[BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.26.2.3, 1.26.2.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv12115/lib/bio/appl/blast

Modified Files:
      Tag: BRANCH-biohackathon2008
	format0.rb 
Log Message:
Merging differences between 1.28 and 1.29 into format0.rb in BRANCH-biohackathon2008.


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.26.2.3
retrieving revision 1.26.2.4
diff -C2 -d -r1.26.2.3 -r1.26.2.4
*** format0.rb	13 May 2008 11:19:42 -0000	1.26.2.3
--- format0.rb	14 May 2008 13:39:41 -0000	1.26.2.4
***************
*** 535,539 ****
                    r = data.first
                    break unless r
!                   if /^Significant alignments for pattern/ =~ r
                      data.shift
                      r = data.first
--- 535,539 ----
                    r = data.first
                    break unless r
!                   while /^Significant alignments for pattern/ =~ r
                      data.shift
                      r = data.first
***************
*** 590,596 ****
                @f0message.each do |r|
                  sc = StringScanner.new(r)
!                 if sc.skip_until(/^ *pattern +(.+)$/) then
                    @pattern = sc[1] unless @pattern
!                   sc.skip_until(/^ at position +(\d+)/)
                    @pattern_positions << sc[1].to_i
                  end
--- 590,596 ----
                @f0message.each do |r|
                  sc = StringScanner.new(r)
!                 if sc.skip_until(/^ *pattern +([^\s]+)/) then
                    @pattern = sc[1] unless @pattern
!                   sc.skip_until(/(?:^ *| +)at position +(\d+) +of +query +sequence/)
                    @pattern_positions << sc[1].to_i
                  end