def get_mapping(tree1, tree2, pos, times):
recomb, coal = arghmm.find_recomb_coal(tree2, tree1, pos=pos)
states1 = list(arghmm.iter_coal_states(tree1, times))
states2 = list(arghmm.iter_coal_states(tree2, times))
for i, (node1, time1) in enumerate(states1):
j = arghmm.get_deterministic_transition(
(node1, time1), states2, times, tree2, tree1, recomb[0],
times.index(recomb[1]), coal[0], times.index(coal[1]))
node2, time2 = states2[j]
yield (node1, time1), (node2, time2)
def get_mapping(tree1, tree2, pos, times):
recomb, coal = arghmm.find_recomb_coal(tree2, tree1, pos=pos)
states1 = list(arghmm.iter_coal_states(tree1, times))
states2 = list(arghmm.iter_coal_states(tree2, times))
for i, (node1, time1) in enumerate(states1):
j = arghmm.get_deterministic_transition(
(node1, time1), states2, times, tree2, tree1,
recomb[0], times.index(recomb[1]),
coal[0], times.index(coal[1]))
node2, time2 = states2[j]
yield (node1, time1), (node2, time2)
win.add_group(argvis.draw_arg(tree, layout2))
recomb = tree[r[0]]
x, y = layout2[recomb]
win.add_group(argvis.draw_mark(x, y, col=(0, 0, 1)))
coal = last_tree[c[0]]
x, y = layout[coal]
win.add_group(argvis.draw_mark(x, y, col=(0, 1, 0)))
mapping = {}
for i, (node1, time1) in enumerate(model.states[pos-1]):
j = arghmm.get_deterministic_transition(
(node1, time1), model.states[pos], model.times, tree, last_tree,
r[0], times.index(r[1]),
c[0], times.index(c[1]))
node2, time2 = model.states[pos][j]
mapping[(node1, time1)] = (node2, time2)
x1 = layout[last_tree[node1]][0]
x2 = layout2[tree[node2]][0]
y1 = model.times[time1]
y2 = model.times[time2]
win.add_group(group(line_strip(color(0,1,0,.5),
x1, y1,
(x1+x2)/2.0, 100+(y1+y2)/2.0,
x2, y2)))
win.home("exact")
layout2[node] = (x + 20, y)
win.add_group(argvis.draw_arg(tree, layout2))
recomb = tree[r[0]]
x, y = layout2[recomb]
win.add_group(argvis.draw_mark(x, y, col=(0, 0, 1)))
coal = last_tree[c[0]]
x, y = layout[coal]
win.add_group(argvis.draw_mark(x, y, col=(0, 1, 0)))
mapping = {}
for i, (node1, time1) in enumerate(model.states[pos - 1]):
j = arghmm.get_deterministic_transition(
(node1, time1), model.states[pos], model.times, tree, last_tree,
r[0], times.index(r[1]), c[0], times.index(c[1]))
node2, time2 = model.states[pos][j]
mapping[(node1, time1)] = (node2, time2)
x1 = layout[last_tree[node1]][0]
x2 = layout2[tree[node2]][0]
y1 = model.times[time1]
y2 = model.times[time2]
win.add_group(
group(
line_strip(color(0, 1, 0, .5), x1, y1, (x1 + x2) / 2.0,
100 + (y1 + y2) / 2.0, x2, y2)))
win.home("exact")
