def testChecksumAfterSaveRestore(self):
"""
A database that has a sequence added to it, which is then saved and
restored, and then has a second sequence is added to it must have the
same checksum as a database that simply has the two sequences added to
it without the intervening save/restore.
"""
seq1 = 'FRRRFRRRFASAASA'
seq2 = 'MMMMMMMMMFRRRFR'
dbParams1 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
db1 = Database(dbParams1)
db1.addSubject(AARead('id1', seq1))
fp = StringIO()
db1.save(fp)
fp.seek(0)
db1 = Database.restore(fp)
db1.addSubject(AARead('id2', seq2))
dbParams2 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
db2 = Database(dbParams2)
db2.addSubject(AARead('id1', seq1))
db2.addSubject(AARead('id2', seq2))
self.assertEqual(db1.checksum(), db2.checksum())
def testChecksumEmptyDatabase(self):
"""
The database checksum must be the same as the checksum for its
parameters plus the default backend name when no subjects have
been added to the database.
"""
dbParams = DatabaseParameters()
expected = Checksum(dbParams.checksum).update([
Backend.DEFAULT_NAME,
])
db = Database(dbParams)
self.assertEqual(expected.value, db.checksum())
def testChecksumAfterSubjectAdded(self):
"""
The database checksum must be as expected when a subject has been
added to the database.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix], trigPoints=[])
db = Database(dbParams)
sequence = 'AFRRRFRRRFASAASA'
subject = AARead('id', sequence)
db.addSubject(subject)
expected = Checksum(dbParams.checksum).update([
Backend.DEFAULT_NAME,
'id',
sequence,
])
self.assertEqual(expected.value, db.checksum())
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())