def luup(x, y):
if x == cl.forest_tnu or y == cl.forest_tnu: return
assert cl.get_checklist(x) != cl.get_checklist(y)
if in_chain(x, y0) and in_chain(y, x0):
bar = best.get(x)
if bar and find_in_chain(bar.cod, y, x0):
if bar.cod == y:
art.proclaim(draft, art.change_relation(bar, rel.eq, "extensional"))
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(draft, art.extensional(y, x, rel.lt, "presumed 0"))
luup(x, cl.get_parent(y))
else:
bar = best.get(y)
if bar and find_in_chain(bar.cod, x, y0):
if bar.cod == y:
art.proclaim(draft, bar)
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(draft, art.extensional(x, y, rel.lt, "presumed 1"))
luup(cl.get_parent(x), y)
else:
# neither x nor y matches by name
art.proclaim(draft, art.extensional(x, y, rel.eq, "presumed mutual"))
luup(cl.get_parent(x), cl.get_parent(y))
def luup(x, y):
if x == cl.forest_tnu or y == cl.forest_tnu: return
assert cl.get_checklist(x) != cl.get_checklist(y)
if in_chain(x, y0) and in_chain(y, x0):
bar = best.get(x)
if bar and find_in_chain(bar.cod, y, x0):
if bar.cod == y:
art.proclaim(proposal, art.change_relation(bar, rel.eq, "extensional"))
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(proposal, art.extensional(y, x, rel.lt, "refines", "refined by"))
luup(x, cl.get_parent(y))
else:
bar = best.get(y)
if bar and find_in_chain(bar.cod, x, y0):
if bar.cod == y:
art.proclaim(proposal, bar)
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(proposal, art.extensional(x, y, rel.lt, "refines*", "refined by*"))
luup(cl.get_parent(x), y)
else:
# neither x nor y matches by name
art.proclaim(proposal, art.extensional(x, y, rel.eq, "similar="))
luup(cl.get_parent(x), cl.get_parent(y))
def alignment_step(x, best, xmrcas, proposal):
def luup(x, y):
if x == cl.forest_tnu or y == cl.forest_tnu: return
assert cl.get_checklist(x) != cl.get_checklist(y)
if in_chain(x, y0) and in_chain(y, x0):
bar = best.get(x)
if bar and find_in_chain(bar.cod, y, x0):
if bar.cod == y:
art.proclaim(proposal, art.change_relation(bar, rel.eq, "extensional"))
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(proposal, art.extensional(y, x, rel.lt, "refines", "refined by"))
luup(x, cl.get_parent(y))
else:
bar = best.get(y)
if bar and find_in_chain(bar.cod, x, y0):
if bar.cod == y:
art.proclaim(proposal, bar)
luup(cl.get_parent(x), cl.get_parent(y))
else:
art.proclaim(proposal, art.extensional(x, y, rel.lt, "refines*", "refined by*"))
luup(cl.get_parent(x), y)
else:
# neither x nor y matches by name
art.proclaim(proposal, art.extensional(x, y, rel.eq, "similar="))
luup(cl.get_parent(x), cl.get_parent(y))
# See is b is in the chain (matching nodes in lineage)
def find_in_chain(b, y, x0):
if y == cl.forest_tnu:
return False
elif in_chain(y, x0):
if b == y:
return True
else:
return find_in_chain(b, cl.get_parent(y), x0)
else:
return False
def in_chain(y, x0):
ar = xmrcas.get(y)
return ar and ar.cod == x0
ar = xmrcas.get(x) # x ~ y0
if ar:
y0 = ar.cod
x0 = xmrcas.get(y0).cod
if xmrcas.get(x0).cod != y0: # x < y0
art.proclaim(proposal, art.extensional(x, y0, rel.lt, "inferred"))
else: # x could be <, =, > y0. figure it out
if x0 < y0:
luup(x0, y0)
else:
pass # pick it up later (or earlier)
def subinfer_partners(x, other):
y = None
for child in cl.get_children(x):
child_ar = subinfer_partners(child, other) # an articulation
if child_ar != None:
child_y = child_ar.cod
if y == None:
y = child_y
else:
y = cl.mrca(y, child_y)
if y != None:
ar = art.extensional(x, y, rel.matches, "cross-mrca")
else:
ar = get_mutual(best, x)
if ar:
assert cl.get_checklist(ar.cod) != cl.get_checklist(x)
if dribble.watch(x):
dribble.log("# Cross-mrca: %s" % (art.express(ar)))
xmrcas[x] = ar
return ar # in B
def extensional_match(node, xmrcas):
partner = xmrcas.get(node) # node in other checklist; 'conode'
if not partner:
# Descendant of a particle
if dribble.watch(node):
dribble.log("# EM: %s is not tipward." % cl.get_unique(node))
return None
back = xmrcas.get(partner) # 'bounce'
if not back:
# Not sure how this can happen but it does (NCBI vs. GBIF)
dribble.log("%s <= %s <= nowhere" % (cl.get_unique(node),
cl.get_unique(partner)))
if dribble.watch(node):
dribble.log("# EM: %s killed because aborted round trip." % cl.get_unique(node))
return None
# node <= partner <= back
how = cl.how_related(node, back) # Alway rcc5
if how == rel.eq:
# Should end up being eq iff name match or unique match
# Can test for unique match by looking at xmrca of parent
# Could be part of a 'monotypic' chain; fix later
how = rel.matches
reason = "mutual-cross-mrca"
elif how == rel.gt:
how = rel.matches
reason = "monotypic-inversion"
elif how == rel.disjoint:
reason = "particle-set-exclusion"
else: # must be rel.lt
# Assume resolution (node < partner) until conflict is proven
reason = "refinement"
# Look for an intersection between any partner-child and node
# x is in A checklist, y is in B checklist
for pchild in cl.get_children(partner):
pchild_back = xmrcas.get(pchild)
if pchild_back == None:
# pchild ! node
pass
else:
(d, e) = cross_compare(node, pchild, xmrcas)
# d < node while e ! node
if d and e:
how = rel.conflict
reason = ("%s is in; its sibling %s is not" %
(cl.get_unique(d), cl.get_unique(e)))
dribble.log("** %s conflicts with %s because\n"
" %s ! %s\n (but sibling %s < %s)" %
(cl.get_unique(node),
cl.get_unique(partner),
cl.get_unique(e),
cl.get_unique(node),
cl.get_unique(d),
cl.get_unique(node)))
break
elif e:
reason = ("%s is not in it" % cl.get_unique(e))
ar = art.extensional(node, partner, how, reason)
if dribble.watch(node):
dribble.log("# Extensional articulation %s" % art.express(ar))
return ar