bio 1.0.0 → 1.1.0

data/lib/bio/tree.rb

@@ -0,0 +1,850 @@
+#
+# = bio/tree.rb - phylogenetic tree data structure class
+#
+# Copyright::   Copyright (C) 2006
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: tree.rb,v 1.8 2007/04/05 23:35:39 trevor Exp $
+#
+
+require 'matrix'
+require 'bio/pathway'
+
+module Bio
+
+  # This is the class for phylogenetic tree.
+  # It stores a phylogenetic tree.
+  # 
+  # Internally, it is based on Bio::Pathway class.
+  # However, users cannot handle Bio::Pathway object directly.
+  #
+  # This is alpha version. Incompatible changes may be made frequently.
+  class Tree
+
+    # Error when there are no path between specified nodes
+    class NoPathError < RuntimeError; end
+
+    # Edge object of each node.
+    # By default, the object doesn't contain any node information.
+    class Edge
+
+      # creates a new edge.
+      def initialize(distance = nil)
+        if distance.kind_of?(Numeric)
+          self.distance = distance
+        elsif distance
+          self.distance_string = distance
+        end
+      end
+
+      # evolutionary distance
+      attr_reader :distance
+
+      # evolutionary distance represented as a string
+      attr_reader :distance_string
+
+      # set evolutionary distance value
+      def distance=(num)
+        @distance = num
+        @distance_string = (num ? num.to_s : num)
+      end
+
+      # set evolutionary distance value from a string
+      def distance_string=(str)
+        if str.to_s.strip.empty?
+          @distance = nil
+          @distance_string = str
+        else
+          @distance = str.to_f
+          @distance_string = str
+        end
+      end
+
+      # visualization of this object
+      def inspect
+        "<Edge distance=#{@distance.inspect}>"
+      end
+
+      # string representation of this object
+      def to_s
+        @distance_string.to_s
+      end
+
+      #---
+      # methods for NHX (New Hampshire eXtended) and/or PhyloXML
+      #+++
+
+      # log likelihood value (:L in NHX)
+      attr_accessor :log_likelihood
+
+      # width of the edge
+      # (<branch width="w"> of PhyloXML, or :W="w" in NHX)
+      attr_accessor :width
+
+      # Other NHX parameters. Returns a Hash.
+      # Note that :L and :W
+      # are not stored here but stored in the proper attributes in this class.
+      # However, if you force to set these parameters in this hash,
+      # the parameters in this hash are preferred when generating NHX.
+      # In addition, If the same parameters are defined at Node object,
+      # the parameters in the node are preferred.
+      def nhx_parameters
+        @nhx_parameters ||= {}
+        @nhx_parameters
+      end
+
+    end #class Edge
+
+    # Gets distance value from the given edge.
+    # Returns float or any other numeric value or nil.
+    def get_edge_distance(edge)
+      begin
+        dist = edge.distance
+      rescue NoMethodError
+        dist = edge
+      end
+      dist
+    end
+
+    # Gets distance string from the given edge.
+    # Returns a string or nil.
+    def get_edge_distance_string(edge)
+      begin
+        dist = edge.distance_string
+      rescue NoMethodError
+        dist = (edge ? edge.to_s : nil)
+      end
+      dist
+    end
+
+    # Returns edge1 + edge2
+    def get_edge_merged(edge1, edge2)
+      dist1 = get_edge_distance(edge1)
+      dist2 = get_edge_distance(edge2)
+      if dist1 and dist2 then
+        Edge.new(dist1 + dist2)
+      elsif dist1 then
+        Edge.new(dist1)
+      elsif dist2 then
+        Edge.new(dist2)
+      else
+        Edge.new
+      end
+    end
+
+    # Node object.
+    class Node
+
+      # Creates a new node.
+      def initialize(name = nil)
+        @name = name if name
+      end
+
+      # name of the node
+      attr_accessor :name
+
+      # bootstrap value
+      attr_reader :bootstrap
+
+      # bootstrap value as a string
+      attr_reader :bootstrap_string
+
+      # sets a bootstrap value
+      def bootstrap=(num)
+        @bootstrap_string = (num ? num.to_s : num)
+        @bootstrap = num
+      end
+
+      # sets a bootstrap value from a string
+      def bootstrap_string=(str)
+        if str.to_s.strip.empty?
+          @bootstrap = nil
+          @bootstrap_string = str
+        else
+          i = str.to_i
+          f = str.to_f
+          @bootstrap = (i == f ? i : f)
+          @bootstrap_string = str
+        end
+      end
+
+      # visualization of this object
+      def inspect
+        if @name and !@name.empty? then
+          str = "(Node:#{@name.inspect}"
+        else
+          str = sprintf('(Node:%x', (self.__id__ << 1) & 0xffffffff)
+        end
+        str += " bootstrap=#{@bootstrap.inspect}" if @bootstrap
+        str += ")"
+        str
+      end
+
+      # string representation of this object
+      def to_s
+        @name.to_s
+      end
+
+      # the order of the node
+      # (lower value, high priority)
+      attr_accessor :order_number
+
+      #---
+      # methods for NHX (New Hampshire eXtended) and/or PhyloXML
+      #+++
+
+      # Phylogenetic events.
+      # Returns an Array of one (or more?) of the following symbols
+      #   :gene_duplication
+      #   :speciation
+      def events
+        @events ||= []
+        @events
+      end
+
+      # EC number (EC_number in PhyloXML, or :E in NHX)
+      attr_accessor :ec_number
+
+      # scientific name (scientific_name in PhyloXML, or :S in NHX)
+      attr_accessor :scientific_name
+
+      # taxonomy identifier (taxonomy_identifier in PhyloXML, or :T in NHX)
+      attr_accessor :taxonomy_id
+
+      # Other NHX parameters. Returns a Hash.
+      # Note that :D, :E, :S, and :T
+      # are not stored here but stored in the proper attributes in this class.
+      # However, if you force to set these parameters in this hash,
+      # the parameters in this hash are preferred when generating NHX.
+      def nhx_parameters
+        @nhx_parameters ||= {}
+        @nhx_parameters
+      end
+
+    end #class Node
+
+    # Gets node name
+    def get_node_name(node)
+      begin
+        node.name
+      rescue NoMethodError
+        node.to_s
+      end
+    end
+
+    def get_node_bootstrap(node)
+      begin
+        node.bootstrap
+      rescue NoMethodError
+        nil
+      end
+    end
+
+    def get_node_bootstrap_string(node)
+      begin
+        node.bootstrap_string
+      rescue NoMethodError
+        nil
+      end
+    end
+
+    # Creates a new phylogenetic tree.
+    # When no arguments are given, it creates a new empty tree.
+    # When a Tree object is given, it copies the tree.
+    # Note that the  new tree shares Node and Edge objects
+    # with the given tree.
+    def initialize(tree = nil)
+      # creates an undirected adjacency list graph
+      @pathway = Bio::Pathway.new([], true)
+      @root = nil
+      @options = {}
+      self.concat(tree) if tree
+    end
+
+    # root node of this tree
+    # (even if unrooted tree, it is used by some methods)
+    attr_accessor :root
+
+    # tree options; mainly used for tree output
+    attr_accessor :options
+
+    # Clears all nodes and edges.
+    # Returns self.
+    # Note that options and root are also cleared.
+    def clear
+      initialize
+      self
+    end
+
+    # Returns all nodes as an array.
+    def nodes
+      @pathway.graph.keys
+    end
+
+    # Number of nodes.
+    def number_of_nodes
+      @pathway.nodes
+    end
+
+    # Iterates over each node of this tree.
+    def each_node(&x) #:yields: node
+      @pathway.graph.each_key(&x)
+      self
+    end
+
+    # Iterates over each edges of this tree.
+    def each_edge #:yields: source, target, edge
+      @pathway.relations.each do |rel|
+        yield rel.node[0], rel.node[1], rel.relation
+      end
+      self
+    end
+
+    # Returns all edges an array of [ node0, node1, edge ]
+    def edges
+      @pathway.relations.collect do |rel|
+        [ rel.node[0], rel.node[1], rel.relation ]
+      end
+    end
+
+    # Returns number of edges in the tree.
+    def number_of_edges
+      @pathway.relations.size
+    end
+
+    # Returns an array of adjacent nodes of the given node.
+    def adjacent_nodes(node)
+      h = @pathway.graph[node]
+      h ? h.keys : []
+    end
+
+    # Returns all connected edges with adjacent nodes.
+    # Returns an array of the array [ source, target, edge ].
+    #
+    # The reason why the method name is "out_edges" is that
+    # it comes from the Boost Graph Library.
+    def out_edges(source)
+      h = @pathway.graph[source]
+      if h
+        h.collect { |key, val| [ source, key, val ] }
+      else
+        []
+      end
+    end
+
+    # Iterates over each connected edges of the given node.
+    # Returns self.
+    #
+    # The reason why the method name is "each_out_edge" is that
+    # it comes from the Boost Graph Library.
+    def each_out_edge(source) #:yields: source, target, edge
+      h = @pathway.graph[source]
+      h.each { |key, val| yield source, key, val } if h
+      self
+    end
+
+    # Returns number of edges in the given node.
+    #
+    # The reason why the method name is "out_degree" is that
+    # it comes from the Boost Graph Library.
+    def out_degree(source)
+      h = @pathway.graph[source]
+      h ? h.size : 0
+    end
+
+    # Returns an edge from source to target.
+    # If source and target are not adjacent nodes, returns nil.
+    def get_edge(source, target)
+      h = @pathway.graph[source]
+      h ? h[target] : nil
+    end
+
+    # Adds a new edge to the tree.
+    # Returns the newly added edge.
+    # If the edge already exists, it is overwritten with new one.
+    def add_edge(source, target, edge = Edge.new)
+      @pathway.append(Bio::Relation.new(source, target, edge))
+      edge
+    end
+
+    # Finds a node in the tree by given name and returns the node.
+    # If the node does not found, returns nil.
+    # If multiple nodes with the same name exist,
+    # the result would be one of those (unspecified).
+    def get_node_by_name(str)
+      self.each_node do |node|
+        if get_node_name(node) == str
+          return node
+        end
+      end
+      nil
+    end
+
+    # Adds a node to the tree.
+    # Returns self.
+    # If the node already exists, it does nothing.
+    def add_node(node)
+      @pathway.graph[node] ||= {}
+      self
+    end
+
+    # If the node exists, returns true.
+    # Otherwise, returns false.
+    def include?(node)
+      @pathway.graph[node] ? true : false
+    end
+
+    # Removes all edges connected with the node.
+    # Returns self.
+    # If the node does not exist, raises IndexError.
+    def clear_node(node)
+      unless self.include?(node)
+        raise IndexError, 'the node does not exist'
+      end
+      @pathway.relations.delete_if do |rel|
+        rel.node.include?(node)
+      end
+      @pathway.graph[node].each_key do |k|
+        @pathway.graph[k].delete(node)
+      end
+      @pathway.graph[node].clear
+      self
+    end
+
+    # Removes the given node from the tree.
+    # All edges connected with the node are also removed.
+    # Returns self.
+    # If the node does not exist, raises IndexError.
+    def remove_node(node)
+      self.clear_node(node)
+      @pathway.graph.delete(node)
+      self
+    end
+
+    # Removes each node if the block returns not nil.
+    # All edges connected with the removed nodes are also removed.
+    # Returns self.
+    def remove_node_if
+      all = self.nodes
+      all.each do |node|
+        if yield node then
+          self.clear_node(node)
+          @pathway.graph.delete(node)
+        end
+      end
+      self
+    end
+
+    # Removes an edge between source and target.
+    # Returns self.
+    # If the edge does not exist, raises IndexError.
+    #---
+    # If two or more edges exists between source and target,
+    # all of them are removed.
+    #+++
+    def remove_edge(source, target)
+      unless self.get_edge(source, target) then
+        raise IndexError, 'edge not found'
+      end
+      fwd = [ source, target ]
+      rev = [ target, source ]
+      @pathway.relations.delete_if do |rel|
+        rel.node == fwd or rel.node == rev
+      end
+      h = @pathway.graph[source]
+      h.delete(target) if h
+      h = @pathway.graph[target]
+      h.delete(source) if h
+      self
+    end
+
+    # Removes each edge if the block returns not nil.
+    # Returns self.
+    def remove_edge_if #:yields: source, target, edge
+      removed_rel = []
+      @pathway.relations.delete_if do |rel|
+        if yield rel.node[0], rel.node[1], edge then
+          removed_rel << rel
+          true
+        end
+      end
+      removed_rel.each do |rel|
+        source = rel[0]
+        target = rel[1]
+        h = @pathway.graph[source]
+        h.delete(target) if h
+        h = @pathway.graph[target]
+        h.delete(source) if h
+      end
+      self
+    end
+
+    # Replaces each node by each block's return value.
+    # Returns self.
+    def collect_node! #:yields: node
+      tr = {}
+      self.each_node do |node|
+        tr[node] = yield node
+      end
+      # replaces nodes in @pathway.relations
+      @pathway.relations.each do |rel|
+        rel.node.collect! { |node| tr[node] }
+      end
+      # re-generates @pathway from relations
+      @pathway.to_list
+      # adds orphan nodes
+      tr.each_value do |newnode|
+        @pathway.graph[newnode] ||= {}
+      end
+      self
+    end
+
+    # Replaces each edge by each block's return value.
+    # Returns self.
+    def collect_edge! #:yields: source, target, edge
+      @pathway.relations.each do |rel|
+        newedge = yield rel.node[0], rel.node[1], rel.relation
+        rel.relation = newedge
+        @pathway.append(rel, false)
+      end
+      self
+    end
+
+    # Gets the sub-tree consisted of given nodes.
+    # _nodes_ must be an array of nodes.
+    # Nodes that do not exist in the original tree are ignored.
+    # Returns a Tree object.
+    # Note that the sub-tree shares Node and Edge objects
+    # with the original tree.
+    def subtree(nodes)
+      nodes = nodes.find_all do |x|
+        @pathway.graph[x]
+      end
+      return self.class.new if nodes.empty?
+      # creates subtree
+      new_tree = self.class.new
+      nodes.each do |x|
+        new_tree.add_node(x)
+      end
+      self.each_edge do |node1, node2, edge|
+        if new_tree.include?(node1) and new_tree.include?(node2) then
+          new_tree.add_edge(node1, node2, edge)
+        end
+      end
+      return new_tree
+    end
+
+    # Gets the sub-tree consisted of given nodes and
+    # all internal nodes connected between given nodes.
+    # _nodes_ must be an array of nodes.
+    # Nodes that do not exist in the original tree are ignored.
+    # Returns a Tree object.
+    # The result is unspecified for cyclic trees.
+    # Note that the sub-tree shares Node and Edge objects
+    # with the original tree.
+    def subtree_with_all_paths(nodes)
+      hash = {}
+      nodes.each { |x| hash[x] = true }
+      nodes.each_index do |i|
+        node1 = nodes[i]
+        (0...i).each do |j|
+          node2 = nodes[j]
+          unless node1 == node2 then
+            begin
+              path = self.path(node1, node2)
+            rescue IndexError, NoPathError
+              path = []
+            end
+            path.each { |x| hash[x] = true }
+          end
+        end
+      end
+      self.subtree(hash.keys)
+    end
+
+    # Concatenates the other tree.
+    # If the same edge exists, the edge in _other_ is used.
+    # Returns self.
+    # The result is unspecified if _other_ isn't a Tree object.
+    # Note that the Node and Edge objects in the _other_ tree are
+    # shared in the concatinated tree.
+    def concat(other)
+      #raise TypeError unless other.kind_of?(self.class)
+      other.each_node do |node|
+        self.add_node(node)
+      end
+      other.each_edge do |node1, node2, edge|
+        self.add_edge(node1, node2, edge)
+      end
+      self
+    end
+
+    # Gets path from node1 to node2.
+    # Retruns an array of nodes, including node1 and node2.
+    # If node1 and/or node2 do not exist, IndexError is raised.
+    # If node1 and node2 are not connected, NoPathError is raised.
+    # The result is unspecified for cyclic trees.
+    def path(node1, node2)
+      raise IndexError, 'node1 not found' unless @pathway.graph[node1]
+      raise IndexError, 'node2 not found' unless @pathway.graph[node2]
+      return [ node1 ] if node1 == node2
+      step, path = @pathway.bfs_shortest_path(node1, node2)
+      unless path[0] == node1 and path[-1] == node2 then
+        raise NoPathError, 'node1 and node2 are not connected'
+      end
+      path
+    end
+
+    # Iterates over each edge from node1 to node2.
+    # The result is unspecified for cyclic trees.
+    def each_edge_in_path(node1, node2)
+      path = self.path(node1, node2)
+      source = path.shift
+      path.each do |target|
+        edge = self.get_edge(source, target)
+        yield source, target, edge
+        source = target
+      end
+      self
+    end
+
+    # Returns distance between node1 and node2.
+    # It would raise error if the edges didn't contain distance values.
+    # The result is unspecified for cyclic trees.
+    def distance(node1, node2)
+      distance = 0
+      self.each_edge_in_path(node1, node2) do |source, target, edge|
+        distance += get_edge_distance(edge)
+      end
+      distance
+    end
+
+    # Gets the parent node of the _node_.
+    # If _root_ isn't specified or _root_ is <code>nil</code>, @root is used.
+    # Returns an <code>Node</code> object or nil.
+    # The result is unspecified for cyclic trees.
+    def parent(node, root = nil)
+      root ||= @root
+      self.path(root, node)[-2]
+    end
+
+    # Gets the adjacent children nodes of the _node_.
+    # If _root_ isn't specified or _root_ is <code>nil</code>, @root is used.
+    # Returns an array of <code>Node</code>s.
+    # The result is unspecified for cyclic trees.
+    def children(node, root = nil)
+      root ||= @root
+      path = self.path(root, node)
+      result = self.adjacent_nodes(node)
+      result -= path
+      result
+    end
+
+    # Gets all descendent nodes of the _node_.
+    # If _root_ isn't specified or _root_ is <code>nil</code>, @root is used.
+    # Returns an array of <code>Node</code>s.
+    # The result is unspecified for cyclic trees.
+    def descendents(node, root = nil)
+      root ||= @root
+      distance, route = @pathway.breadth_first_search(root)
+      d = distance[node]
+      result = []
+      distance.each do |key, val|
+        if val > d then
+          x = key
+          while x = route[x]
+            if x == node then
+              result << key
+              break
+            end
+            break if distance[x] <= d
+          end
+        end
+      end
+      result
+    end
+
+    # If _node_ is nil, returns an array of 
+    # all leaves (nodes connected with one edge).
+    # Otherwise, gets all descendent leaf nodes of the _node_.
+    # If _root_ isn't specified or _root_ is <code>nil</code>, @root is used.
+    # Returns an array of <code>Node</code>s.
+    # The result is unspecified for cyclic trees.
+    def leaves(node = nil, root = nil)
+      unless node then
+        nodes = []
+        self.each_node do |x|
+          nodes << x if self.out_degree(x) == 1
+        end
+        return nodes
+      else
+        root ||= @root
+        self.descendents(node, root).find_all do |x|
+          self.adjacent_nodes(x).size == 1
+        end
+      end
+    end
+
+    # Gets all ancestral nodes of the _node_.
+    # If _root_ isn't specified or _root_ is <code>nil</code>, @root is used.
+    # Returns an array of <code>Node</code>s.
+    # The result is unspecified for cyclic trees.
+    def ancestors(node, root = nil)
+      root ||= @root
+      (self.path(root, node) - [ node ]).reverse
+    end
+
+    # Gets the lowest common ancestor of the two nodes.
+    # If _root_ isn't specified or _root_ is <code>nil</code>, @root is used.
+    # Returns a <code>Node</code> object or nil.
+    # The result is unspecified for cyclic trees.
+    def lowest_common_ancestor(node1, node2, root = nil)
+      root ||= @root
+      distance, route = @pathway.breadth_first_search(root)
+      x = node1; r1 = []
+      begin; r1 << x; end while x = route[x]
+      x = node2; r2 = []
+      begin; r2 << x; end while x = route[x]
+      return (r1 & r2).first
+    end
+
+    # Returns total distance of all edges.
+    # It would raise error if some edges didn't contain distance values.
+    def total_distance
+      distance = 0
+      self.each_edge do |source, target, edge|
+        distance += get_edge_distance(edge)
+      end
+      distance
+    end
+
+    # Calculates distance matrix of given nodes.
+    # If _nodes_ is nil, or is ommited, it acts the same as
+    # tree.distance_matrix(tree.leaves).
+    # Returns a matrix object.
+    # The result is unspecified for cyclic trees.
+    # Note 1: The diagonal values of the matrix are 0.
+    # Note 2: If the distance cannot be calculated, nil will be set.
+    def distance_matrix(nodes = nil)
+      nodes ||= self.leaves
+      matrix = []
+      nodes.each_index do |i|
+        row = []
+        nodes.each_index do |j|
+          if i == j then
+            distance = 0
+          elsif r = matrix[j] and val = r[i] then
+            distance = val
+          else
+            distance = (self.distance(nodes[i], nodes[j]) rescue nil)
+          end
+          row << distance
+        end
+        matrix << row
+      end
+      Matrix.rows(matrix, false)
+    end
+
+    # Shows the adjacency matrix representation of the tree.
+    # It shows matrix only for given nodes.
+    # If _nodes_ is nil or is ommitted,
+    # it acts the same as tree.adjacency_matrix(tree.nodes).
+    # If a block is given, for each edge,
+    # it yields _source_, _target_, and _edge_, and
+    # uses the returned value of the block.
+    # Without blocks, it uses edge.
+    # Returns a matrix object.
+    def adjacency_matrix(nodes = nil,
+                         default_value = nil,
+                         diagonal_value = nil) #:yields: source, target, edge
+      nodes ||= self.nodes
+      size = nodes.size
+      hash = {}
+      nodes.each_with_index { |x, i| hash[x] = i }
+      # prepares an matrix
+      matrix = Array.new(size, nil)
+      matrix.collect! { |x| Array.new(size, default_value) }
+      (0...size).each { |i| matrix[i][i] = diagonal_value }
+      # fills the matrix from each edge
+      self.each_edge do |source, target, edge|
+        i_source = hash[source]
+        i_target = hash[target]
+        if i_source and i_target then
+          val = block_given? ? (yield source, target, edge) : edge
+          matrix[i_source][i_target] = val
+          matrix[i_target][i_source] = val
+        end
+      end
+      Matrix.rows(matrix, false)
+    end
+
+    # Removes all nodes that are not branches nor leaves.
+    # That is, removes nodes connected with exactly two edges.
+    # For each removed node, two adjacent edges are merged and
+    # a new edge are created.
+    # Returns removed nodes.
+    # Note that orphan nodes are still kept unchanged.
+    def remove_nonsense_nodes
+      hash = {}
+      self.each_node do |node|
+        hash[node] = true if @pathway.graph[node].size == 2
+      end
+      hash.each_key do |node|
+        adjs = @pathway.graph[node].keys
+        edges = @pathway.graph[node].values
+        new_edge = get_edge_merged(edges[0], edges[1])
+        @pathway.graph[adjs[0]].delete(node)
+        @pathway.graph[adjs[1]].delete(node)
+        @pathway.graph.delete(node)
+        @pathway.append(Bio::Relation.new(adjs[0], adjs[1], new_edge))
+      end
+      #@pathway.to_relations
+      @pathway.relations.reject! do |rel|
+        hash[rel.node[0]] or hash[rel.node[1]]
+      end
+      return hash.keys
+    end
+
+    # Insert a new node between adjacent nodes node1 and node2.
+    # The old edge between node1 and node2 are changed to the edge
+    # between new_node and node2.
+    # The edge between node1 and new_node is newly created.
+    #
+    # If new_distance is specified, the distance between
+    # node1 and new_node is set to new_distance, and
+    # distance between new_node and node2 is set to
+    # <code>tree.get_edge(node1, node2).distance - new_distance</code>.
+    #
+    # Returns self.
+    # If node1 and node2 are not adjacent, raises IndexError.
+    #
+    # If new_node already exists in the tree, the tree would become
+    # circular. In addition, if the edge between new_node and
+    # node1 (or node2) already exists, it will be erased.
+    def insert_node(node1, node2, new_node, new_distance = nil)
+      unless edge = self.get_edge(node1, node2) then
+        raise IndexError, 'nodes not found or two nodes are not adjacent'
+      end
+      new_edge = Edge.new(new_distance)
+      self.remove_edge(node1, node2)
+      self.add_edge(node1, new_node, new_edge)
+      if new_distance and old_distance = get_edge_distance(edge) then
+        old_distance -= new_distance
+        begin
+          edge.distance = old_distance
+        rescue NoMethodError
+          edge = old_distance
+        end
+      end
+      self.add_edge(new_node, node2, edge)
+      self
+    end
+  end #class Tree
+end #module Bio
+
+#---
+# temporary added
+#+++
+require 'bio/db/newick'
+