def setUp(self):
s1 = Sequence("<STR_LIT>", "<STR_LIT>", <NUM_LIT:100>, <NUM_LIT>)<EOL>s2 = Sequence("<STR_LIT>", "<STR_LIT>", <NUM_LIT:1000>, <NUM_LIT>)<EOL>s3 = Sequence("<STR_LIT>", "<STR_LIT>", <NUM_LIT>, <NUM_LIT>, "<STR_LIT:->")<EOL>self.pa1 = PairwiseAlignment(s1, s2)<EOL>self.pa2 = PairwiseAlignment(s1, s3)<EOL>self.msa1 = MultipleSequenceAlignment([s1, s2, s3])<EOL>
Set up a few alignments to use in the tests.