[BioRuby-cvs] bioruby/lib/bio/appl/bl2seq report.rb,1.1,1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq
In directory pub.open-bio.org:/tmp/cvs-serv6477/lib/bio/appl/bl2seq

Modified Files:
	report.rb 
Log Message:
* renamed to Bio::Blast::Bl2seq (from Bio::Bl2seq)


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq/report.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** report.rb	7 Aug 2005 16:42:28 -0000	1.1
--- report.rb	10 Aug 2005 12:55:41 -0000	1.2
***************
*** 29,32 ****
--- 29,34 ----
  
  module Bio
+ class Blast
+ 
    class Bl2seq
      class Report < Bio::Blast::Default::Report
***************
*** 97,100 ****
--- 99,104 ----
      end #class Report
    end #class Bl2seq
+ 
+ end #class Blast
  end #module Bio
  
***************
*** 103,110 ****
  if __FILE__ == $0
  
!   Bio::FlatFile.open(Bio::Bl2seq::Report, ARGF) do |ff|
    ff.each do |rep|
  
!   print "# === Bio::Bl2seq::Report\n"
    puts
    #@#print "  rep.program           #=> "; p rep.program
--- 107,114 ----
  if __FILE__ == $0
  
!   Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, ARGF) do |ff|
    ff.each do |rep|
  
!   print "# === Bio::Blast::Bl2seq::Report\n"
    puts
    #@#print "  rep.program           #=> "; p rep.program
***************
*** 171,175 ****
    rep.iterations.each do |itr|
        
!   print "# --- Bio::Bl2seq::Report::Iteration\n"
    puts
  
--- 175,179 ----
    rep.iterations.each do |itr|
        
!   print "# --- Bio::Blast::Bl2seq::Report::Iteration\n"
    puts
  
***************
*** 194,198 ****
    itr.hits.each_with_index do |hit, i|
  
!   print "# --- Bio::Bl2seq::Default::Report::Hit"
    print " ([#{i}])\n"
    puts
--- 198,202 ----
    itr.hits.each_with_index do |hit, i|
  
!   print "# --- Bio::Blast::Bl2seq::Default::Report::Hit"
    print " ([#{i}])\n"
    puts
***************
*** 245,249 ****
    hit.hsps.each_with_index do |hsp, j|
  
!   print "# --- Bio::Blast::Default::Report::HSP (Bio::Bl2seq::Report::HSP)"
    print " ([#{j}])\n"
    puts
--- 249,253 ----
    hit.hsps.each_with_index do |hsp, j|
  
!   print "# --- Bio::Blast::Default::Report::HSP (Bio::Blast::Bl2seq::Report::HSP)"
    print " ([#{j}])\n"
    puts
***************
*** 295,299 ****
  =begin
  
! = Bio::Bl2seq::Default::Report
  
      NCBI bl2seq (BLAST 2 sequences) output parser
--- 299,303 ----
  =begin
  
! = Bio::Blast::Bl2seq::Report
  
      NCBI bl2seq (BLAST 2 sequences) output parser