted_token_lcase(self):
nr = newickreader.NewickReader(rooting="force-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&r"), False)
def test_with_rooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&R"), False)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&u"), False)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&U"), False)
def test_with_meaningless_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-unrooted")
self.assertIs(nr._parse_tree_rooting_state("zz"), False)
class RootingInterpreterForceRootedTestCase(unittest.TestCase):
def test_with_no_token(self):
nr = newickreader.NewickReader(rooting="force-rooted")
self.assertIs(nr._parse_tree_rooting_state(""), True)
def test_with_no_token2(self):
nr = newickreader.NewickReader(rooting="force-rooted")
self.assertIs(nr._parse_tree_rooting_state(), True)
def test_with_rooted_token_lcase(self):
nr = newickreader.NewickReader(rooting="force-rooted")
self.assertIs(nr._parse_tree_rooting_state("&r"), True)
def test_with_rooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-rooted")
self.assertIs(nr._parse_tree_rooting_state("&R"), True)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-rooted")
self.assertIs(nr._parse_tree_rooting_state("&u"), True)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-rooted")
self.assertIs(nr._parse_tree_rooting_state("&U"), True)
def test_with_meaningless_token_ucase(self):
nr = newickreader.NewickReader(rooting="force-rooted")
self.assertIs(nr._parse_tree_rooting_state("zz"), True)
class RootingInterpreterDefaultUnrootedTestCase(unittest.TestCase):
def test_with_no_token(self):
nr = newickreader.NewickReader(rooting="default-unrooted")
self.assertIs(nr._parse_tree_rooting_state(""), False)
def test_with_no_token2(self):
nr = newickreader.NewickReader(rooting="default-unrooted")
self.assertIs(nr._parse_tree_rooting_state(), False)
def test_with_rooted_token_lcase(self):
nr = newickreader.NewickReader(rooting="default-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&r"), True)
def test_with_rooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&R"), True)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&u"), False)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-unrooted")
self.assertIs(nr._parse_tree_rooting_state("&U"), False)
def test_with_meaningless_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-unrooted")
self.assertIs(nr._parse_tree_rooting_state("zz"), False)
class RootingInterpreterDefaultRootedTestCase(unittest.TestCase):
def test_with_no_token(self):
nr = newickreader.NewickReader(rooting="default-rooted")
self.assertIs(nr._parse_tree_rooting_state(""), True)
def test_with_no_token2(self):
nr = newickreader.NewickReader(rooting="default-rooted")
self.assertIs(nr._parse_tree_rooting_state(), True)
def test_with_rooted_token_lcase(self):
nr = newickreader.NewickReader(rooting="default-rooted")
self.assertIs(nr._parse_tree_rooting_state("&r"), True)
def test_with_rooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-rooted")
self.assertIs(nr._parse_tree_rooting_state("&R"), True)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-rooted")
self.assertIs(nr._parse_tree_rooting_state("&u"), False)
def test_with_unrooted_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-rooted")
self.assertIs(nr._parse_tree_rooting_state("&U"), False)
def test_with_meaningless_token_ucase(self):
nr = newickreader.NewickReader(rooting="default-rooted")
self.assertIs(nr._parse_tree_rooting_state("zz"), True)
if __name__ == "__main__":
unittest.main()
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