+
+ # Connects two vertices, creating and storing a new edge
+ # Also adds the vertices, unless they're already in the graph
+ def connect(vertex1, vertex2, edge_attributes = {})
+ self.vertices << vertex1 unless self.vertices.include? vertex1
+ self.vertices << vertex2 unless self.vertices.include? vertex2
+ edge = Edge.new(edge_attributes)
+ self.edges << edge
+ edge << vertex1 << vertex2
+ end
+
+ # Form a product graph of this graph and the other.
+ # Return the product graph.
+ def product(other)
+ product_graph = Graph.new
+ self.vertices.each do |v1|
+ other.vertices.each do |v2|
+ product_graph << Vertex.new({:g1_vertex => v1, :g2_vertex => v2})
+ end
+ end
+ self.edges.each do |e1|
+ e1_vertices = e1.vertices
+ other.edges.each do |e2|
+ if e1.type == e2.type
+ e2_vertices = e2.vertices
+ source = product_graph.vertices.find {|v| v.g1_vertex == e1_vertices[0] and v.g2_vertex == e2_vertices[0]}
+ destination = product_graph.vertices.find {|v| v.g1_vertex == e1_vertices[1] and v.g2_vertex == e2_vertices[1]}
+ product_graph.connect source, destination
+ source = product_graph.vertices.find {|v| v.g1_vertex == e1_vertices[0] and v.g2_vertex == e2_vertices[1]}
+ destination = product_graph.vertices.find {|v| v.g1_vertex == e1_vertices[1] and v.g2_vertex == e2_vertices[0]}
+ product_graph.connect source, destination
+ end
+ end
+ end
+ product_graph.vertices.reject! {|v| v.neighbours.empty?}
+ product_graph
+ end
+
+
+ def initial_similarity
+ self.vertices.each do |v|
+ if block_given?
+ v.initial_similarity = yield v
+ else
+ v.initial_similarity = 1.0
+ end
+ v.similarity = v.initial_similarity
+ end
+ end
+
+ # Performs similarity flooding on a graph
+ # Assumes that the initial similarity has already been calculated
+ def similarity_flood(opts = {})
+ max_iterations = opts[:iterations] || 100
+ max_residual = opts[:max_residual] || 0.001
+ iteration = 1
+ residual = max_residual + 1
+ while residual > max_residual and iteration <= max_iterations
+ $log.debug { "Starting iteration #{iteration}" }
+ self.vertices.each do |v|
+ v.last_similarity = v.similarity
+ end
+ self.vertices.each do |v|
+ if block_given?
+ v.similarity = yield v
+ else
+ $log.debug { "Processing vertex #{v.name}" }
+ edge_groups = v.edges.group_by {|e| e.type }
+ $log.debug { " Edge groups {#{edge_groups.keys.map {|t| t.to_s + ' => {' + edge_groups[t].map {|e| e.to_s}.join(', ')}.join('; ')}}" }
+ edge_groups.each do |type, edges|
+ $log.debug { " Processing group type #{type}" }
+ n = edges.length
+ edges.each do |e|
+ e.other_end(v).similarity += v.last_similarity / n
+ end
+ end
+ end
+ end
+# self.vertices.each do |v|
+# n = v.neighbours.length
+# v.neighbours.each do |neighbour|
+# neighbour.similarity += v.last_similarity / n
+# end
+# end
+ max_similarity = vertices.map {|v| v.similarity}.max
+ self.vertices.each do |v|
+ v.similarity = v.similarity / max_similarity
+ end
+ residual = Math.sqrt(self.vertices.reduce(0) {|a, v| a += (v.similarity - v.last_similarity) ** 2})
+ $log.debug { puts "Residual = #{residual.round(3)}, sims = #{self.vertices.map {|v| v.name + " = " + v.similarity.round(2).to_s}}" }
+ iteration += 1
+ end
+
+ end
+
+ end # class