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#
# Methods which edit the graph components without traversal
#
module RGFATools::InvertibleSegments
# Selects a random orientation for all invertible segments
# @return [RGFA] self
def randomly_orient_invertibles
segment_names.each do |sn|
if segment_same_links_both_ends?(sn)
randomly_orient_proven_invertible_segment(sn)
end
end
self
end
# Selects a random orientation for an invertible segment
# @return [RGFA] self
# @!macro segment_param
def randomly_orient_invertible(segment)
segment_name = segment.kind_of?(RGFA::Line) ? segment.name : segment
if !segment_same_links_both_ends?(segment_name)
raise "Only segments with links to the same or equivalent segments "+
"at both ends can be randomly oriented"
end
randomly_orient_proven_invertible_segment(segment_name)
self
end
private
def randomly_orient_proven_invertible_segment(segment_name)
parts = partitioned_links_of([segment_name, :E])
if parts.size == 2
tokeep1_other_end = parts[0][0].other_end([segment_name, :E])
tokeep2_other_end = parts[1][0].other_end([segment_name, :E])
elsif parts.size == 1 and parts[0].size == 2
tokeep1_other_end = parts[0][0].other_end([segment_name, :E])
tokeep2_other_end = parts[0][1].other_end([segment_name, :E])
else
return
end
return if links_of(tokeep1_other_end).size < 2
return if links_of(tokeep2_other_end).size < 2
delete_other_links([segment_name, :E], tokeep1_other_end)
delete_other_links([segment_name, :B], tokeep2_other_end)
annotate_random_orientation(segment_name)
end
def link_targets_for_cmp(segment_end)
links_of(segment_end).map {|l| l.other_end(segment_end).join}
end
def segment_same_links_both_ends?(segment_name)
e_links = link_targets_for_cmp([segment_name, :E])
b_links = link_targets_for_cmp([segment_name, :B])
return e_links == b_links
end
def segment_signature(segment_end)
s = segment!(segment_end[0])
link_targets_for_cmp(segment_end).join(",")+"\t"+
link_targets_for_cmp(segment_end.invert_end_type).join(",")+"\t"+
[:or].map do |field|
s.send(field)
end.join("\t")
end
def partitioned_links_of(segment_end)
links_of(segment_end).group_by do |l|
other_end = l.other_end(segment_end)
sig = segment_signature(other_end)
sig
end.map {|sig, par| par}
end
def annotate_random_orientation(segment_name)
segment = segment!(segment_name)
n = segment.name.to_s.split("_")
pairs = 0
pos = [1, segment.LN]
if segment.or
o = segment.or.to_s.split(",")
if o.size > 2
while o.last == o.first + "^" or o.last + "^" == o.first
pairs += 1
o.pop
o.shift
end
end
if segment.mp
pos = [segment.mp[pairs*2], segment.mp[-1-pairs*2]]
end
end
rn = segment.rn
rn ||= []
rn += pos
segment.rn = rn
n[pairs] = "(" + n[pairs]
n[-1-pairs] = n[-1-pairs] + ")"
rename(segment.name, n.join("_"))
end
end
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