def testOneAlignment(self):
"""
When one alignment is present that alignment must be returned by
bestAlignment.
"""
alignment = Alignment(44, 'Seq 1')
alignment.addHsp(HSP(10))
alignment.addHsp(HSP(9))
alignments = [alignment]
hit = ReadAlignments(Read('id1', 'aaa'), alignments)
best = bestAlignment(hit)
self.assertEqual('Seq 1', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
def testOneAlignment(self):
"""
When one alignment is present that alignment must be returned by
bestAlignment.
"""
alignment = Alignment(44, 'Seq 1')
alignment.addHsp(HSP(10))
alignment.addHsp(HSP(9))
alignments = [alignment]
hit = ReadAlignments(Read('id1', 'aaa'), alignments)
best = bestAlignment(hit)
self.assertEqual('Seq 1', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
def testThreeAlignments(self):
"""
When three alignments are present, the one with the highest first HSP
must be returned by bestAlignment.
"""
alignment1 = Alignment(33, 'Seq 1')
alignment1.addHsp(HSP(10))
alignment1.addHsp(HSP(9))
alignment2 = Alignment(44, 'Seq 2')
alignment2.addHsp(HSP(30))
alignment2.addHsp(HSP(29))
alignment3 = Alignment(55, 'Seq 3')
alignment3.addHsp(HSP(20))
alignment3.addHsp(HSP(19))
alignments = [alignment1, alignment2, alignment3]
hit = ReadAlignments(Read('id1', 'aaa'), alignments)
best = bestAlignment(hit)
self.assertEqual('Seq 2', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
def testThreeAlignments(self):
"""
When three alignments are present, the one with the highest first HSP
must be returned by bestAlignment.
"""
alignment1 = Alignment(33, 'Seq 1')
alignment1.addHsp(HSP(10))
alignment1.addHsp(HSP(9))
alignment2 = Alignment(44, 'Seq 2')
alignment2.addHsp(HSP(30))
alignment2.addHsp(HSP(29))
alignment3 = Alignment(55, 'Seq 3')
alignment3.addHsp(HSP(20))
alignment3.addHsp(HSP(19))
alignments = [alignment1, alignment2, alignment3]
hit = ReadAlignments(Read('id1', 'aaa'), alignments)
best = bestAlignment(hit)
self.assertEqual('Seq 2', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
