[BioRuby-cvs] bioruby/lib/bio alignment.rb,1.23,1.24

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv17518/lib/bio

Modified Files:
	alignment.rb 
Log Message:
* Ruby 1.9 compliant: in EnumerableExtension#each_window and
  OriginalAlignment#index methods, local variable names outside the
  iterator loops are changed not to be shadowed by iterator variables.
* Warning messages for uninitialized instance variables of
  @gap_regexp, @gap_char, @missing_char, and @seqclass are suppressed.


Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** alignment.rb	16 Jul 2007 12:21:39 -0000	1.23
--- alignment.rb	26 Dec 2007 14:08:02 -0000	1.24
***************
*** 94,98 ****
        # Returns regular expression for checking gap.
        def gap_regexp
!         @gap_regexp or GAP_REGEXP
        end
        # regular expression for checking gap
--- 94,98 ----
        # Returns regular expression for checking gap.
        def gap_regexp
!         ((defined? @gap_regexp) ? @gap_regexp : nil) or GAP_REGEXP
        end
        # regular expression for checking gap
***************
*** 101,105 ****
        # Gap character.
        def gap_char
!         @gap_char or GAP_CHAR
        end
        # gap character
--- 101,105 ----
        # Gap character.
        def gap_char
!         ((defined? @gap_char) ? @gap_char : nil) or GAP_CHAR
        end
        # gap character
***************
*** 108,112 ****
        # Character if the site is missing or unknown.
        def missing_char
!         @missing_char or MISSING_CHAR
        end
        # Character if the site is missing or unknown.
--- 108,112 ----
        # Character if the site is missing or unknown.
        def missing_char
!         ((defined? @missing_char) ? @missing_char : nil) or MISSING_CHAR
        end
        # Character if the site is missing or unknown.
***************
*** 119,123 ****
        # If no sequences are found, returns nil.
        def seqclass
!         @seqclass or String
        end
  
--- 119,123 ----
        # If no sequences are found, returns nil.
        def seqclass
!         ((defined? @seqclass) ? @seqclass : nil) or String
        end
  
***************
*** 348,352 ****
        # If no sequences are found, returns nil.
        def seqclass
!         if @seqclass then
            @seqclass
          else
--- 348,352 ----
        # If no sequences are found, returns nil.
        def seqclass
!         if (defined? @seqclass) and @seqclass then
            @seqclass
          else
***************
*** 482,490 ****
          return nil if window_size < 0
          if step_size >= 0 then
!           i = nil
            0.step(alignment_length - window_size, step_size) do |i|
              yield alignment_window(i, window_size)
            end
!           alignment_window((i+window_size)..-1)
          else
            i = alignment_length - window_size
--- 482,491 ----
          return nil if window_size < 0
          if step_size >= 0 then
!           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((last_step + window_size)..-1)
          else
            i = alignment_length - window_size
***************
*** 1821,1826 ****
        def index(seq)
          #(Hash-like)
!         k = nil
          self.each_pair do |k, s|
            if s.class == seq.class then
              r = (s == seq)
--- 1822,1828 ----
        def index(seq)
          #(Hash-like)
!         last_key = nil
          self.each_pair do |k, s|
+           last_key = k
            if s.class == seq.class then
              r = (s == seq)
***************
*** 1830,1834 ****
            break if r
          end
!         k
        end
  
--- 1832,1836 ----
            break if r
          end
!         last_key
        end