lib/bio/db/kegg/common.rb in bio-1.4.0 vs lib/bio/db/kegg/common.rb in bio-1.4.1

@@ -1,9 +1,9 @@
 #
 # = bio/db/kegg/common.rb - Common methods for KEGG database classes
 #
-# Copyright::  Copyright (C) 2003-2007 Toshiaki Katayama <[e-mail]>
+# Copyright::  Copyright (C) 2001-2007 Toshiaki Katayama <[e-mail]>
 # Copyright::  Copyright (C) 2003 Masumi Itoh <[e-mail]>
 # Copyright::  Copyright (C) 2009 Kozo Nishida <[e-mail]>
 # License::    The Ruby License
 #
 #
@@ -21,10 +21,73 @@
 class KEGG
 
   # Namespace for methods commonly used in the Bio::KEGG::* classes.
   module Common
 
+    # The module provides references method.
+    module References
+      # REFERENCE -- Returns contents of the REFERENCE records as an Array of
+      # Bio::Reference objects.
+      def references
+        unless @data['REFERENCE']
+          ary = []
+          toptag2array(get('REFERENCE')).each do |ref|
+            hash = Hash.new
+            subtag2array(ref).each do |field|
+              case tag_get(field)
+              when /REFERENCE/
+                cmnt = tag_cut(field).chomp
+                if /^\s*PMID\:(\d+)\s*/ =~ cmnt then
+                  hash['pubmed'] = $1
+                  cmnt = $'
+                end
+                if cmnt and !cmnt.empty? then
+                  hash['comments'] ||= []
+                  hash['comments'].push(cmnt)
+                end
+              when /AUTHORS/
+                authors = truncate(tag_cut(field))
+                authors = authors.split(/\, /)
+                authors[-1] = authors[-1].split(/\s+and\s+/) if authors[-1]
+                authors = authors.flatten.map { |a| a.sub(',', ', ') }
+                hash['authors']	= authors
+              when /TITLE/
+                hash['title']	= truncate(tag_cut(field))
+              when /JOURNAL/
+                journal = truncate(tag_cut(field))
+                case journal
+                  # KEGG style
+                when /(.*) (\d*(?:\([^\)]+\))?)\:(\d+\-\d+) \((\d+)\)$/
+                  hash['journal'] = $1
+                  hash['volume']  = $2
+                  hash['pages']   = $3
+                  hash['year']    = $4
+                  # old KEGG style
+                when /(.*) (\d+):(\d+\-\d+) \((\d+)\) \[UI:(\d+)\]$/
+                  hash['journal'] = $1
+                  hash['volume']  = $2
+                  hash['pages']   = $3
+                  hash['year']    = $4
+                  hash['medline'] = $5
+                  # Only journal name and year are available
+                when /(.*) \((\d+)\)$/
+                  hash['journal'] = $1
+                  hash['year']    = $2
+                else
+                  hash['journal'] = journal
+                end
+              end
+            end
+            ary.push(Reference.new(hash))
+          end
+          @data['REFERENCE'] = ary #.extend(Bio::References::BackwardCompatibility)
+
+        end
+        @data['REFERENCE']
+      end
+    end #module References
+
     # The module providing dblinks_as_hash methods.
     #
     # Bio::KEGG::* internal use only.
     module DblinksAsHash
 
@@ -52,11 +115,12 @@
       # Returns a Hash of the pathway ID and name in PATHWAY field.
       def pathways_as_hash
         unless defined? @pathways_as_hash then
           hash = {}
           pathways_as_strings.each do |line|
-            sign, entry_id, name = line.split(/\s+/, 3)
+            line = line.sub(/\APATH\:\s+/, '')
+            entry_id, name = line.split(/\s+/, 2)
             hash[entry_id] = name
           end
           @pathways_as_hash = hash
         end
         @pathways_as_hash
@@ -70,13 +134,13 @@
 
       # Returns a Hash of the orthology ID and definition in ORTHOLOGY field.
       def orthologs_as_hash
         unless defined? @orthologs_as_hash
           kos = {}
-          orthologs_as_strings.each do |ko|
-            entry = ko.scan(/K[0-9]{5}/)[0]
-            sign, entry_id, definition = ko.split(/\s+/, 3)
+          orthologs_as_strings.each do |line|
+            ko = line.sub(/\AKO\:\s+/, '')
+            entry_id, definition = ko.split(/\s+/, 2)
             kos[entry_id] = definition
           end
           @orthologs_as_hash = kos
         end
         @orthologs_as_hash
@@ -103,9 +167,49 @@
           @genes_as_hash = hash
         end
         @genes_as_hash
       end
     end #module GenesAsHash
+
+    # This module provides modules_as_hash method.
+    #
+    # Bio::KEGG::* internal use only.
+    module ModulesAsHash
+      # Returns MODULE field as a Hash.
+      # Each key of the hash is KEGG MODULE ID,
+      # and each value is the name of the Pathway Module.
+      # ---
+      # *Returns*:: Hash
+      def modules_as_hash
+        unless defined? @modules_s_as_hash then
+          hash = {}
+          modules_as_strings.each do |line|
+            entry_id, name = line.split(/\s+/, 2)
+            hash[entry_id] = name
+          end
+          @modules_as_hash = hash
+        end
+        @modules_as_hash
+      end
+    end #module ModulesAsHash
+
+    # This module provides strings_as_hash private method.
+    #
+    # Bio::KEGG::* internal use only.
+    module StringsAsHash
+      # (Private) Creates a hash from lines.
+      # Each line is consisted of two components, ID and description,
+      # separated with spaces. IDs must be unique with each other.
+      def strings_as_hash(lines)
+        hash = {}
+        lines.each do |line|
+          entry_id, definition = line.split(/\s+/, 2)
+          hash[entry_id] = definition
+        end
+        return hash
+      end
+      private :strings_as_hash
+    end #module StringsAsHash
 
   end #module Common
 end #class KEGG
 end #module Bio