bio 1.4.2 → 1.4.3

data/lib/bio/db/newick.rb

@@ -6,7 +6,6 @@
 #               Daniel Amelang <dan@amelang.net>
 # License::     The Ruby License
 #
-# $Id:$
 #
 # == Description
 #
@@ -22,249 +21,6 @@ require 'strscan'
 require 'bio/tree'
 
 module Bio
-  class Tree
-
-    #---
-    # newick output
-    #+++
-
-    # default options
-    DEFAULT_OPTIONS =
-      { :indent => '  ' }
-
-    def __get_option(key, options)
-      if (r = options[key]) != nil then
-        r
-      elsif @options && (r = @options[key]) != nil then
-        r
-      else
-        DEFAULT_OPTIONS[key]
-      end
-    end
-    private :__get_option
-
-
-    # formats Newick label (unquoted_label or quoted_label)
-    def __to_newick_format_label(str, options)
-      if __get_option(:parser, options) == :naive then
-        return str.to_s
-      end
-      str = str.to_s
-      if /([\(\)\,\:\[\]\_\'\x00-\x1f\x7f])/ =~ str then
-        # quoted_label
-        return "\'" + str.gsub(/\'/, "\'\'") + "\'"
-      end
-      # unquoted_label
-      return str.gsub(/ /, '_')
-    end
-    private :__to_newick_format_label
-
-    # formats leaf
-    def __to_newick_format_leaf(node, edge, options)
-
-      label = __to_newick_format_label(get_node_name(node), options)
-
-      dist = get_edge_distance_string(edge)
-
-      bs = get_node_bootstrap_string(node)
-
-      if  __get_option(:branch_length_style, options) == :disabled
-        dist = nil
-      end
-     
-      case __get_option(:bootstrap_style, options)
-      when :disabled
-        label + (dist ? ":#{dist}" : '')
-      when :molphy
-        label + (dist ? ":#{dist}" : '') + (bs ? "[#{bs}]" : '')
-      when :traditional
-        label + (bs ? bs : '') + (dist ? ":#{dist}" : '')
-      else
-        # default: same as molphy style
-        label + (dist ? ":#{dist}" : '') + (bs ? "[#{bs}]" : '')
-      end
-    end
-    private :__to_newick_format_leaf
-
-    # formats leaf for NHX
-    def __to_newick_format_leaf_NHX(node, edge, options)
-
-      label = __to_newick_format_label(get_node_name(node), options)
-
-      dist = get_edge_distance_string(edge)
-
-      bs = get_node_bootstrap_string(node)
-
-      if  __get_option(:branch_length_style, options) == :disabled
-        dist = nil
-      end
-
-      nhx = {}
-
-      # bootstrap
-      nhx[:B] = bs if bs and !(bs.empty?)
-      # EC number
-      nhx[:E] = node.ec_number if node.instance_eval {
-        defined?(@ec_number) && self.ec_number
-      }
-      # scientific name
-      nhx[:S] = node.scientific_name if node.instance_eval {
-        defined?(@scientific_name) && self.scientific_name
-      }
-      # taxonomy id
-      nhx[:T] = node.taxonomy_id if node.instance_eval {
-        defined?(@taxonomy_id) && self.taxonomy_id
-      }
-
-      # :D (gene duplication or speciation)
-      if node.instance_eval { defined?(@events) && !(self.events.empty?) } then
-        if node.events.include?(:gene_duplication)
-          nhx[:D] = 'Y'
-        elsif node.events.include?(:speciation)
-          nhx[:D] = 'N'
-        end
-      end
-
-      # log likelihood
-      nhx[:L] = edge.log_likelihood if edge.instance_eval {
-        defined?(@log_likelihood) && self.log_likelihood }
-      # width
-      nhx[:W] = edge.width if edge.instance_eval {
-        defined?(@width) && self.width }
-
-      # merges other parameters
-      flag = node.instance_eval { defined? @nhx_parameters }
-      nhx.merge!(node.nhx_parameters) if flag
-      flag = edge.instance_eval { defined? @nhx_parameters }
-      nhx.merge!(edge.nhx_parameters) if flag
-
-      nhx_string = nhx.keys.sort{ |a,b| a.to_s <=> b.to_s }.collect do |key|
-        "#{key.to_s}=#{nhx[key].to_s}"
-      end.join(':')
-      nhx_string = "[&&NHX:" + nhx_string + "]" unless nhx_string.empty?
-     
-      label + (dist ? ":#{dist}" : '') + nhx_string
-    end
-    private :__to_newick_format_leaf_NHX
-
-    #
-    def __to_newick(parents, source, depth, format_leaf,
-                    options, &block)
-      result = []
-      if indent_string = __get_option(:indent, options) then
-        indent0 = indent_string * depth
-        indent  = indent_string * (depth + 1)
-        newline = "\n"
-      else
-        indent0 = indent = newline = ''
-      end
-      out_edges = self.out_edges(source)
-      if block_given? then
-        out_edges.sort! { |edge1, edge2| yield(edge1[1], edge2[1]) }
-      else
-        out_edges.sort! do |edge1, edge2|
-          o1 = edge1[1].order_number
-          o2 = edge2[1].order_number
-          if o1 and o2 then
-            o1 <=> o2
-          else
-            edge1[1].name.to_s <=> edge2[1].name.to_s
-          end
-        end
-      end
-      out_edges.each do |src, tgt, edge|
-        if parents.include?(tgt) then
-          ;;
-        elsif self.out_degree(tgt) == 1 then
-          result << indent + __send__(format_leaf, tgt, edge, options)
-        else
-          result << 
-            __to_newick([ src ].concat(parents), tgt, depth + 1,
-                        format_leaf, options) +
-            __send__(format_leaf, tgt, edge, options)
-        end
-      end
-      indent0 + "(" + newline + result.join(',' + newline) +
-        (result.size > 0 ? newline : '') + indent0 + ')'
-    end
-    private :__to_newick
-
-    # Returns a newick formatted string.
-    # If block is given, the order of the node is sorted
-    # (as the same manner as Enumerable#sort).
-    #
-    # Available options:
-    # <tt>:indent</tt>::
-    #     indent string; set false to disable (default: '  ')
-    # <tt>:bootstrap_style</tt>::
-    #     <tt>:disabled</tt> disables bootstrap representations.
-    #     <tt>:traditional</tt> for traditional style.
-    #     <tt>:molphy</tt> for Molphy style (default).
-    def output_newick(options = {}, &block) #:yields: node1, node2
-      root = @root
-      root ||= self.nodes.first
-      return '();' unless root
-      __to_newick([], root, 0, :__to_newick_format_leaf, options, &block) +
-        __to_newick_format_leaf(root, Edge.new, options) +
-        ";\n"
-    end
-
-    alias newick output_newick
-      
-
-    # Returns a NHX (New Hampshire eXtended) formatted string.
-    # If block is given, the order of the node is sorted
-    # (as the same manner as Enumerable#sort).
-    #
-    # Available options:
-    # <tt>:indent</tt>::
-    #     indent string; set false to disable (default: '  ')
-    #
-    def output_nhx(options = {}, &block) #:yields: node1, node2
-      root = @root
-      root ||= self.nodes.first
-      return '();' unless root
-      __to_newick([], root, 0,
-                  :__to_newick_format_leaf_NHX, options, &block) +
-        __to_newick_format_leaf_NHX(root, Edge.new, options) +
-        ";\n"
-    end
-
-    # Returns formatted text (or something) of the tree
-    # Currently supported format is: :newick, :nhx
-    def output(format, *arg, &block)
-      case format
-      when :newick
-        output_newick(*arg, &block)
-      when :nhx
-        output_nhx(*arg, &block)
-      when :phylip_distance_matrix
-        output_phylip_distance_matrix(*arg, &block)
-      else
-        raise 'Unknown format'
-      end
-    end
-
-    #---
-    # This method isn't suitable to written in this file?
-    #+++
-
-    # Generates phylip-style distance matrix as a string.
-    # if nodes is not given, all leaves in the tree are used.
-    # If the names of some of the given (or default) nodes
-    # are not defined or are empty, the names are automatically generated.
-    def output_phylip_distance_matrix(nodes = nil, options = {})
-      nodes = self.leaves unless nodes
-      names = nodes.collect do |x|
-        y = get_node_name(x)
-        y = sprintf("%x", x.__id__.abs) if y.empty?
-        y
-      end
-      m = self.distance_matrix(nodes)
-      Bio::Phylip::DistanceMatrix.generate(m, names, options)
-    end
-
-  end #class Tree
 
   #---
   # newick parser

data/lib/bio/db/pdb.rb

@@ -5,14 +5,11 @@
 # 		GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
 # License::	The Ruby License
 #
-# $Id: pdb.rb,v 1.8 2007/04/05 23:35:40 trevor Exp $
 #
 
-require 'bio/db'
-
 # definition of the PDB class
 module Bio
-  class PDB #< DB
+  class PDB
 
     autoload :ChemicalComponent, 'bio/db/pdb/chemicalcomponent'
 

data/lib/bio/db/pdb/atom.rb

@@ -6,7 +6,6 @@
 #              Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: atom.rb,v 1.8 2007/04/05 23:35:41 trevor Exp $
 #
 # = Bio::PDB::Coordinate
 #
@@ -19,9 +18,11 @@
 #
 
 require 'matrix'
-require 'bio/db/pdb'
 
 module Bio
+
+  require 'bio/db/pdb' unless const_defined?(:PDB)
+
   class PDB
 
     # Bio::PDB::Coordinate is a class to store a 3D coordinate.

data/lib/bio/db/pdb/chain.rb

@@ -6,17 +6,16 @@
 #             Naohisa Goto <ng@bioruby.org>
 # License::   The Ruby License
 # 
-# $Id: chain.rb,v 1.10 2008/04/01 10:36:44 ngoto Exp $
 #
 # = Bio::PDB::Chain
 # 
 # Please refer Bio::PDB::Chain.
 #
 
-require 'bio/db/pdb'
-
 module Bio
 
+  require 'bio/db/pdb' unless const_defined?(:PDB)
+
   class PDB
 
     # Bio::PDB::Chain is a class to store a chain.

data/lib/bio/db/pdb/chemicalcomponent.rb

@@ -5,7 +5,6 @@
 #             GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
 # License::   The Ruby License
 #
-# $Id: chemicalcomponent.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
 #
 # = About Bio::PDB::ChemicalComponent
 #
@@ -17,9 +16,11 @@
 # * http://deposit.pdb.org/het_dictionary.txt
 #
 
-require 'bio/db/pdb/pdb'
 
 module Bio
+
+  require 'bio/db/pdb' unless const_defined?(:PDB)
+
   class PDB
 
     # Bio::PDB::ChemicalComponet is a parser for a entry of

data/lib/bio/db/pdb/model.rb

@@ -6,17 +6,17 @@
 #             Naohisa Goto <ng@bioruby.org>
 # License::   The Ruby License
 #
-# $Id: model.rb,v 1.10 2007/12/18 13:48:42 ngoto Exp $
 #
 # = Bio::PDB::Model
 #
 # Please refer Bio::PDB::Model.
 #
 
-require 'bio/db/pdb'
 
 module Bio
 
+  require 'bio/db/pdb' unless const_defined?(:PDB)
+
   class PDB
 
     # Bio::PDB::Model is a class to store a model.

data/lib/bio/db/pdb/pdb.rb

@@ -22,11 +22,12 @@
 # This is beta version. Specs shall be changed frequently.
 #
 
-require 'bio/db/pdb'
 require 'bio/data/aa'
 
 module Bio
 
+  require 'bio/db/pdb' unless const_defined?(:PDB)
+
   # This is the main PDB class which takes care of parsing, annotations
   # and is the entry way to the co-ordinate data held in models.
   #

data/lib/bio/db/pdb/residue.rb

@@ -6,17 +6,17 @@
 #              Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
 #
 # = Bio::PDB::Residue
 #
 # = Bio::PDB::Heterogen
 #
 
-require 'bio/db/pdb'
 
 module Bio
 
+  require 'bio/db/pdb' unless const_defined?(:PDB)
+
   class PDB
 
     # Bio::PDB::Residue is a class to store a residue.

data/lib/bio/db/pdb/utils.rb

@@ -6,7 +6,6 @@
 #              Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: utils.rb,v 1.7 2007/04/05 23:35:41 trevor Exp $
 #
 # = Bio::PDB::Utils
 #
@@ -38,9 +37,12 @@
 #
 
 require 'matrix'
-require 'bio/db/pdb'
 
-module Bio; class PDB
+module Bio
+
+require 'bio/db/pdb' unless const_defined?(:PDB)
+
+class PDB
 
   # Utility methods for PDB data.
   # The methods in this mixin should be applicalbe to all PDB objects.
@@ -395,5 +397,6 @@ module Bio; class PDB
     end
   end #module HeterogenFinder
 
-end; end #module Bio; class PDB
+end #class PDB
+end #module Bio
 

data/lib/bio/db/phyloxml/phyloxml_parser.rb

@@ -78,15 +78,27 @@ module PhyloXML
     # Initializes LibXML::Reader and reads the file until it reaches the first
     # phylogeny element.
     #
-    # Create a new Bio::PhyloXML::Parser object.
+    # Example: Create a new Bio::PhyloXML::Parser object.
     #
     #   p = Bio::PhyloXML::Parser.open("./phyloxml_examples.xml")
     #
+    # If the optional code block is given, Bio::PhyloXML object is passed to
+    # the block as an argument. When the block terminates, the Bio::PhyloXML
+    # object is automatically closed, and the open method returns the value
+    # of the block.
+    #
+    # Example: Get the first tree in the file.
+    #
+    #   tree = Bio::PhyloXML::Parser.open("example.xml") do |px|
+    #     px.next_tree
+    #   end
+    #
     # ---
     # *Arguments*:
     # * (required) _filename_: Path to the file to parse.
     # * (optional) _validate_: Whether to validate the file against schema or not. Default value is true.
-    # *Returns*:: Bio::PhyloXML::Parser object
+    # *Returns*:: (without block) Bio::PhyloXML::Parser object
+    # *Returns*:: (with block) the value of the block
     def self.open(filename, validate=true)
       obj = new(nil, validate)
       obj.instance_eval {
@@ -98,7 +110,16 @@ module PhyloXML
                                      LibXML::XML::Parser::Options::NONET })
         _skip_leader
       }
-      obj
+      if block_given? then
+        begin
+          ret = yield obj
+        ensure
+          obj.close if obj and !obj.closed?
+        end
+        ret
+      else
+        obj
+      end
     end
 
     # Initializes LibXML::Reader and reads the file until it reaches the first
@@ -108,11 +129,17 @@ module PhyloXML
     #
     #   p = Bio::PhyloXML::Parser.open_uri("http://www.phyloxml.org/examples/apaf.xml")
     #
+    # If the optional code block is given, Bio::PhyloXML object is passed to
+    # the block as an argument. When the block terminates, the Bio::PhyloXML
+    # object is automatically closed, and the open_uri method returns the
+    # value of the block.
+    #
     # ---
     # *Arguments*:
     # * (required) _uri_: (URI or String) URI to the data to parse
     # * (optional) _validate_: For URI reader, the "validate" option is ignored and no validation is executed.
-    # *Returns*:: Bio::PhyloXML::Parser object
+    # *Returns*:: (without block) Bio::PhyloXML::Parser object
+    # *Returns*:: (with block) the value of the block
     def self.open_uri(uri, validate=true)
       case uri
       when URI
@@ -129,7 +156,15 @@ module PhyloXML
         @reader = XML::Reader.file(uri)
         _skip_leader
       }
-      obj
+      if block_given? then
+        begin
+          ret = yield obj
+        ensure
+          obj.close if obj and !obj.closed?
+        end
+      else
+        obj
+      end
     end
 
     # Special class for closed PhyloXML::Parser object.
@@ -156,6 +191,18 @@ module PhyloXML
       nil
     end
 
+    # If the object is closed by using the close method or equivalent,
+    # returns true. Otherwise, returns false.
+    # ---
+    # *Returns*:: true or false
+    def closed?
+      if @reader.kind_of?(ClosedPhyloXMLParser) then
+        true
+      else
+        false
+      end
+    end
+
     # Initializes LibXML::Reader and reads from the IO until it reaches
     # the first phylogeny element.
     #