def foo_test_mc_trees(self):
print 'testing mc trees:'
k = 4
for i in range(4, 4 + k):
print 'N:', i
all_bifurcating_trees = splitalg.get_bifurcating_trees(i)
all_quartets = splitalg.get_quartets(i)
# get multifurcating trees using the nine rules
mc_trees_ben = set(get_mc_trees_ben(i))
print 'number of mc trees using the nine rules:', len(mc_trees_ben)
tree_set_sets_ben = set(
frozenset(mc_tree_to_trees(tree, all_bifurcating_trees))
for tree in mc_trees_ben)
print 'number of unique bifurcating tree sets generated by these mc trees:', len(
tree_set_sets_ben)
# get multifurcating trees using a naive method
mc_trees = set(get_mc_trees(i))
print 'number of mc trees using a naive search:', len(mc_trees)
tree_set_sets = set(
frozenset(mc_tree_to_trees(tree, all_bifurcating_trees))
for tree in mc_trees)
print 'number of unique bifurcating tree sets generated by these mc trees:', len(
tree_set_sets)
# compare subsets
symmetric_difference = mc_trees_ben ^ mc_trees
print 'number of trees in the symmetric difference set:', len(
symmetric_difference)
if mc_trees_ben - mc_trees:
print 'an mc tree using the rules but not the naive:'
print(mc_trees_ben - mc_trees).pop()
if mc_trees - mc_trees_ben:
print 'an mc tree using the naive but not the rules:'
print(mc_trees - mc_trees_ben).pop()
# Look for a naive mc tree that generates a set of bifurcating trees that
# is not representable by a multiconnected tree constructed from the rules.
weird_naive_mc_trees = set()
for mc_tree in mc_trees:
if frozenset(mc_tree_to_trees(
mc_tree,
all_bifurcating_trees)) not in tree_set_sets_ben:
weird_naive_mc_trees.add(mc_tree)
if weird_naive_mc_trees:
weird_tree = weird_naive_mc_trees.pop()
print 'a naive mc tree that represents a set of trees not representable by any real mc tree:'
print weird_tree
mytrees = set(all_bifurcating_trees)
for split in weird_tree:
mytrees = get_compatible_trees(split, mytrees)
print len(mytrees), 'trees compatible with the weird tree:'
for tree in mytrees:
print tree
# find the quartets implied by the trees
quartets = get_splits_implied_by_trees(mytrees, all_quartets)
print len(
quartets
), 'quartets implied by the set of bifurcating trees:'
for q in quartets:
print q
print
def foo_test_mc_trees(self):
print 'testing mc trees:'
k = 4
for i in range(4, 4+k):
print 'N:', i
all_bifurcating_trees = splitalg.get_bifurcating_trees(i)
all_quartets = splitalg.get_quartets(i)
# get multifurcating trees using the nine rules
mc_trees_ben = set(get_mc_trees_ben(i))
print 'number of mc trees using the nine rules:', len(mc_trees_ben)
tree_set_sets_ben = set(frozenset(mc_tree_to_trees(tree, all_bifurcating_trees)) for tree in mc_trees_ben)
print 'number of unique bifurcating tree sets generated by these mc trees:', len(tree_set_sets_ben)
# get multifurcating trees using a naive method
mc_trees = set(get_mc_trees(i))
print 'number of mc trees using a naive search:', len(mc_trees)
tree_set_sets = set(frozenset(mc_tree_to_trees(tree, all_bifurcating_trees)) for tree in mc_trees)
print 'number of unique bifurcating tree sets generated by these mc trees:', len(tree_set_sets)
# compare subsets
symmetric_difference = mc_trees_ben ^ mc_trees
print 'number of trees in the symmetric difference set:', len(symmetric_difference)
if mc_trees_ben - mc_trees:
print 'an mc tree using the rules but not the naive:'
print (mc_trees_ben - mc_trees).pop()
if mc_trees - mc_trees_ben:
print 'an mc tree using the naive but not the rules:'
print (mc_trees - mc_trees_ben).pop()
# Look for a naive mc tree that generates a set of bifurcating trees that
# is not representable by a multiconnected tree constructed from the rules.
weird_naive_mc_trees = set()
for mc_tree in mc_trees:
if frozenset(mc_tree_to_trees(mc_tree, all_bifurcating_trees)) not in tree_set_sets_ben:
weird_naive_mc_trees.add(mc_tree)
if weird_naive_mc_trees:
weird_tree = weird_naive_mc_trees.pop()
print 'a naive mc tree that represents a set of trees not representable by any real mc tree:'
print weird_tree
mytrees = set(all_bifurcating_trees)
for split in weird_tree:
mytrees = get_compatible_trees(split, mytrees)
print len(mytrees), 'trees compatible with the weird tree:'
for tree in mytrees:
print tree
# find the quartets implied by the trees
quartets = get_splits_implied_by_trees(mytrees, all_quartets)
print len(quartets), 'quartets implied by the set of bifurcating trees:'
for q in quartets:
print q
print
def __init__(self, N):
self.N = N
self.all_quartets = list(splitalg.get_quartets(N))
self.all_splits = list(splitalg.get_informative_partial_splits(N))
def __init__(self, N):
self.N = N
self.all_quartets = list(splitalg.get_quartets(N))
self.all_splits = list(splitalg.get_informative_partial_splits(N))