bio 1.2.0 → 1.2.1

data/lib/bio.rb

@@ -5,12 +5,12 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id: bio.rb,v 1.87 2007/12/14 16:04:54 k Exp $
+# $Id: bio.rb,v 1.88 2007/12/29 19:19:07 k Exp $
 #
 
 module Bio
 
-  BIORUBY_VERSION = [1, 2, 0].extend(Comparable)
+  BIORUBY_VERSION = [1, 2, 1].extend(Comparable)
 
   ### Basic data types
 

data/lib/bio/alignment.rb

@@ -6,7 +6,7 @@
 #
 # License:: The Ruby License
 #
-#  $Id: alignment.rb,v 1.23 2007/07/16 12:21:39 ngoto Exp $
+#  $Id: alignment.rb,v 1.24 2007/12/26 14:08:02 ngoto Exp $
 #
 # = About Bio::Alignment
 #
@@ -93,21 +93,21 @@ module Bio
 
       # Returns regular expression for checking gap.
       def gap_regexp
-        @gap_regexp or GAP_REGEXP
+        ((defined? @gap_regexp) ? @gap_regexp : nil) or GAP_REGEXP
       end
       # regular expression for checking gap
       attr_writer :gap_regexp
 
       # Gap character.
       def gap_char
-        @gap_char or GAP_CHAR
+        ((defined? @gap_char) ? @gap_char : nil) or GAP_CHAR
       end
       # gap character
       attr_writer :gap_char
 
       # Character if the site is missing or unknown.
       def missing_char
-        @missing_char or MISSING_CHAR
+        ((defined? @missing_char) ? @missing_char : nil) or MISSING_CHAR
       end
       # Character if the site is missing or unknown.
       attr_writer :missing_char
@@ -118,7 +118,7 @@ module Bio
       # Otherwise, returns the first sequence's class.
       # If no sequences are found, returns nil.
       def seqclass
-        @seqclass or String
+        ((defined? @seqclass) ? @seqclass : nil) or String
       end
 
       # The class of the sequence.
@@ -347,7 +347,7 @@ module Bio
       # Otherwise, returns the first sequence's class.
       # If no sequences are found, returns nil.
       def seqclass
-        if @seqclass then
+        if (defined? @seqclass) and @seqclass then
           @seqclass
         else
           klass = nil
@@ -481,11 +481,12 @@ module Bio
       def each_window(window_size, step_size = 1)
         return nil if window_size < 0
         if step_size >= 0 then
-          i = nil
+          last_step = nil
           0.step(alignment_length - window_size, step_size) do |i|
             yield alignment_window(i, window_size)
+            last_step = i
           end
-          alignment_window((i+window_size)..-1)
+          alignment_window((last_step + window_size)..-1)
         else
           i = alignment_length - window_size
           while i >= 0
@@ -1820,8 +1821,9 @@ module Bio
       # Returns the key for a given sequence. If not found, returns nil.
       def index(seq)
         #(Hash-like)
-        k = nil
+        last_key = nil
         self.each_pair do |k, s|
+          last_key = k
           if s.class == seq.class then
             r = (s == seq)
           else
@@ -1829,7 +1831,7 @@ module Bio
           end
           break if r
         end
-        k
+        last_key
       end
 
       # Sequences in the alignment are duplicated.

data/lib/bio/appl/blast/format0.rb

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2003-2006 GOTO Naohisa <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: format0.rb,v 1.24 2007/12/14 16:12:17 k Exp $
+# $Id: format0.rb,v 1.25 2007/12/27 17:28:57 ngoto Exp $
 #
 # == Description
 #
@@ -223,11 +223,22 @@ module Bio
         end
 
         # Returns the bibliography reference of the BLAST software. 
+        # Note that this method shows only the first reference.
+        # When you want to get additional references,
+        # you can use <tt>references</tt> method.
         def reference
-          unless defined?(@reference)
-            @reference = @f0reference.to_s.gsub(/\s+/, ' ').strip
+          references[0]
+        end
+
+        # Returns the bibliography references of the BLAST software. 
+        # Returns an array of strings.
+        def references
+          unless defined?(@references)
+            @references = @f0references.collect do |x|
+              x.to_s.gsub(/\s+/, ' ').strip
+            end
           end #unless
-          @reference
+          @references
         end
 
         # Returns the name (filename or title) of the database.
@@ -276,7 +287,10 @@ module Bio
         # database line.
         def format0_split_headers(data)
           @f0header = data.shift
-          @f0reference = data.shift
+          @f0references = []
+          while data[0] and /\AQuery\=/ !~ data[0]
+            @f0references.push data.shift
+          end
           @f0query = data.shift
           @f0database = data.shift
         end
@@ -1020,6 +1034,10 @@ module Bio
                   pv = sc[2]
                   pv = '1' + pv if pv[0] == ?e
                   @pvalue = pv.to_f
+                elsif sc.skip(/Method\:\s*(.+)/) then
+                  # signature of composition-based statistics method
+                  # for example, "Method: Composition-based stats."
+                  @stat_method = sc[1]
                 else
                   raise ScanError
                 end
@@ -1089,6 +1107,13 @@ module Bio
           attr_reader              :hit_strand if false #dummy
           method_after_parse_score :hit_strand
 
+          # statistical method for calculating evalue and/or score
+          # (nil or a string)
+          # (note that composition-based statistics for blastp or tblastn
+          # were enabled by default after NCBI BLAST 2.2.17)
+          attr_reader              :stat_method if false #dummy
+          method_after_parse_score :stat_method
+
           # Parses alignments.
           def parse_alignment
             unless defined?(@parse_alignment)

data/lib/bio/appl/blast/wublast.rb

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2003 GOTO Naohisa <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: wublast.rb,v 1.11 2007/04/21 08:58:17 ngoto Exp $
+# $Id: wublast.rb,v 1.12 2007/12/27 17:28:57 ngoto Exp $
 #
 # == Description
 #
@@ -70,10 +70,11 @@ module Bio
         # Splits headers.
         def format0_split_headers(data)
           @f0header = data.shift
+          @f0references = []
           while r = data.first
             case r
             when /^Reference\: /
-              @f0reference = data.shift
+              @f0references.push data.shift
             when /^Copyright /
               @f0copyright = data.shift
             when /^Notice\: /

data/lib/bio/db/medline.rb

@@ -5,7 +5,7 @@
 #              Toshiaki Katayama <k@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: medline.rb,v 1.16 2007/04/05 23:35:40 trevor Exp $
+# $Id: medline.rb,v 1.17 2007/12/21 05:12:41 k Exp $
 #
 
 require 'bio/db'
@@ -25,7 +25,6 @@ module Bio
 #
 class MEDLINE < NCBIDB
 
-  # 
   def initialize(entry)
     @pubmed = Hash.new('')
 
@@ -37,6 +36,7 @@ class MEDLINE < NCBIDB
       @pubmed[tag] += line[6..-1] if line.length > 6
     end
   end
+  attr_reader :pubmed
 
 
   # returns a Reference object.
@@ -187,12 +187,18 @@ class MEDLINE < NCBIDB
   end
   alias affiliations ad
 
-
-  ### Other MEDLINE tags
-
   # AID  - Article Identifier
   #   Article ID values may include the pii (controlled publisher identifier)
   #   or doi (Digital Object Identifier).
+  def doi
+    @pubmed['AID'][/(\S+) \[doi\]/, 1]
+  end
+
+  def pii
+    @pubmed['AID'][/(\S+) \[pii\]/, 1]
+  end
+
+  ### Other MEDLINE tags
 
   # CI   - Copyright Information
   #   Copyright statement.

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

@@ -6,7 +6,7 @@
 #             Naohisa Goto <ng@bioruby.org>
 # License::   The Ruby License
 # 
-# $Id: chain.rb,v 1.8 2007/04/05 23:35:41 trevor Exp $
+# $Id: chain.rb,v 1.9 2007/12/18 13:48:42 ngoto Exp $
 #
 # = Bio::PDB::Chain
 # 
@@ -172,6 +172,12 @@ module Bio
         @residues.join('') + "TER\n" + @heterogens.join('')
       end
 
+      # returns a string containing human-readable representation
+      # of this object.
+      def inspect
+        "#<#{self.class.to_s} id=#{chain_id.inspect} model.serial=#{(model ? model.serial : nil).inspect} residues.size=#{residues.size} heterogens.size=#{heterogens.size} aaseq=#{aaseq.inspect}>"
+      end
+
       # gets an amino acid sequence of this chain from ATOM records
       def aaseq
         unless defined? @aaseq

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

@@ -6,7 +6,7 @@
 #             Naohisa Goto <ng@bioruby.org>
 # License::   The Ruby License
 #
-# $Id: model.rb,v 1.9 2007/04/05 23:35:41 trevor Exp $
+# $Id: model.rb,v 1.10 2007/12/18 13:48:42 ngoto Exp $
 #
 # = Bio::PDB::Model
 #
@@ -134,6 +134,12 @@ module Bio
         end
         return string
       end
+
+      # returns a string containing human-readable representation
+      # of this object.
+      def inspect
+        "#<#{self.class.to_s} serial=#{serial.inspect} chains.size=#{chains.size}>"
+      end
       
     end #class Model
 

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

@@ -6,7 +6,7 @@
 #             Alex Gutteridge <alexg@ebi.ac.uk>
 # License::   The Ruby License
 #
-#  $Id: pdb.rb,v 1.23 2007/07/10 10:44:46 ngoto Exp $
+#  $Id: pdb.rb,v 1.27 2007/12/28 14:43:44 ngoto Exp $
 #
 # = About Bio::PDB
 #
@@ -233,7 +233,7 @@ module Bio
         }
         klass.module_eval {
           symbolary.each do |x|
-            define_method(x) { do_parse; super }
+            define_method(x) { do_parse; super() }
           end
         }
         klass
@@ -267,7 +267,7 @@ module Bio
         }
         klass.module_eval {
           define_method(:initialize_from_string) { |str|
-            r = super
+            r = super(str)
             do_parse
             r
           }
@@ -437,7 +437,8 @@ module Bio
       def self.create_definition_hash
         hash = {}
         constants.each do |x|
-          hash[x] =  const_get(x) if /\A[A-Z][A-Z0-9]+\z/ =~ x
+          x = x.intern # keep compatibility both Ruby 1.8 and 1.9
+          hash[x] = const_get(x) if /\A[A-Z][A-Z0-9]+\z/ =~ x.to_s
         end
         if x = const_get(:Default) then
           hash.default = x
@@ -1380,22 +1381,27 @@ module Bio
       End = 
         def_rec([  2,  1, Pdb_Integer, :serial ]) # dummy field (always 0)
 
-      Definition['END'] = End
+      Definition['END'.intern] = End
 
       # Basically just look up the class in Definition hash
       # do some munging for JRNL and REMARK
       def self.get_record_class(str)
         t = fetch_record_name(str)
+        t = t.intern unless t.empty?
         if d = Definition[t] then
           return d
         end
         case t
-        when 'JRNL'
-          d = Jrnl::Definition[str[12..15].to_s.strip]
-        when 'REMARK'
+        when :JRNL
+          ts = str[12..15].to_s.strip
+          ts = ts.intern unless ts.empty?
+          d = Jrnl::Definition[ts]
+        when :REMARK
           case str[7..9].to_i
           when 1
-            d = Remark1::Definition[str[12..15].to_s.strip]
+            ts = str[12..15].to_s.strip
+            ts = ts.intern unless ts.empty?
+            d = Remark1::Definition[ts]
           when 2
             if str[28..37] == 'ANGSTROMS.' then
               d = Remark2::ANGSTROMS
@@ -1417,13 +1423,21 @@ module Bio
 
     Coordinate_fileds = {
       'MODEL'  => true,
+      :MODEL   => true,
       'ENDMDL' => true,
+      :ENDMDL  => true,
       'ATOM'   => true,
+      :ATOM    => true,
       'HETATM' => true,
+      :HETATM  => true,
       'SIGATM' => true,
+      :SIGATM  => true,
       'SIGUIJ' => true,
+      :SIGUIJ  => true,
       'ANISOU' => true,
+      :ANISOU  => true,
       'TER'    => true,
+      :TER     => true,
     }
 
     # Creates a new Bio::PDB object from given <em>str</em>.
@@ -1876,6 +1890,12 @@ module Bio
       f ? f.modNum : nil
     end
 
+    # returns a string containing human-readable representation
+    # of this object.
+    def inspect
+      "#<#{self.class.to_s} entry_id=#{entry_id.inspect}>"
+    end
+
   end #class PDB
 
 end #module Bio

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

@@ -6,7 +6,7 @@
 #              Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: residue.rb,v 1.13 2007/04/23 16:03:25 ngoto Exp $
+# $Id: residue.rb,v 1.14 2007/12/18 13:48:42 ngoto Exp $
 #
 # = Bio::PDB::Residue
 #
@@ -129,6 +129,12 @@ module Bio
         @atoms.join('')
       end
 
+      # returns a string containing human-readable representation
+      # of this object.
+      def inspect
+        "#<#{self.class.to_s} resName=#{resName.inspect} id=#{residue_id.inspect} chain.id=#{(chain ? chain.id : nil).inspect} resSeq=#{resSeq.inspect} iCode=#{iCode.inspect} atoms.size=#{atoms.size}>"
+      end
+
       # Always returns false.
       #
       # If the residue is HETATM, returns true.

data/lib/bio/sequence/common.rb

@@ -6,7 +6,7 @@
 #               Ryan Raaum <ryan@raaum.org>
 # License::     The Ruby License
 #
-# $Id: common.rb,v 1.5 2007/12/03 06:19:12 nakao Exp $
+# $Id: common.rb,v 1.6 2007/12/27 17:36:02 ngoto Exp $
 #
 
 module Bio
@@ -177,11 +177,12 @@ module Common
   # * (optional) _step_size_: Fixnum (default 1)
   # *Returns*:: new Bio::Sequence::NA/AA object
   def window_search(window_size, step_size = 1)
-    i = 0
+    last_step = 0
     0.step(self.length - window_size, step_size) do |i| 
       yield self[i, window_size]                        
+      last_step = i
     end                          
-    return self[i + window_size .. -1] 
+    return self[last_step + window_size .. -1] 
   end
 
   # Returns a float total value for the sequence given a hash of

data/test/unit/bio/test_alignment.rb

@@ -6,7 +6,7 @@
 #              2005 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_alignment.rb,v 1.11 2007/04/05 23:35:42 trevor Exp $
+#  $Id: test_alignment.rb,v 1.12 2007/12/26 13:55:40 ngoto Exp $
 #
 
 require 'pathname'
@@ -426,7 +426,7 @@ module Bio
         Sequence::AA.new('MNSA'),
         Sequence::AA.new('MHTL'),
         Sequence::AA.new('MQNV'),
-        Sequence::AA.new('MKKW'),
+        Sequence::AA.new('MKKW')
       ]
       assert_equal('*:. ', a.match_line)
       assert_equal('*:. ', a.match_line(:type => :aa))

metadata

@@ -3,8 +3,8 @@ rubygems_version: 0.9.4
 specification_version: 1
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 1.2.0
-date: 2007-12-15 00:00:00 +09:00
+  version: 1.2.1
+date: 2007-12-30 00:00:00 +09:00
 summary: Bioinformatics library
 require_paths: 
 - lib