def find_right_bound(range_interval, align, node_index, tree_info, mapping_t,
neighbors_ranges, ret_tuple_as_trans_desc):
right_bound = cur_pos = range_interval.upper_bound
while True:
if cur_pos < range_interval.lower_bound:
return -1
move = align[cur_pos]
if not align_utils.is_log_move(move, ret_tuple_as_trans_desc):
if align_utils.move_in_subtree(move,
tree_info[node_index].tree_range,
mapping_t):
break
move_in_right_neighbors = neighbors_ranges.is_in_range(
align_utils.move_index(move, mapping_t,
ret_tuple_as_trans_desc))
if align_utils.is_sync_move(
move, ret_tuple_as_trans_desc) and move_in_right_neighbors:
right_bound = cur_pos - 1
elif align_utils.is_model_move(
move, ret_tuple_as_trans_desc) and move_in_right_neighbors:
if cur_pos != right_bound:
move_move(align, cur_pos, right_bound)
right_bound -= 1
cur_pos -= 1
return right_bound
def find_left_bound(range_interval, align, node_index, tree_info, mapping_t, ret_tuple_as_trans_desc):
left_bound = range_interval.lower_bound
tree_range = tree_info[node_index].tree_range
while True:
if left_bound > range_interval.upper_bound:
return -1
move = align[left_bound]
if not align_utils.is_log_move(move, ret_tuple_as_trans_desc):
model_index = align_utils.move_index(move, mapping_t, ret_tuple_as_trans_desc)
if tree_range.is_in_range(model_index):
break
left_bound += 1
return left_bound
def remove_first_log_move(align, begin, mapping_t, subtree_range,
ret_tuple_as_trans_desc):
left_bound = begin
while True:
if left_bound == len(align):
return None
move = align[left_bound]
if not align_utils.is_log_move(move, ret_tuple_as_trans_desc):
move_cur_index = align_utils.move_index(move, mapping_t,
ret_tuple_as_trans_desc)
if subtree_range.is_in_range(move_cur_index):
break
left_bound += 1
return RangeInterval(left_bound, len(align) - 1)
def find_right_bound(range_interval, align, node_index, tree_info, mapping_t, ret_tuple_as_trans_desc):
right_bound = cur_index = range_interval.upper_bound
tree_range = tree_info[node_index].tree_range
while True:
if cur_index < range_interval.lower_bound:
return -1
move = align[cur_index]
if not align_utils.is_log_move(move, ret_tuple_as_trans_desc):
model_index = align_utils.move_index(move, mapping_t, ret_tuple_as_trans_desc)
if tree_range.is_in_range(model_index):
break
else:
right_bound = cur_index - 1
cur_index -= 1
return right_bound
def apply(align, tree_info, mapping_t, com_res, stop_condition,
ret_tuple_as_trans_desc):
ranges = list()
subtree_range = tree_info[com_res.subtree1.index].tree_range
anchor = True
range_interval = remove_first_log_move(align, 0, mapping_t, subtree_range,
ret_tuple_as_trans_desc)
if range_interval is not None:
cur_index = left_bound = right_bound = range_interval.lower_bound
while cur_index < len(align):
move = align[cur_index]
if align_utils.is_log_move(move, ret_tuple_as_trans_desc):
if anchor:
right_bound += 1
else:
move_cur_index = align_utils.move_index(
move, mapping_t, ret_tuple_as_trans_desc)
if subtree_range.is_in_range(move_cur_index):
anchor = True
right_bound = cur_index
elif stop_condition[0].is_in_range(
move_cur_index) or stop_condition[1].is_in_range(
move_cur_index):
ranges.append(RangeInterval(left_bound, right_bound))
anchor = True
range_interval = remove_first_log_move(
align, cur_index, mapping_t, subtree_range,
ret_tuple_as_trans_desc)
if range_interval is None:
break
cur_index = left_bound = right_bound = range_interval.lower_bound
else:
anchor = False
if cur_index == len(align) - 1:
ranges.append(RangeInterval(left_bound, right_bound))
cur_index += 1
return ranges
def compute_ranges_for_loop(align, tree_info, mapping_t, node_index, ranges, ret_tuple_as_trans_desc):
parent_node_index = tree_info[node_index].tree.parent.index
if node_index == parent_node_index + 1:
ub = tree_info[parent_node_index].tree_range.upper_bound
nei_ranges = RangeInterval(tree_info[node_index].tree_range.upper_bound + 1, ub)
else:
lb = tree_info[parent_node_index].tree_range.lower_bound
nei_ranges = RangeInterval(lb, tree_info[node_index].tree_range.lower_bound - 1)
new_ranges = list()
for range_interval in ranges:
ri = compute_one_range_for_sequence(align, tree_info, mapping_t, node_index, range_interval,
ret_tuple_as_trans_desc)
if ri is not None:
cur_pos = left_bound = ri.lower_bound
while cur_pos <= ri.upper_bound:
move = align[cur_pos]
if not align_utils.is_log_move(move, ret_tuple_as_trans_desc):
move_cur_index = align_utils.move_index(move, mapping_t, ret_tuple_as_trans_desc)
move_in_nei = nei_ranges.is_in_range(move_cur_index)
else:
move_in_nei = False
if move_in_nei or cur_pos == ri.upper_bound:
new_ranges.append(compute_one_range_for_sequence(align, tree_info, mapping_t, node_index,
RangeInterval(left_bound, cur_pos),
ret_tuple_as_trans_desc))
ri = compute_one_range_for_sequence(align, tree_info, mapping_t, node_index,
RangeInterval(cur_pos + 1, ri.upper_bound),
ret_tuple_as_trans_desc)
if ri is None:
break
elif ri.upper_bound == ri.lower_bound:
new_ranges.append(RangeInterval(ri.lower_bound, ri.upper_bound))
left_bound = cur_pos = ri.lower_bound
cur_pos += 1
return new_ranges
def compute_ranges_for_loop(align, tree_info, mapping_t, node_index, ranges,
ret_tuple_as_trans_desc):
parent_node_index = tree_info[node_index].tree.parent.index
if node_index == parent_node_index + 1:
ub = tree_info[parent_node_index].tree_range.upper_bound
nei_ranges = RangeInterval(
tree_info[node_index].tree_range.upper_bound + 1, ub)
else:
lb = tree_info[parent_node_index].tree_range.lower_bound
nei_ranges = RangeInterval(
lb, tree_info[node_index].tree_range.lower_bound - 1)
new_ranges = list()
for range_interval in ranges:
ri = compute_one_range_for_sequence(align, tree_info, mapping_t,
node_index, range_interval,
nei_ranges, nei_ranges,
ret_tuple_as_trans_desc)
if ri is not None:
left_bound = cur_pos = ri.lower_bound
scatter_align = False
while cur_pos <= ri.upper_bound:
move = align[cur_pos]
move_in_nei = True
if not align_utils.is_log_move(move, ret_tuple_as_trans_desc):
move_cur_index = align_utils.move_index(
move, mapping_t, ret_tuple_as_trans_desc)
move_in_nei = nei_ranges.is_in_range(move_cur_index)
scatter_align = True if move_in_nei else scatter_align
if scatter_align and align_utils.move_in_subtree(
move, tree_info[node_index].tree_range, mapping_t):
new_ranges.append(
compute_one_range_for_sequence(
align, tree_info, mapping_t, node_index,
RangeInterval(left_bound,
cur_pos - 1), nei_ranges,
nei_ranges, ret_tuple_as_trans_desc))
ri = compute_one_range_for_sequence(
align, tree_info, mapping_t, node_index,
RangeInterval(cur_pos, ri.upper_bound), nei_ranges,
nei_ranges, ret_tuple_as_trans_desc)
if ri is None:
break
left_bound = cur_pos = ri.lower_bound
scatter_align = False
if (align_utils.is_sync_move(move, True)
and move_in_nei) or cur_pos == ri.upper_bound:
new_ranges.append(
compute_one_range_for_sequence(
align, tree_info, mapping_t, node_index,
RangeInterval(left_bound, cur_pos), nei_ranges,
nei_ranges, ret_tuple_as_trans_desc))
ri = compute_one_range_for_sequence(
align, tree_info, mapping_t, node_index,
RangeInterval(cur_pos + 1, ri.upper_bound), nei_ranges,
nei_ranges, ret_tuple_as_trans_desc)
if ri is None:
break
left_bound = cur_pos = ri.lower_bound
scatter_align = False
else:
cur_pos += 1
return new_ranges