def testAddSameSubjectLeavesDatabaseSizeTheSame(self):
"""
If an identical subject is added multiple times, the database size
does not increase.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix], trigPoints=[])
db = Database(dbParams)
db.addSubject(AARead('id', 'FRRRFRRRF'))
self.assertEqual(1, db.subjectCount())
db.addSubject(AARead('id', 'FRRRFRRRF'))
self.assertEqual(1, db.subjectCount())
def testInitialStatistics(self):
"""
The database statistics must be initially correct.
"""
dbParams = DatabaseParameters()
db = Database(dbParams)
self.assertEqual(0, db.subjectCount())
self.assertEqual(0, db.totalResidues())
self.assertEqual(0, db.totalCoveredResidues())
def testOneReadTwoLandmarksStatistics(self):
"""
If one subject is added, the database statistics must be correct.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix], trigPoints=[])
db = Database(dbParams)
db.addSubject(AARead('id', 'FRRRFRRRFAAAAAAAAAAAAAAFRRRFRRRFRRRF'))
self.assertEqual(1, db.subjectCount())
self.assertEqual(36, db.totalResidues())
self.assertEqual(22, db.totalCoveredResidues())
def testTwoReadsTwoLandmarksStatistics(self):
"""
If two identical reads are added, the database statistics must be
correct.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix], trigPoints=[])
db = Database(dbParams)
db.addSubject(AARead('id1', 'FRRRFRRRFAAAAAAAAAAAAAAFRRRFRRRFRRRF'))
db.addSubject(AARead('id2', 'FRRRFRRRFAAAAAAAAAAAAAAFRRRFRRRFRRRF'))
self.assertEqual(2, db.subjectCount())
self.assertEqual(72, db.totalResidues())
self.assertEqual(44, db.totalCoveredResidues())
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())