def testConflict(self): taxa = TaxonSet([str(i) for i in xrange(1,7)]) o = ['(1,5,(2,((3,6),4)));', '(2,1,(3,(6,4)));', ] m = [o[0], o[1], '(1,5,(2,(3,6,4)));'] trees = trees_from_newick_str_list(m) self.kernelOfTest(trees) rng = RepeatedRandom() for i in xrange(50): trees = trees_from_newick_str_list(m) for t in trees: randomly_reorient_tree(t, rng=rng) self.kernelOfTest(trees)
def runTest(self): n = '(Basichlsac,(Lamprothma,Mougeotisp),(((Haplomitr2,Petalaphy),((Angiopteri,(((Azollacaro,((Dennstasam,(Oleandrapi,Polypodapp)),Dicksonant)),Vittarifle),Botrychbit)),(Isoetesmel,((((Agathismac,Agathisova),Pseudotsu),(((Libocedrus,Juniperusc),Callitris),Athrotaxi)),((Liriodchi,Nelumbo),Sagittari))))),Thuidium));' k = dendropy.TreeList(stream=StringIO(n), schema="newick")[0] trees = dendropy.TreeList(stream=StringIO(n+n), schema="newick", encode_splits=True, taxon_set=k.taxon_set) ref = trees[0] changing = trees[1] rng = RepeatedRandom() for i in xrange(50): treemanip.randomly_reorient_tree(changing, rng=rng, splits=True) self.assertNotEqual(str(changing), n) changing.debug_check_tree(logger_obj=_LOG, splits=True) if treecalc.symmetric_difference(ref, changing) != 0: self.fail("\n%s\n!=\n%s" % (str(ref), str(changing)))
def testConflict(self): taxa = TaxonSet([str(i) for i in xrange(1, 7)]) o = [ '(1,5,(2,((3,6),4)));', '(2,1,(3,(6,4)));', ] m = [o[0], o[1], '(1,5,(2,(3,6,4)));'] trees = trees_from_newick_str_list(m) self.kernelOfTest(trees) rng = RepeatedRandom() for i in xrange(50): trees = trees_from_newick_str_list(m) for t in trees: randomly_reorient_tree(t, rng=rng) self.kernelOfTest(trees)