def testNotTooManyFeaturesByDefault(self):
"""
A new instance of L{_FeatureAdder} must be marked on creation as not
having too many features to plot.
"""
featureAdder = _FeatureAdder()
self.assertFalse(featureAdder.tooManyFeaturesToPlot)
def testTooManyFeatures(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns too many
features, the C{text} and C{axis} methods on the figure must be called
correctly and the C{add} call must return the sequences.
"""
def fetcher(title, db="database"):
feature = SeqFeature(type="site", qualifiers={"a": ["b"]})
return SeqRecord(None, features=[feature] * 100)
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ("site",)
fig = plt.subplot(111)
fig.text = MagicMock()
fig.axis = MagicMock()
result = featureAdder.add(fig, "title", 0, 300, identity, sequenceFetcher=fetcher)
fig.text.assert_called_with(
0.5,
0.5,
"Too many features to plot",
horizontalalignment="center",
verticalalignment="center",
transform=ANY,
fontsize=20,
)
fig.axis.assert_called_with([0, 300, -1, 1])
self.assertTrue(isinstance(result, _FeatureList))
self.assertEqual(100, len(result))
def testNoFeatures(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns no features
the C{text} and C{axis} methods on the fig must both be called
correctly and the C{add} method must return C{[]}.
"""
def fetcher(title, db='database'):
return SeqRecord(None)
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ('site', )
fig = plt.subplot(111, label=_randomLabel())
fig.text = MagicMock()
fig.axis = MagicMock()
result = featureAdder.add(fig,
'title',
0,
300,
sequenceFetcher=fetcher)
fig.text.assert_called_with(0.5,
0.5,
'No features found',
horizontalalignment='center',
verticalalignment='center',
transform=ANY,
fontsize=20)
fig.axis.assert_called_with([0, 300, -1, 1])
self.assertEqual([], result)
def testNotTooManyFeaturesByDefault(self):
"""
A new instance of L{_FeatureAdder} must be marked on creation as not
having too many features to plot.
"""
featureAdder = _FeatureAdder()
self.assertFalse(featureAdder.tooManyFeaturesToPlot)
def testOneFeatureRaisesNotImplementedError(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns a feature,
the C{add} method must raise C{NotImplementedError} because the
C{_displayFeatures} method is not implemented.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
subfeature = SeqFeature(type='region',
qualifiers={'a': ['b']},
location=location)
feature = SeqFeature(type='site',
qualifiers={'a': ['b']},
sub_features=[subfeature],
location=location)
return SeqRecord(None, features=[feature])
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ('site', )
fig = plt.subplot(111)
self.assertRaises(NotImplementedError,
featureAdder.add,
fig,
'title',
0,
300,
sequenceFetcher=fetcher)
def testTooManyFeatures(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns too many
features, the C{text} and C{axis} methods on the figure must be called
correctly and the C{add} call must return the sequences.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
feature = SeqFeature(type='site', qualifiers={'a': ['b']},
location=location)
return SeqRecord(None, features=[feature] * 100)
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ('site',)
fig = plt.subplot(111)
fig.text = MagicMock()
fig.axis = MagicMock()
result = featureAdder.add(fig, 'title', 0, 300,
sequenceFetcher=fetcher)
fig.text.assert_called_with(0.5, 0.5,
'Too many features to plot',
horizontalalignment='center',
verticalalignment='center',
transform=ANY, fontsize=20)
fig.axis.assert_called_with([0, 300, -1, 1])
self.assertTrue(isinstance(result, FeatureList))
self.assertEqual(100, len(result))
def testTooManyFeatures(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns too many
features, the C{text} and C{axis} methods on the figure must be called
correctly and the C{add} call must return the sequences.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
feature = SeqFeature(type='site',
qualifiers={'a': ['b']},
location=location)
return SeqRecord(None, features=[feature] * 100)
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ('site', )
fig = plt.subplot(111, label=_randomLabel())
fig.text = MagicMock()
fig.axis = MagicMock()
result = featureAdder.add(fig,
'title',
0,
300,
sequenceFetcher=fetcher)
fig.text.assert_called_with(0.5,
0.5,
'Too many features to plot',
horizontalalignment='center',
verticalalignment='center',
transform=ANY,
fontsize=20)
fig.axis.assert_called_with([0, 300, -1, 1])
self.assertTrue(isinstance(result, FeatureList))
self.assertEqual(100, len(result))
def testYTicks(self):
"""
A L{_FeatureAdder} must set the title of its figure.
"""
fetcher = lambda title, db='database': None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.set_yticks = MagicMock()
featureAdder.add(fig, 'title', 0, 100, sequenceFetcher=fetcher)
fig.set_yticks.assert_called_with([])
def testTitle(self):
"""
A L{_FeatureAdder} must set the title of its figure.
"""
fetcher = lambda title, db="database": None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.set_title = MagicMock()
featureAdder.add(fig, "title", 0, 100, identity, sequenceFetcher=fetcher)
fig.set_title.assert_called_with("Target sequence features", fontsize=16)
def testYTicks(self):
"""
A L{_FeatureAdder} must set the title of its figure.
"""
fetcher = lambda title, db="database": None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.set_yticks = MagicMock()
featureAdder.add(fig, "title", 0, 100, identity, sequenceFetcher=fetcher)
fig.set_yticks.assert_called_with([])
def testTitle(self):
"""
A L{_FeatureAdder} must set the title of its figure.
"""
fetcher = lambda title, db='database': None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.set_title = MagicMock()
featureAdder.add(fig, 'title', 0, 100, sequenceFetcher=fetcher)
fig.set_title.assert_called_with('Target sequence features',
fontsize=16)
def testYTicks(self):
"""
A L{_FeatureAdder} must set the title of its figure.
"""
def fetcher(title, db='database'):
return None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.set_yticks = MagicMock()
featureAdder.add(fig, 'title', 0, 100, sequenceFetcher=fetcher)
fig.set_yticks.assert_called_with([])
def testYTicks(self):
"""
A L{_FeatureAdder} must set the title of its figure.
"""
def fetcher(title, db='database'):
return None
featureAdder = _FeatureAdder()
fig = plt.subplot(111, label=_randomLabel())
fig.set_yticks = MagicMock()
featureAdder.add(fig, 'title', 0, 100, sequenceFetcher=fetcher)
fig.set_yticks.assert_called_with([])
def testTitle(self):
"""
A L{_FeatureAdder} must set the title of its figure.
"""
def fetcher(title, db='database'):
return None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.set_title = MagicMock()
featureAdder.add(fig, 'title', 0, 100, sequenceFetcher=fetcher)
fig.set_title.assert_called_with('Target sequence features',
fontsize=16)
def testOffline(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns C{None},
the C{add} method of the L{_FeatureAdder} must return C{None}. The
C{text} and C{axis} methods on the fig must both be called correctly.
"""
fetcher = lambda title, db="database": None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.text = MagicMock()
fig.axis = MagicMock()
featureAdder.add(fig, "title", 0, 300, identity, sequenceFetcher=fetcher)
fig.text.assert_called_with(100, 0, "You (or Genbank) appear to be offline.", fontsize=20)
fig.axis.assert_called_with([0, 300, -1, 1])
def testOffline(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns C{None},
the C{add} method of the L{_FeatureAdder} must return C{None}. The
C{text} and C{axis} methods on the fig must both be called correctly.
"""
fetcher = lambda title, db='database': None
featureAdder = _FeatureAdder()
fig = plt.subplot(111)
fig.text = MagicMock()
fig.axis = MagicMock()
featureAdder.add(fig, 'title', 0, 300, sequenceFetcher=fetcher)
fig.text.assert_called_with(100,
0,
'You (or Genbank) appear to be offline.',
fontsize=20)
fig.axis.assert_called_with([0, 300, -1, 1])
def testOneFeatureRaisesNotImplementedError(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns a feature,
the C{add} method must raise C{NotImplementedError} because the
C{_displayFeatures} method is not implemented.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
feature = SeqFeature(type='site', qualifiers={'a': ['b']},
location=location)
return SeqRecord(None, features=[feature])
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ('site',)
fig = plt.subplot(111)
self.assertRaises(NotImplementedError, featureAdder.add, fig, 'title',
0, 300, sequenceFetcher=fetcher)
def testOneFeatureRaisesNotImplementedError(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns a feature,
the C{add} method must raise C{NotImplementedError} because the
C{_displayFeatures} method is not implemented.
"""
def fetcher(title, db="database"):
subfeature = SeqFeature(type="region", qualifiers={"a": ["b"]})
feature = SeqFeature(type="site", qualifiers={"a": ["b"]}, sub_features=[subfeature])
return SeqRecord(None, features=[feature])
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ("site",)
fig = plt.subplot(111)
self.assertRaises(
NotImplementedError, featureAdder.add, fig, "title", 0, 300, identity, sequenceFetcher=fetcher
)
def testNoFeatures(self):
"""
If the sequence fetcher used by a L{_FeatureAdder} returns no features
the C{text} and C{axis} methods on the fig must both be called
correctly and the C{add} method must return C{[]}.
"""
fetcher = lambda title, db='database': SeqRecord(None)
featureAdder = _FeatureAdder()
featureAdder.WANTED_TYPES = ('site',)
fig = plt.subplot(111)
fig.text = MagicMock()
fig.axis = MagicMock()
result = featureAdder.add(fig, 'title', 0, 300,
sequenceFetcher=fetcher)
fig.text.assert_called_with(0.5, 0.5,
'No features found',
horizontalalignment='center',
verticalalignment='center',
transform=ANY, fontsize=20)
fig.axis.assert_called_with([0, 300, -1, 1])
self.assertEqual([], result)
