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#
# = sample/demo_pathway.rb - demonstration of Bio::Pathway
#
# Copyright: Copyright (C) 2001
# Toshiaki Katayama <k@bioruby.org>,
# Shuichi Kawashima <shuichi@hgc.jp>
# License:: The Ruby License
#
#
# == Description
#
# Demonstration of Bio::Pathway, an implementation of the graph data structure
# and graph algorithms.
#
# == Usage
#
# Simply run this script.
#
# $ ruby demo_pathway.rb
#
# == Development information
#
# The code was moved from lib/bio/pathway.rb.
#
require 'bio'
#if __FILE__ == $0
puts "--- Test === method true/false"
r1 = Bio::Relation.new('a', 'b', 1)
r2 = Bio::Relation.new('b', 'a', 1)
r3 = Bio::Relation.new('b', 'a', 2)
r4 = Bio::Relation.new('a', 'b', 1)
p r1 === r2
p r1 === r3
p r1 === r4
p [ r1, r2, r3, r4 ].uniq
p r1.eql?(r2)
p r3.eql?(r2)
# Sample Graph :
# +----------------+
# | |
# v |
# +---------(q)-->(t)------->(y)<----(r)
# | | | ^ |
# v | v | |
# +--(s)<--+ | (x)<---+ (u)<-----+
# | | | | |
# v | | v |
# (v)----->(w)<---+ (z)----+
data = [
[ 'q', 's', 1, ],
[ 'q', 't', 1, ],
[ 'q', 'w', 1, ],
[ 'r', 'u', 1, ],
[ 'r', 'y', 1, ],
[ 's', 'v', 1, ],
[ 't', 'x', 1, ],
[ 't', 'y', 1, ],
[ 'u', 'y', 1, ],
[ 'v', 'w', 1, ],
[ 'w', 's', 1, ],
[ 'x', 'z', 1, ],
[ 'y', 'q', 1, ],
[ 'z', 'x', 1, ],
]
ary = []
puts "--- List of relations"
data.each do |x|
ary << Bio::Relation.new(*x)
end
p ary
puts "--- Generate graph from list of relations"
graph = Bio::Pathway.new(ary)
p graph
puts "--- Test to_matrix method"
p graph.to_matrix
puts "--- Test dump_matrix method"
puts graph.dump_matrix(0)
puts "--- Test dump_list method"
puts graph.dump_list
puts "--- Labeling some nodes"
hash = { 'q' => "L1", 's' => "L2", 'v' => "L3", 'w' => "L4" }
graph.label = hash
p graph
puts "--- Extract subgraph by label"
p graph.subgraph
puts "--- Extract subgraph by list"
p graph.subgraph(['q', 't', 'x', 'y', 'z'])
puts "--- Test cliquishness of the node 'q'"
p graph.cliquishness('q')
puts "--- Test cliquishness of the node 'q' (undirected)"
u_graph = Bio::Pathway.new(ary, 'undirected')
p u_graph.cliquishness('q')
puts "--- Test small_world histgram"
p graph.small_world
puts "--- Test breadth_first_search method"
distance, predecessor = graph.breadth_first_search('q')
p distance
p predecessor
puts "--- Test bfs_shortest_path method"
step, path = graph.bfs_shortest_path('y', 'w')
p step
p path
puts "--- Test depth_first_search method"
timestamp, tree, back, cross, forward = graph.depth_first_search
p timestamp
print "tree edges : "; p tree
print "back edges : "; p back
print "cross edges : "; p cross
print "forward edges : "; p forward
puts "--- Test dfs_topological_sort method"
#
# Professor Bumstead topologically sorts his clothing when getting dressed.
#
# "undershorts" "socks"
# | | |
# v | v "watch"
# "pants" --+-------> "shoes"
# |
# v
# "belt" <----- "shirt" ----> "tie" ----> "jacket"
# | ^
# `---------------------------------------'
#
dag = Bio::Pathway.new([
Bio::Relation.new("undeershorts", "pants", true),
Bio::Relation.new("undeershorts", "shoes", true),
Bio::Relation.new("socks", "shoes", true),
Bio::Relation.new("watch", "watch", true),
Bio::Relation.new("pants", "belt", true),
Bio::Relation.new("pants", "shoes", true),
Bio::Relation.new("shirt", "belt", true),
Bio::Relation.new("shirt", "tie", true),
Bio::Relation.new("tie", "jacket", true),
Bio::Relation.new("belt", "jacket", true),
])
p dag.dfs_topological_sort
puts "--- Test dijkstra method"
distance, predecessor = graph.dijkstra('q')
p distance
p predecessor
puts "--- Test dijkstra method by weighted graph"
#
# 'a' --> 'b'
# | 1 | 3
# |5 v
# `----> 'c'
#
r1 = Bio::Relation.new('a', 'b', 1)
r2 = Bio::Relation.new('a', 'c', 5)
r3 = Bio::Relation.new('b', 'c', 3)
w_graph = Bio::Pathway.new([r1, r2, r3])
p w_graph
p w_graph.dijkstra('a')
puts "--- Test bellman_ford method by negative weighted graph"
#
# ,-- 'a' --> 'b'
# | | 1 | 3
# | |5 v
# | `----> 'c'
# | ^
# |2 | -5
# `--> 'd' ----'
#
r4 = Bio::Relation.new('a', 'd', 2)
r5 = Bio::Relation.new('d', 'c', -5)
w_graph.append(r4)
w_graph.append(r5)
p w_graph.bellman_ford('a')
p graph.bellman_ford('q')
#end
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