[BioRuby-cvs] bioruby/lib/bio/util sirna.rb,1.3,1.4

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory pub.open-bio.org:/tmp/cvs-serv9021/lib/bio/util

Modified Files:
	sirna.rb 
Log Message:
* expanded tab at the line head


Index: sirna.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/sirna.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** sirna.rb	9 Aug 2005 05:40:44 -0000	1.3
--- sirna.rb	8 Sep 2005 01:22:12 -0000	1.4
***************
*** 75,82 ****
          target_stop  = target_start + @target_size
  
! 	antisense_gc_percent = antisense.gc_percent
! 	next if antisense_gc_percent > @max_gc_percent
! 	next if antisense_gc_percent < @min_gc_percent
! 	
          case rule
          when 'uitei'
--- 75,82 ----
          target_stop  = target_start + @target_size
  
!         antisense_gc_percent = antisense.gc_percent
!         next if antisense_gc_percent > @max_gc_percent
!         next if antisense_gc_percent < @min_gc_percent
!         
          case rule
          when 'uitei'
***************
*** 86,93 ****
          else
            raise NotImplementedError
! 	end
  
          pair = Bio::SiRNA::Pair.new(target, sense, antisense, target_start, target_stop, rule, antisense_gc_percent)
! 	@pairs.push(pair)
        end
        return @pairs
--- 86,93 ----
          else
            raise NotImplementedError
!         end
  
          pair = Bio::SiRNA::Pair.new(target, sense, antisense, target_start, target_stop, rule, antisense_gc_percent)
!         @pairs.push(pair)
        end
        return @pairs
***************
*** 98,108 ****
  
        def initialize(target, sense, antisense, start, stop, rule, gc_percent)
! 	@target     = target
! 	@sense      = sense
! 	@antisense  = antisense
! 	@start      = start
! 	@stop       = stop
! 	@rule       = rule
! 	@gc_percent = gc_percent
        end
        attr_accessor :target, :sense, :antisense, :start, :stop, :rule, :gc_percent
--- 98,108 ----
  
        def initialize(target, sense, antisense, start, stop, rule, gc_percent)
!         @target     = target
!         @sense      = sense
!         @antisense  = antisense
!         @start      = start
!         @stop       = stop
!         @rule       = rule
!         @gc_percent = gc_percent
        end
        attr_accessor :target, :sense, :antisense, :start, :stop, :rule, :gc_percent
***************
*** 110,121 ****
        # human readable report
        def report
! 	report =  "### siRNA\n"
! 	report << 'Start: ' + @start.to_s + "\n"
! 	report << 'Stop:  ' + @stop.to_s  + "\n"
! 	report << 'Rule:  ' + @rule.to_s  + "\n"
! 	report << 'GC %:  ' + @gc_percent.to_s  + "\n"
! 	report << 'Target:    '        + @target.upcase + "\n"
! 	report << 'Sense:     ' + '  ' + @sense.upcase  + "\n"
! 	report << 'Antisense: '        + @antisense.reverse.upcase + "\n"
        end
  
--- 110,121 ----
        # human readable report
        def report
!         report =  "### siRNA\n"
!         report << 'Start: ' + @start.to_s + "\n"
!         report << 'Stop:  ' + @stop.to_s  + "\n"
!         report << 'Rule:  ' + @rule.to_s  + "\n"
!         report << 'GC %:  ' + @gc_percent.to_s  + "\n"
!         report << 'Target:    '        + @target.upcase + "\n"
!         report << 'Sense:     ' + '  ' + @sense.upcase  + "\n"
!         report << 'Antisense: '        + @antisense.reverse.upcase + "\n"
        end
  
***************
*** 138,143 ****
          case method
          when 'BLOCK-iT'
! 	  block_it
! 	else
            raise NotImplementedError
          end
--- 138,143 ----
          case method
          when 'BLOCK-iT'
!           block_it
!         else
            raise NotImplementedError
          end
***************
*** 165,173 ****
          if /^G/i =~ fwd
    	  @top_strand    = top + fwd + loop_fwd + rev
! 	  @bottom_strand = bot + fwd + loop_rev + rev
! 	else
    	  @top_strand    = top + 'G' + fwd + loop_fwd + rev
! 	  @bottom_strand = bot + fwd + loop_rev + rev + 'C'
! 	end
        end
        
--- 165,173 ----
          if /^G/i =~ fwd
    	  @top_strand    = top + fwd + loop_fwd + rev
!           @bottom_strand = bot + fwd + loop_rev + rev
!         else
    	  @top_strand    = top + 'G' + fwd + loop_fwd + rev
!           @bottom_strand = bot + fwd + loop_rev + rev + 'C'
!         end
        end