lib/bio/db/kegg/reaction.rb in bio-1.3.1 vs lib/bio/db/kegg/reaction.rb in bio-1.4.0

@@ -1,82 +1,135 @@
 #
 # = bio/db/kegg/reaction.rb - KEGG REACTION database class
 #
 # Copyright::  Copyright (C) 2004 Toshiaki Katayama <[e-mail]>
+# Copyright::  Copyright (C) 2009 Kozo Nishida <[e-mail]>
 # License::    The Ruby License
 #
-# $Id: reaction.rb,v 1.6 2007/06/28 11:27:24 k Exp $
+# $Id:$
 #
 
 require 'bio/db'
+require 'bio/db/kegg/common'
+require 'enumerator'
 
 module Bio
 class KEGG
 
 class REACTION < KEGGDB
 
   DELIMITER	= RS = "\n///\n"
   TAGSIZE	= 12
 
+  include Common::PathwaysAsHash
+  # Returns a Hash of the pathway ID and name in PATHWAY field.
+  def pathways_as_hash; super; end if false #dummy for RDoc
+  alias pathways pathways_as_hash
+
+  include Common::OrthologsAsHash
+  # Returns a Hash of the orthology ID and definition in ORTHOLOGY field.
+  def orthologs_as_hash; super; end if false #dummy for RDoc
+  alias orthologs orthologs_as_hash
+
+  # Creates a new Bio::KEGG::REACTION object.
+  # ---
+  # *Arguments*:
+  # * (required) _entry_: (String) single entry as a string
+  # *Returns*:: Bio::KEGG::REACTION object
   def initialize(entry)
     super(entry, TAGSIZE)
   end
 
-  # ENTRY
+  # ID of the entry, described in the ENTRY line.
+  # ---
+  # *Returns*:: String
   def entry_id
     field_fetch('ENTRY')[/\S+/]
   end
 
-  # NAME
+  # Name of the reaction, described in the NAME line.
+  # ---
+  # *Returns*:: String
   def name
-    field_fetch('NAME') 
+    field_fetch('NAME')
   end
 
-  # DEFINITION
+  # Definition of the reaction, described in the DEFINITION line.
+  # ---
+  # *Returns*:: String
   def definition
     field_fetch('DEFINITION')
   end
 
-  # EQUATION
+  # Chemical equation, described in the EQUATION line.
+  # ---
+  # *Returns*:: String
   def equation
     field_fetch('EQUATION')
   end
 
-  # RPAIR
-  def rpairs
-    unless @data['RPAIR']
-      @data['RPAIR'] = fetch('RPAIR').split(/\s+/)
+  # KEGG RPAIR (ReactantPair) information, described in the RPAIR lines.
+  # ---
+  # *Returns*:: Array containing String
+  def rpairs_as_strings
+    lines_fetch('RPAIR')
+  end
+
+  # KEGG RPAIR (ReactantPair) information, described in the RPAIR lines.
+  # Returns a hash of RPair IDs and [ name, type ] informations, for example,
+  #   { "RP12733" => [ "C00022_C00900", "trans" ],
+  #     "RP05698" => [ "C00011_C00022", "leave" ],
+  #     "RP00440" => [ "C00022_C00900", "main" ]
+  #   }
+  # ---
+  # *Returns*:: Hash
+  def rpairs_as_hash
+    unless defined? @rpairs_as_hash
+      rps = {}
+      rpairs_as_strings.each do |line|
+        namespace, entry_id, name, rptype = line.split(/\s+/)
+        rps[entry_id] = [ name, rptype ]
+      end
+      @rpairs_as_hash = rps
     end
-    @data['RPAIR']
+    @rpairs_as_hash
   end
 
-  # PATHWAY
-  def pathways
-    lines_fetch('PATHWAY') 
+  alias rpairs rpairs_as_hash
+
+  # Returns the content of the RPAIR entry as tokens
+  # (RPair signature, RPair ID, , RPair type).
+  # ---
+  # *Returns*:: Array containing String
+  def rpairs_as_tokens
+    fetch('RPAIR').split(/\s+/)
   end
 
-  # ENZYME
+  # Pathway information, described in the PATHWAY lines.
+  # ---
+  # *Returns*:: Array containing String
+  def pathways_as_strings
+    lines_fetch('PATHWAY')
+  end
+
+  # Enzymes described in the ENZYME line.
+  # ---
+  # *Returns*:: Array containing String
   def enzymes
     unless @data['ENZYME']
       @data['ENZYME'] = fetch('ENZYME').scan(/\S+/)
     end
     @data['ENZYME']
   end
 
+  # Orthologs described in the ORTHOLOGY lines.
+  # ---
+  # *Returns*:: Array containing String
+  def orthologs_as_strings
+    lines_fetch('ORTHOLOGY')
+  end
+
 end # REACTION
 
 end # KEGG
 end # Bio
-
-
-if __FILE__ == $0
-  entry = ARGF.read
-  rn = Bio::KEGG::REACTION.new(entry)
-  p rn.entry_id
-  p rn.name
-  p rn.definition
-  p rn.equation
-  p rn.rpairs
-  p rn.pathways
-  p rn.enzymes
-end