def testPrint(self):
"""
The print_ function should produce the expected output.
"""
self.maxDiff = None
subject = AARead('subject', 'FRRRFRRRFASAASA')
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs],
limitPerLandmark=16,
maxDistance=10,
minDistance=0,
distanceBase=1,
randomLandmarkDensity=0.6,
randomTrigPointDensity=0.4,
acAlphaHelixFilename='xxx',
acAlphaHelix310Filename='yyy',
acAlphaHelixCombinedFilename='bbb',
acAlphaHelixPiFilename='zzz',
acExtendedStrandFilename='aaa')
db = Database(dbParams)
db.addSubject(subject)
expected = ('Parameters:\n'
' Landmark finders:\n'
' AlphaHelix\n'
' BetaStrand\n'
' Trig point finders:\n'
' Peaks\n'
' Troughs\n'
' Limit per landmark: 16\n'
' Max distance: 10\n'
' Min distance: 0\n'
' Distance base: 1.000000\n'
' Feature length base: 1.350000\n'
' Random landmark density: 0.600000\n'
' Random trig point density: 0.400000\n'
' AC AlphaHelix filename: xxx\n'
' AC AlphaHelix 3-10 filename: yyy\n'
' AC AlphaHelix Combined filename: bbb\n'
' AC AlphaHelix pi filename: zzz\n'
' AC ExtendedStrand filename: aaa\n'
'Connector class: SimpleConnector\n'
'Subject count: 1\n'
'Hash count: 3\n'
'Total residues: 15\n'
'Coverage: 73.33%\n'
'Checksum: 3162290961\n'
'Connector:')
self.assertEqual(expected, db.print_())
def testPrintNoHashes(self):
"""
The print_ function should report the expected result if no hashes are
found in the subject.
"""
self.maxDiff = None
subject = AARead('subject', '')
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs],
limitPerLandmark=16,
maxDistance=10,
minDistance=0,
distanceBase=1)
db = Database(dbParams)
db.addSubject(subject)
expected = (
'Parameters:\n'
' Landmark finders:\n'
' AlphaHelix\n'
' BetaStrand\n'
' Trig point finders:\n'
' Peaks\n'
' Troughs\n'
' Limit per landmark: 16\n'
' Max distance: 10\n'
' Min distance: 0\n'
' Distance base: 1.000000\n'
' Feature length base: 1.350000\n'
' Random landmark density: 0.100000\n'
' Random trig point density: 0.100000\n'
' AC AlphaHelix filename: ac-alpha-helix-substrings-20-0.85\n'
' AC AlphaHelix 3-10 filename: ac-alpha-helix-3-10-substrings-'
'1-0.5\n'
' AC AlphaHelix Combined filename: ac-alpha-helix-combined-'
'substrings-20-0.85\n'
' AC AlphaHelix pi filename: ac-alpha-helix-pi-substrings-1-0.5\n'
' AC ExtendedStrand filename: ac-extended-strand-substrings-'
'10-0.5\n'
'Connector class: SimpleConnector\n'
'Subject count: 1\n'
'Hash count: 0\n'
'Total residues: 0\n'
'Coverage: 0.00%\n'
'Checksum: 3786852290\n'
'Connector:')
self.assertEqual(expected, db.print_())
def testPrintWithHashes(self):
"""
The print_ function should produce the expected output when asked to
print hash information.
"""
self.maxDiff = None
subject = AARead('subject-id', 'FRRRFRRRFASAASA')
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs],
limitPerLandmark=16,
maxDistance=10,
minDistance=0,
distanceBase=1)
db = Database(dbParams)
db.addSubject(subject)
expected = (
'Parameters:\n'
' Landmark finders:\n'
' AlphaHelix\n'
' BetaStrand\n'
' Trig point finders:\n'
' Peaks\n'
' Troughs\n'
' Limit per landmark: 16\n'
' Max distance: 10\n'
' Min distance: 0\n'
' Distance base: 1.000000\n'
' Feature length base: 1.350000\n'
' Random landmark density: 0.100000\n'
' Random trig point density: 0.100000\n'
' AC AlphaHelix filename: ac-alpha-helix-substrings-20-0.85\n'
' AC AlphaHelix 3-10 filename: ac-alpha-helix-3-10-substrings-'
'1-0.5\n'
' AC AlphaHelix Combined filename: ac-alpha-helix-combined-'
'substrings-20-0.85\n'
' AC AlphaHelix pi filename: ac-alpha-helix-pi-substrings-1-0.5\n'
' AC ExtendedStrand filename: ac-extended-strand-substrings-'
'10-0.5\n'
'Connector class: SimpleConnector\n'
'Subject count: 1\n'
'Hash count: 3\n'
'Total residues: 15\n'
'Coverage: 73.33%\n'
'Checksum: 2751160351\n'
'Connector:\n'
'Backends:\n'
' Name: backend\n'
' Hash count: 3\n'
' Checksum: 2751160351\n'
' Subjects (with offsets) by hash:\n'
' A2:P:10\n'
' 0 [[0, 9, 10, 1]]\n'
' A2:T:4\n'
' 0 [[0, 9, 4, 1]]\n'
' A2:T:8\n'
' 0 [[0, 9, 8, 1]]\n'
' Landmark symbol counts:\n'
' AlphaHelix (A2): 3\n'
' Trig point symbol counts:\n'
' Peaks (P): 1\n'
' Troughs (T): 2')
self.assertEqual(expected, db.print_(printHashes=True))
