def testCompareDifferentLimitPerLandmark(self):
"""
The compare method must return a description of parameter differences
when two parameter instances have different limit per landmark.
"""
dbParams1 = DatabaseParameters(limitPerLandmark=10)
dbParams2 = DatabaseParameters(limitPerLandmark=20)
expected = ("Summary of differences:\n"
" Param 'limitPerLandmark' values 10 and 20 differ.")
self.assertEqual(expected, dbParams1.compare(dbParams2))
def testCompareDifferentMinDistance(self):
"""
The compare method must return a description of parameter differences
when two parameter instances have different min distances.
"""
dbParams1 = DatabaseParameters(minDistance=10)
dbParams2 = DatabaseParameters(minDistance=20)
expected = ("Summary of differences:\n"
" Param 'minDistance' values 10 and 20 differ.")
self.assertEqual(expected, dbParams1.compare(dbParams2))
def testCompareDifferentFeatureLengthBase(self):
"""
The compare method must return a description of parameter differences
when two parameter instances have different featureLength bases.
"""
dbParams1 = DatabaseParameters(featureLengthBase=1.0)
dbParams2 = DatabaseParameters(featureLengthBase=2.0)
expected = ("Summary of differences:\n"
" Param 'featureLengthBase' values 1.0 and 2.0 differ.")
self.assertEqual(expected, dbParams1.compare(dbParams2))
def testCompareDifferentMaxDistanceAndMinDistance(self):
"""
The compare method must return a description of parameter differences
when two parameter instances have multiple different attributes.
"""
dbParams1 = DatabaseParameters(maxDistance=10, minDistance=30)
dbParams2 = DatabaseParameters(maxDistance=20, minDistance=40)
expected = ("Summary of differences:\n"
" Param 'maxDistance' values 10 and 20 differ.\n"
" Param 'minDistance' values 30 and 40 differ.")
self.assertEqual(expected, dbParams1.compare(dbParams2))
def testCompareDifferentTrigPointFinders(self):
"""
The compare method must return a description of parameter differences
when two parameter instances have different trig point finders.
"""
dbParams1 = DatabaseParameters(trigPoints=[Peaks, Troughs])
dbParams2 = DatabaseParameters(trigPoints=[Peaks])
expected = ("Summary of differences:\n"
" Param 'trigPoints' values "
"['Peaks', 'Troughs'] and ['Peaks'] differ.")
self.assertEqual(expected, dbParams1.compare(dbParams2))
def testCompareDifferentLandmarkFinders(self):
"""
The compare method must return a description of parameter differences
when two parameter instances have different landmark finders.
"""
dbParams1 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand])
dbParams2 = DatabaseParameters(landmarks=[AlphaHelix])
expected = ("Summary of differences:\n"
" Param 'landmarks' values "
"['AlphaHelix', 'BetaStrand'] and ['AlphaHelix'] differ.")
self.assertEqual(expected, dbParams1.compare(dbParams2))
def testCompareDifferentRandomTrigPointDensity(self):
"""
The compare method must return a description of parameter differences
when two parameter instances have different randomTrigPointDensity
values.
"""
dbParams1 = DatabaseParameters(randomTrigPointDensity=0.2)
dbParams2 = DatabaseParameters(randomTrigPointDensity=0.4)
expected = (
"Summary of differences:\n"
" Param 'randomTrigPointDensity' values 0.2 and 0.4 differ.")
self.assertEqual(expected, dbParams1.compare(dbParams2))
def testSaveRestoreWithNonDefaultParameters(self):
"""
When asked to save and then restore a backend with non-default
parameters, a backend with the correct parameters must result.
"""
dbParams = DatabaseParameters(landmarks=[], trigPoints=[],
limitPerLandmark=16, maxDistance=17,
minDistance=18, distanceBase=19.0)
be = Backend()
be.configure(dbParams)
fp = StringIO()
be.save(fp)
fp.seek(0)
result = be.restore(fp)
self.assertIs(None, dbParams.compare(result.dbParams))
def testSaveRestoreEmpty(self):
"""
When asked to save and then restore an empty database, the correct
database must result.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix],
trigPoints=[Peaks])
db = Database(dbParams)
fp = StringIO()
db.save(fp)
fp.seek(0)
result = db.restore(fp)
self.assertEqual(0, result.subjectCount())
self.assertEqual(0, result.totalCoveredResidues())
self.assertEqual(0, result.totalResidues())
self.assertIs(None, dbParams.compare(result.dbParams))
def testSaveContentHasFourParts(self):
"""
When a simple database saves, its content must include parts for the
database parameters, the database state, the backend parameters and
the backend state.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix],
trigPoints=[Peaks])
db = Database(dbParams)
fp = StringIO()
db.save(fp)
fp.seek(0)
dbParams = DatabaseParameters.restore(fp)
loads(fp.readline()[:-1])
backendParams = DatabaseParameters.restore(fp)
loads(fp.readline()[:-1])
self.assertIs(None, dbParams.compare(backendParams))
def testSaveRestoreNonEmpty(self):
"""
When asked to save and then restore a non-empty database, the correct
database must result.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
db = Database(dbParams)
db.addSubject(AARead('id', 'FRRRFRRRFASAASA'))
fp = StringIO()
db.save(fp)
fp.seek(0)
result = db.restore(fp)
self.assertIs(None, dbParams.compare(result.dbParams))
self.assertEqual(db.subjectCount(), result.subjectCount())
self.assertEqual(db.totalCoveredResidues(),
result.totalCoveredResidues())
self.assertEqual(db.totalResidues(), result.totalResidues())
self.assertEqual(db.checksum(), result.checksum())
def testCompareIdentical(self):
"""
The compare method must return None when two parameter instances
have the same values.
"""
dbParams1 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs],
distanceBase=3.0,
featureLengthBase=3.9,
limitPerLandmark=10,
maxDistance=77,
minDistance=66,
randomLandmarkDensity=0.1,
randomTrigPointDensity=0.2)
dbParams2 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs],
distanceBase=3.0,
featureLengthBase=3.9,
limitPerLandmark=10,
maxDistance=77,
minDistance=66,
randomLandmarkDensity=0.1,
randomTrigPointDensity=0.2)
self.assertIs(None, dbParams1.compare(dbParams2))