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require_relative "error"
#
# Methods for the RGFA class, which allow to handle links in the graph.
#
module RGFA::Links
def add_link(gfa_line)
gfa_line = gfa_line.to_rgfa_line(validate: @validate)
gfa_line.canonicize!
l = nil
if segment(gfa_line.from) and segment(gfa_line.to)
l = link_from_to(gfa_line.oriented_from,
gfa_line.oriented_to,
gfa_line.overlap)
end
if l.nil?
@links << gfa_line
[:from, :to].each do |dir|
segment_name = gfa_line.send(dir).to_sym
orient = gfa_line.send(:"#{dir}_orient").to_sym
if !@segments.has_key?(segment_name)
raise RGFA::LineMissingError if @segments_first_order
@segments[segment_name] =
RGFA::Line::Segment.new({:name => segment_name},
virtual: true)
end
@segments[segment_name].links[dir][orient] << gfa_line
gfa_line.send(:"#{dir}=", @segments[segment_name])
end
elsif l.virtual?
l.real!(gfa_line)
else
return
end
end
protected :add_link
# Deletes a link and all paths depending on it
#
# @param l [RGFA::Line::Link] link instance
# @return [RGFA] self
def delete_link(l)
@links.delete(l)
segment(l.from).links[:from][l.from_orient].delete(l)
segment(l.to).links[:to][l.to_orient].delete(l)
l.paths.each {|pt, orient| delete_path(pt)}
end
# Remove all links of a segment end end except that to the other specified
# segment end.
# @param segment_end [RGFA::SegmentEnd] the segment end
# @param other_end [RGFA::SegmentEnd] the other segment end
# @param conserve_components [Boolean] <i>(defaults to: +false+)</i>
# Do not remove links if removing them breaks the graph into unconnected
# components.
# @return [RGFA] self
def delete_other_links(segment_end, other_end, conserve_components: false)
other_end = other_end.to_segment_end
links_of(segment_end).each do |l|
if l.other_end(segment_end) != other_end
if !conserve_components or !cut_link?(l)
delete_link(l)
end
end
end
end
# All links of the graph
# @return [Array<RGFA::Line::Link>]
def links
@links
end
# Finds links of the specified end of segment.
#
# @param [RGFA::SegmentEnd] segment_end a segment end
#
# @return [Array<RGFA::Line::Link>] if segment_end[1] == :E,
# links from sn with from_orient + and to sn with to_orient -
# @return [Array<RGFA::Line::Link>] if segment_end[1] == :B,
# links to sn with to_orient + and from sn with from_orient -
#
# @note to add or remove links, use the appropriate methods;
# adding or removing links from the returned array will not work
def links_of(segment_end)
segment_end = segment_end.to_segment_end
s = segment!(segment_end.segment)
o = segment_end.end_type == :E ? [:+,:-] : [:-,:+]
s.links[:from][o[0]] + s.links[:to][o[1]]
end
# Finds segment ends connected to the specified segment end.
#
# @param [RGFA::SegmentEnd] segment_end a segment end
#
# @return [Array<RGFA::SegmentEnd>>] segment ends connected by links
# to +segment_end+
def neighbours(segment_end)
links_of(segment_end).map {|l| l.other_end(segment_end) }
end
# Searches all links between +segment_end1+ and +segment_end2+
#
# @!macro [new] two_segment_ends
# @param segment_end1 [RGFA::SegmentEnd] a segment end
# @param segment_end2 [RGFA::SegmentEnd] a segment end
# @return [Array<RGFA::Line::Link>] (possibly empty)
def links_between(segment_end1, segment_end2)
segment_end1 = segment_end1.to_segment_end
segment_end2 = segment_end2.to_segment_end
links_of(segment_end1).select do |l|
l.other_end(segment_end1) == segment_end2
end
end
# @!macro [new] link
# Searches a link between +segment_end1+ and +segment_end2+
# @!macro two_segment_ends
# @return [RGFA::Line::Link] the first link found
# @return [nil] if no link is found.
def link(segment_end1, segment_end2)
segment_end1 = segment_end1.to_segment_end
segment_end2 = segment_end2.to_segment_end
links_of(segment_end1).each do |l|
return l if l.other_end(segment_end1) == segment_end2
end
return nil
end
# @!macro link
# @raise [RGFA::LineMissingError] if no link is found.
def link!(segment_end1, segment_end2)
l = link(segment_end1, segment_end2)
raise RGFA::LineMissingError,
"No link was found: "+
"#{segment_end1.to_s} -- "+
"#{segment_end2.to_s}" if l.nil?
l
end
# Find links from the segment in the specified orientation
# (or the equivalent links, i.e. to the segment in opposite orientation).
#
# @param [RGFA::OrientedSegment] oriented_segment a segment with orientation
# @param equivalent [Boolean] return also equivalent links.
# @return [Array<RGFA::Line::Link>]
# @note to add or remove links, use the appropriate methods;
# adding or removing links from the returned array will not work
def links_from(oriented_segment, equivalent = true)
oriented_segment = oriented_segment.to_oriented_segment
s = segment!(oriented_segment.segment)
retval = s.links[:from][oriented_segment.orient]
if equivalent
retval + s.links[:to][oriented_segment.orient_inverted]
else
retval
end
end
# Find links to the segment in the specified orientation
# (or the equivalent links, i.e. from the segment in opposite orientation).
#
# @param [RGFA::OrientedSegment] oriented_segment a segment with orientation
# @param equivalent [Boolean] return also equivalent links.
# @return [Array<RGFA::Line::Link>]
# @note to add or remove links, use the appropriate methods;
# adding or removing links from the returned array will not work
def links_to(oriented_segment, equivalent = true)
oriented_segment = oriented_segment.to_oriented_segment
s = segment!(oriented_segment.segment)
retval = s.links[:to][oriented_segment.orient]
if equivalent
retval + s.links[:from][oriented_segment.orient_inverted]
else
retval
end
end
# Search all links from a segment S1 in a given orientation
# to another segment S2 in a given, or the equivalent
# links from S2 to S1 with inverted orientations.
#
# @param [RGFA::OrientedSegment] oriented_segment1 a segment with orientation
# @param [RGFA::OrientedSegment] oriented_segment2 a segment with orientation
# @param [RGFA::CIGAR] cigar shall match if not empty/undef
# @param equivalent [Boolean] return also equivalent links.
# @return [Array<RGFA::Line::Link>]
# @note to add or remove links, use the appropriate methods;
# adding or removing links from the returned array will not work
def links_from_to(oriented_segment1, oriented_segment2,
cigar = [], equivalent = true)
oriented_segment1 = oriented_segment1.to_oriented_segment
oriented_segment2 = oriented_segment2.to_oriented_segment
links_from(oriented_segment1, equivalent).select do |l|
l.compatible?(oriented_segment1, oriented_segment2, cigar, equivalent)
end
end
# Search the link from a segment S1 in a given orientation
# to another segment S2 in a given, or the equivalent
# link from S2 to S1 with inverted orientations.
#
# @param [RGFA::OrientedSegment] oriented_segment1 a segment with orientation
# @param [RGFA::OrientedSegment] oriented_segment2 a segment with orientation
# @param [RGFA::CIGAR] cigar shall match if not empty/undef
# @param equivalent [Boolean] return also equivalent links.
# @return [RGFA::Line::Link] the first link found
# @return [nil] if no link is found.
def link_from_to(oriented_segment1, oriented_segment2,
cigar = [], equivalent = true)
oriented_segment1 = oriented_segment1.to_oriented_segment
oriented_segment2 = oriented_segment2.to_oriented_segment
links_from(oriented_segment1, equivalent).select do |l|
return l if l.compatible?(oriented_segment1, oriented_segment2,
cigar, equivalent)
end
return nil
end
# Search the link from a segment S1 in a given orientation
# to another segment S2 in a given, or the equivalent
# link from S2 to S1 with inverted orientations.
#
# @param [RGFA::OrientedSegment] oriented_segment1 a segment with orientation
# @param [RGFA::OrientedSegment] oriented_segment2 a segment with orientation
# @param [RGFA::CIGAR] cigar shall match if not empty/undef
# @param equivalent [Boolean] return also equivalent links.
# @return [RGFA::Line::Link] the first link found
# @raise [RGFA::LineMissingError] if no link is found.
def link_from_to!(oriented_segment1, oriented_segment2,
cigar = [], equivalent = true)
l = link_from_to(oriented_segment1, oriented_segment2,
cigar, equivalent)
raise RGFA::LineMissingError,
"No link was found: "+
"#{oriented_segment1.join(":")} -> "+
"#{oriented_segment2.join(":")}" if l.nil?
l
end
end
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