[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/analysis fragment.rb, 1.2, 1.3 sequence_range.rb, 1.3, 1.4 tags.rb, 1.3, NONE

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis
In directory dev.open-bio.org:/tmp/cvs-serv628/restriction_enzyme/analysis

Modified Files:
	fragment.rb sequence_range.rb 
Removed Files:
	tags.rb 
Log Message:
Removed skeleton code of tags feature in RestrictionEnzyme.

--- tags.rb DELETED ---

Index: fragment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis/fragment.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** fragment.rb	31 Dec 2006 21:50:31 -0000	1.2
--- fragment.rb	1 Jan 2007 02:31:22 -0000	1.3
***************
*** 12,16 ****
  $:.unshift(libpath) unless $:.include?(libpath)
  
- require 'bio/util/restriction_enzyme/analysis/tags'
  require 'bio/util/restriction_enzyme/analysis/cut_ranges'
  require 'bio/util/restriction_enzyme/analysis/horizontal_cut_range'
--- 12,15 ----
***************
*** 31,46 ****
  
    attr_reader :size
- #  attr_reader :tags
  
    def initialize( primary_bin, complement_bin )
- #    @tags = []
      @primary_bin = primary_bin
      @complement_bin = complement_bin
    end
  
- #  def add_tag( index, info=nil )
- #    @tags[index] = info
- #  end
- 
    DisplayFragment = Struct.new(:primary, :complement)
  
--- 30,39 ----

Index: sequence_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis/sequence_range.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** sequence_range.rb	1 Jan 2007 02:16:05 -0000	1.3
--- sequence_range.rb	1 Jan 2007 02:31:22 -0000	1.4
***************
*** 37,41 ****
    attr_reader :left, :right
    attr_reader :size
-   attr_reader :tags
    attr_reader :cut_ranges
  
--- 37,40 ----
***************
*** 62,66 ****
      @size = (@right - @left) + 1 unless @left == nil or @right == nil
  
-     @tags = Tags.new
      @cut_ranges = CutRanges.new
    end
--- 61,64 ----
***************
*** 158,162 ****
      bins.sort.each do |k, bin|
        fragment = Fragment.new( bin.p, bin.c )
-       @tags.each { |k,v| fragment.add_tag(k,v) if (ts.left..ts.right).include?(k) }
        fragments << fragment
      end
--- 156,159 ----
***************
*** 169,179 ****
      return fragments
    end
-   
-   def add_tag( index, info=nil )
-     @__fragments_current = false
- 
-     raise IndexError unless index >= @left and index <= @right
-     @tags[index] = info
-   end
  
  # Cut occurs immediately after the index supplied.
--- 166,169 ----