[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.8, 1.9 analysis_basic.rb, 1.1, 1.2 double_stranded.rb, 1.4, 1.5

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv2656/restriction_enzyme

Modified Files:
	analysis.rb analysis_basic.rb double_stranded.rb 
Log Message:


Index: analysis_basic.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** analysis_basic.rb	1 Jan 2007 23:47:27 -0000	1.1
--- analysis_basic.rb	2 Jan 2007 00:13:07 -0000	1.2
***************
*** 43,47 ****
  
  require 'bio/util/restriction_enzyme'
! require 'bio/util/restriction_enzyme/analysis/sequence_range'
  
  class Bio::RestrictionEnzyme
--- 43,47 ----
  
  require 'bio/util/restriction_enzyme'
! require 'bio/util/restriction_enzyme/range/sequence_range'
  
  class Bio::RestrictionEnzyme
***************
*** 83,87 ****
      enzyme_actions = tmp[0].merge(tmp[1])
  
!     sr_with_cuts = SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
      enzyme_actions.each do |id, enzyme_action|
        enzyme_action.cut_ranges.each do |cut_range|
--- 83,87 ----
      enzyme_actions = tmp[0].merge(tmp[1])
  
!     sr_with_cuts = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
      enzyme_actions.each do |id, enzyme_action|
        enzyme_action.cut_ranges.each do |cut_range|
***************
*** 167,171 ****
        other_cut_ranges.each do |key, cut_ranges|
          cut_ranges.each do |cut_range|
!           next unless cut_range.class == VerticalCutRange  # we aren't concerned with horizontal cuts
            previous_cut_left = cut_range.range.first 
            previous_cut_right = cut_range.range.last
--- 167,171 ----
        other_cut_ranges.each do |key, cut_ranges|
          cut_ranges.each do |cut_range|
!           next unless cut_range.class == Bio::RestrictionEnzyme::Range::VerticalCutRange  # we aren't concerned with horizontal cuts
            previous_cut_left = cut_range.range.first 
            previous_cut_right = cut_range.range.last

Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** analysis.rb	1 Jan 2007 23:47:27 -0000	1.8
--- analysis.rb	2 Jan 2007 00:13:07 -0000	1.9
***************
*** 64,68 ****
  
      if permutations.empty?
!       sr_with_cuts = SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
        initial_cuts.each { |key, enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sr_with_cuts.add_cut_range(cut_range) } }
        hash_of_sequence_ranges_with_cuts[0] = sr_with_cuts
--- 64,68 ----
  
      if permutations.empty?
!       sr_with_cuts = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
        initial_cuts.each { |key, enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sr_with_cuts.add_cut_range(cut_range) } }
        hash_of_sequence_ranges_with_cuts[0] = sr_with_cuts
***************
*** 71,75 ****
      permutations.each do |permutation|
        previous_cut_ranges = []
!       sr_with_cuts = SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
        initial_cuts.each { |enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sr_with_cuts.add_cut_range(cut_range) } }
  
--- 71,75 ----
      permutations.each do |permutation|
        previous_cut_ranges = []
!       sr_with_cuts = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
        initial_cuts.each { |enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sr_with_cuts.add_cut_range(cut_range) } }
  
***************
*** 86,90 ****
          # so all cut locations must be checked that would fall underneath.
          previous_cut_ranges.each do |cut_range|
!           next unless cut_range.class == VerticalCutRange  # we aren't concerned with horizontal cuts
            previous_cut_left = cut_range.range.first 
            previous_cut_right = cut_range.range.last
--- 86,90 ----
          # so all cut locations must be checked that would fall underneath.
          previous_cut_ranges.each do |cut_range|
!           next unless cut_range.class == Bio::RestrictionEnzyme::Range::VerticalCutRange  # we aren't concerned with horizontal cuts
            previous_cut_left = cut_range.range.first 
            previous_cut_right = cut_range.range.last

Index: double_stranded.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** double_stranded.rb	1 Jan 2007 23:47:27 -0000	1.4
--- double_stranded.rb	2 Jan 2007 00:13:07 -0000	1.5
***************
*** 14,18 ****
  require 'bio/db/rebase'
  require 'bio/util/restriction_enzyme'
! require 'bio/util/restriction_enzyme/analysis/sequence_range'
  
  require 'bio/util/restriction_enzyme/cut_symbol'
--- 14,18 ----
  require 'bio/db/rebase'
  require 'bio/util/restriction_enzyme'
! require 'bio/util/restriction_enzyme/range/sequence_range'
  
  require 'bio/util/restriction_enzyme/cut_symbol'
***************
*** 247,251 ****
    # Defines a single enzyme action, in this case being a range that correlates
    # to the DNA sequence that may contain it's own internal cuts.
!   class EnzymeAction < Bio::RestrictionEnzyme::Analysis::SequenceRange
    end
  
--- 247,251 ----
    # Defines a single enzyme action, in this case being a range that correlates
    # to the DNA sequence that may contain it's own internal cuts.
!   class EnzymeAction < Bio::RestrictionEnzyme::Range::SequenceRange
    end