[BioRuby-cvs] bioruby/lib/bio alignment.rb,1.13,1.14

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv25760/lib/bio

Modified Files:
	alignment.rb 
Log Message:
fixed bugs in EnumerableExtension#alignment_rstrip! and #remove_all_gaps!.


Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** alignment.rb	2 Dec 2005 07:01:37 -0000	1.13
--- alignment.rb	2 Dec 2005 12:01:28 -0000	1.14
***************
*** 735,739 ****
          each_site_step(len - 1, 0, -1) do |a|
            a.remove_gaps!
!           if a.empty then
              newlen -= 1
            else
--- 735,739 ----
          each_site_step(len - 1, 0, -1) do |a|
            a.remove_gaps!
!           if a.empty? then
              newlen -= 1
            else
***************
*** 743,747 ****
          return nil if newlen >= len
          each_seq do |s|
!           s[len..-1] = '' if s.length > len
          end
          self
--- 743,747 ----
          return nil if newlen >= len
          each_seq do |s|
!           s[newlen..-1] = '' if s.length > newlen
          end
          self
***************
*** 792,796 ****
          ret = nil
          each_seq do |s|
!           ret ||= s.gsub!(gap_regexp, '')
          end
          ret ? self : nil
--- 792,797 ----
          ret = nil
          each_seq do |s|
!           x = s.gsub!(gap_regexp, '')
!           ret ||= x
          end
          ret ? self : nil