def are_disjoint(tnu1, tnu2): assert table.is_record(tnu1) assert table.is_record(tnu2) if tnu1 == forest_tnu: return False if tnu2 == forest_tnu: return False if tnu1 == tnu2: return False (tnu1, tnu2) = find_peers(tnu1, tnu2) return tnu1 != tnu2
def mrca(tnu1, tnu2):
while True:
if tnu1 == forest_tnu: return forest_tnu
if tnu2 == forest_tnu: return forest_tnu
assert table.is_record(tnu1)
assert table.is_record(tnu2)
# to_accepted ??
if tnu1 == tnu2: return tnu1
(tnu1, tnu2) = find_peers(tnu1, tnu2)
assert get_mutex(tnu1) == get_mutex(tnu2)
def how_related(tnu1, tnu2):
if tnu1 == tnu2:
# If in differently checklists, this could be an incompatibility
return rel.eq
assert table.is_record(tnu1)
assert table.is_record(tnu2)
assert get_checklist(tnu1) == get_checklist(tnu2)
(peer1, peer2) = find_peers(tnu1, tnu2)
if peer1 == peer2:
if peer1 == tnu1:
return rel.gt
elif peer2 == tnu2:
return rel.lt
return rel.disjoint
def to_accepted(tnu):
if not table.is_record(tnu):
print ("Not a record: %s" % tnu)
assert False
probe = get_accepted(tnu)
if probe:
return probe
else:
return tnu
def find_peers(tnu_1, tnu_2):
assert table.is_record(tnu_1)
assert table.is_record(tnu_2)
tnu1 = to_accepted(tnu_1)
tnu2 = to_accepted(tnu_2)
if tnu1 == forest_tnu or tnu2 == forest_tnu:
return (forest_tnu, forest_tnu)
assert get_checklist(tnu1) == get_checklist(tnu2) #?
mutex1 = get_mutex(tnu1)
mutex2 = get_mutex(tnu2)
if mutex1 == mutex2:
if debug:
print ("# Kludge %s %s" % (get_unique(tnu1), get_unique(tnu2)))
tnu1 = get_parent(tnu1)
mutex1 = get_mutex(tnu1)
#print("# Mutexes are %s %s" % (mutex1, mutex2))
# Mutex of the forest is 0. Going in 0-ward direction.
while mutex1 != mutex2:
assert mutex1 >= 0
assert mutex2 >= 0
if mutex1 > mutex2:
# If p2 is closer to the root, try going rootward from p1
if tnu1 == forest_tnu: return (forest_tnu, forest_tnu)
tnu1 = get_parent(tnu1)
mutex1 = get_mutex(tnu1)
else: # mutex1 < mutex2:
# If p1 is closer to the root, try going rootward from p2
if tnu2 == forest_tnu: return (forest_tnu, forest_tnu)
tnu2 = get_parent(tnu2)
mutex2 = get_mutex(tnu2)
if debug:
print("# find_peers(%s, %s) = %s, %s" % \
(get_unique(tnu_1), get_unique(tnu_2),
get_unique(tnu1), get_unique(tnu2)))
return (tnu1, tnu2)
def get_spaceless(tnu):
if tnu == None: return "none"
if tnu == forest_tnu: return "forest"
assert table.is_record(tnu)
checklist = get_checklist(tnu)
name = get_name(tnu)
tnus_with_this_name = \
get_nodes_with_value(checklist, canonical_name, name)
if len(tnus_with_this_name) > 1:
# TBD: what if id is None? Use id of accepted?
name = name + "#" + get_taxon_id(tnu)
if not is_accepted(tnu):
name = "?" + name
# Not sure about this??
# name = name.replace(" ", "_")
return name