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begin
require "rgl/adjacency"
require "rgl/implicit"
require_relative "error"
#
# Conversion to RGL graphs
#
module RGFA::RGL
# Creates an RGL graph.
#
# @param oriented [Boolean] (defaults to: <i>+true+</i>) may the graph
# contain links of segments in different orientation?
# @return [RGL::ImplicitGraph] an rgl implicit directed graph
def to_rgl(oriented: true)
if oriented
to_rgl_oriented
else
to_rgl_unoriented
end
end
# Creates an RGL graph, including links orientations.
#
# @return [RGL::ImplicitGraph] an rgl implicit directed graph;
# where vertices are [RGFA::Segment, orientation] pairs
# (instances of the RGFA::OrientedSegment subclass of Array)
def to_rgl_oriented
RGL::ImplicitGraph.new do |g|
g.vertex_iterator do |block|
self.each_segment do |segment|
[:+, :-].each do |orient|
block.call([segment, orient].to_oriented_segment)
end
end
end
g.adjacent_iterator do |oriented_segment, block|
s = segment(oriented_segment.segment)
o = oriented_segment.orient
s.links[:from][o].each do |l|
os = [segment(l.to), l.to_orient].to_oriented_segment
block.call(os)
end
o = oriented_segment.invert_orient
s.links[:to][o].each do |l|
os = [segment(l.from), l.from_orient].to_oriented_segment
block.call(os.invert_orient)
end
end
g.directed = true
end
end
# Creates an RGL graph, assuming that all links orientations
# are "+".
#
# @raise [RGFA::RGL::ValueError] if the graph contains any link where
# from_orient or to_orient is :-
# @return [RGL::ImplicitGraph] an rgl implicit directed graph;
# where vertices are RGFA::Segment objects
def to_rgl_unoriented
RGL::ImplicitGraph.new do |g|
g.vertex_iterator {|block| self.each_segment {|s| block.call(s)}}
g.adjacent_iterator do |s, bl|
s = segment(s)
s.links[:from][:+].each do |l|
if l.to_orient == :-
raise RGFA::RGL::ValueError,
"Graph contains links with segments in reverse orientations"
end
bl.call(segment(l.to))
end
if s.links[:from][:-].size > 0
raise RGFA::RGL::ValueError,
"Graph contains links with segments in reverse orientations"
end
end
g.directed = true
end
end
def self.included(base)
base.extend(ClassMethods)
end
module ClassMethods
# @param g [RGL::ImplicitGraph, RGL::DirectedAdjacencyGraph] an RGL graph.
#
# @!macro[new] from_rgl
# <b>Accepted vertex formats</b>:
#
# - RGFA::OrientedSegment, or Array which can be converted to it;
# where the first element is a <i>segment specifier</i> (see below)
# - <i>segment specifier</i> alone: the orientation is assumed to be :+
#
# The <i>segment specifier</i> can be:
# - RGFA::Segment instance
# - String, segment representation (e.g. "S\tsegment\t*")
# - String, valid segment name (e.g. "segment")
#
# @raise [RGFA::RGL::InvalidFormatError] if the graph cannot be
# converted
#
# @return [RGFA] a new RGFA instance
def from_rgl(g)
gfa = RGFA.new
if not (g.respond_to?(:each_vertex) and
g.respond_to?(:each_edge))
raise RGFA::RGL::InvalidFormatError,
"#{g} is not a valid RGL graph"
end
if not g.directed?
raise RGFA::RGL::InvalidFormatError,
"#{g} is not a directed graph"
end
g.each_vertex {|v| add_segment_if_new(gfa, v)}
g.each_edge do |s, t|
gfa << RGFA::Line::Link.new(segment_name_and_orient(s) +
segment_name_and_orient(t) +
["*"])
end
gfa
end
private
def add_segment_if_new(gfa, v)
# RGFA::OrientedSegment or GFA::GraphVertex
v = v.segment if v.respond_to?(:segment)
if v.kind_of?(Symbol)
# segment name as symbol
return if gfa.segment_names.include?(v)
v = RGFA::Line::Segment.new([v.to_s, "*"])
elsif v.kind_of?(String)
a = v.split("\t")
if a[0] == "S"
# string representation of segment
return if gfa.segment_names.include?(a[1].to_sym)
v = RGFA::Line::Segment.new(a[1..-1])
else
# segment name as string
return if gfa.segment_names.include?(v.to_sym)
v = RGFA::Line::Segment.new([v, "*"])
end
end
return if gfa.segment_names.include?(v.name)
gfa << v
end
def segment_name_and_orient(s)
# default orientation
o = s.respond_to?(:orient) ? s.orient.to_s : "+"
# RGFA::Line::Segment (also embedded in RGFA::OrientedSegment)
if s.respond_to?(:name)
s = s.name.to_s
elsif s.respond_to?(:segment)
# GFA::GraphVertex
s = s.segment.to_s
elsif s.respond_to?(:split)
a = s.split("\t")
s = a[1] if a[0] == "S"
else
s = s.to_s
end
return s, o
end
end
end
module RGL::Graph
# @!macro from_rgl
def to_rgfa
RGFA.from_rgl(self)
end
end
# Exception raised if conversion is impossible due to unexpected values
class RGFA::RGL::ValueError < RGFA::Error; end
# Exception raised if conversion is impossible due to general format problems
class RGFA::RGL::InvalidFormatError < RGFA::Error; end
rescue LoadError
module RGFA::RGL
end
end
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