[BioRuby-cvs] bioruby/lib/bio/appl/hmmer report.rb,1.4,1.5

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/hmmer
In directory pub.open-bio.org:/tmp/cvs-serv1761

Modified Files:
	report.rb 
Log Message:
* bug fixed by Masashi Fujita (2005/5/26) -- sometimes sequence position
  in HMMER report becomes '-' instead of digits according to the alignment.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/hmmer/report.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** report.rb	26 Feb 2003 02:58:23 -0000	1.4
--- report.rb	9 Aug 2005 09:58:19 -0000	1.5
***************
*** 62,66 ****
          $1.split(/^\S+.*?\n/).slice(1..-1).each_with_index do |al,k|
            al2 = al.gsub(/\n\n/,"\n").to_s.collect { |l|
! 	    l.sub(/^.{19}/,'').sub(/\s\d+\s*$/,'')
  	  }
            align = ['', '', '']
--- 62,66 ----
          $1.split(/^\S+.*?\n/).slice(1..-1).each_with_index do |al,k|
            al2 = al.gsub(/\n\n/,"\n").to_s.collect { |l|
! 	    l.sub(/^.{19}/,'').sub(/\s(\d+|-)\s*$/,'')
  	  }
            align = ['', '', '']
***************
*** 121,125 ****
          def initialize(data, is_hmmsearch)
            @is_hmmsearch = is_hmmsearch
!          
  	  @accession, @domain, seq_f, seq_t, @seq_ft, hmm_f, hmm_t, @hmm_ft,
  	    score, evalue = data.split(' ')
--- 121,125 ----
          def initialize(data, is_hmmsearch)
            @is_hmmsearch = is_hmmsearch
! 
  	  @accession, @domain, seq_f, seq_t, @seq_ft, hmm_f, hmm_t, @hmm_ft,
  	    score, evalue = data.split(' ')