[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.14, 1.15 analysis_basic.rb, 1.7, 1.8 double_stranded.rb, 1.6, 1.7

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv16002/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 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** analysis_basic.rb	5 Jan 2007 06:11:15 -0000	1.7
--- analysis_basic.rb	5 Jan 2007 06:33:01 -0000	1.8
***************
*** 51,59 ****
  class Analysis
  
-   def self.cut( sequence, *args )
-     # Just a placeholder, actually defined in bio/util/restriction_enzyme/analysis.rb
-     #self.new.cut( sequence, *args )
-   end
- 
    # See cut_without_permutations instance method
    def self.cut_without_permutations( sequence, *args )
--- 51,54 ----
***************
*** 73,77 ****
    # accurate.
    #
!   # This code is mainly included as an example for those interested to study
    # without having to wade through the extra layer of complexity added by the
    # permutations.
--- 68,72 ----
    # accurate.
    #
!   # This code is mainly included as an academic example
    # without having to wade through the extra layer of complexity added by the
    # permutations.
***************
*** 90,94 ****
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to SequenceRange::Fragments)
    def cut_without_permutations( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
--- 85,89 ----
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments)
    def cut_without_permutations( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
***************
*** 118,123 ****
      fragments_for_display( {0 => sequence_range} )
    end
- 
- 
    
    #########
--- 113,116 ----
***************
*** 125,129 ****
    #########
  
- 
    # Take the fragments from SequenceRange objects generated from add_cut_range
    # and return unique results as a Bio::RestrictionEnzyme::Analysis::Fragment object.
--- 118,121 ----

Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** analysis.rb	5 Jan 2007 06:11:15 -0000	1.14
--- analysis.rb	5 Jan 2007 06:33:01 -0000	1.15
***************
*** 51,55 ****
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects.   (Note: unrelated to SequenceRange::Fragments)
    def cut( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
--- 51,55 ----
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects.   (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments)
    def cut( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?

Index: double_stranded.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** double_stranded.rb	5 Jan 2007 06:03:22 -0000	1.6
--- double_stranded.rb	5 Jan 2007 06:33:01 -0000	1.7
***************
*** 148,152 ****
    end
  
!   # Returns +true+ if the cut pattern creates blunt fragments
    def blunt?
      as = aligned_strands_with_cuts
--- 148,153 ----
    end
  
!   # Returns +true+ if the cut pattern creates blunt fragments.
!   # (opposite of sticky)
    def blunt?
      as = aligned_strands_with_cuts
***************
*** 158,162 ****
    end
  
!   # Returns +true+ if the cut pattern creates sticky fragments
    def sticky?
      !blunt?
--- 159,164 ----
    end
  
!   # Returns +true+ if the cut pattern creates sticky fragments.
!   # (opposite of blunt)
    def sticky?
      !blunt?
***************
*** 239,242 ****
--- 241,250 ----
    # This would be represented by two EnzymeActions - one for each
    # RestrictionEnzyme.
+   # 
+   # This is, however, subject to competition.  If the second enzyme reaches
+   # the target first, the the first enzyme will not be able to find the
+   # appropriate bind site.
+   # 
+   # FIXME complete these docs
    #
    # To initialize an EnzymeAction you must first instantiate it with the
***************
*** 262,266 ****
      # * Reflect cuts that are in enzyme notation
      # * 0 is not a valid enzyme index, decrement 0 and all negative
- #    c_cl = p_cl.collect { |n| s.length - n }.collect { |n| n <= 0 ? n - 1 : n } #wrong.
      c_cl = p_cl.collect {|n| (n >= s.length or n < 1) ? ((s.length - n) - 1) : (s.length - n)}
  
--- 270,273 ----