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)
