[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.17, 1.18

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv23466/lib/bio/util/restriction_enzyme

Modified Files:
	analysis.rb 
Log Message:
Support user specification of maximum allowable permutations.

It's becoming apparent that we need some sort of standardized logging mechanism for warnings.


Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** analysis.rb	5 Apr 2007 23:35:42 -0000	1.17
--- analysis.rb	23 Apr 2007 19:42:55 -0000	1.18
***************
*** 47,55 ****
    # * +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?
      # Format the fragments for the user
!     fragments_for_display( cut_and_return_by_permutations( sequence, *args ) )
    end
  
--- 47,56 ----
    # * +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) or a +Symbol+ containing an error code
    def cut( sequence, *args )
!     res = cut_and_return_by_permutations( sequence, *args )
!     return res if res.class == Symbol
      # Format the fragments for the user
!     fragments_for_display( res )
    end
  
***************
*** 64,76 ****
    # * +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*:: +Hash+ Keys are a permutation ID, values are SequenceRange objects that have cuts applied.
    def cut_and_return_by_permutations( sequence, *args )
      my_hash = {}
      
!     return my_hash if !sequence.kind_of?(String) or sequence.empty?
      sequence = Bio::Sequence::NA.new( sequence )
      
      enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args )
!     return my_hash if enzyme_actions.empty? and initial_cuts.empty?
      
      if enzyme_actions.size > 1
--- 65,113 ----
    # * +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.
+   # May also supply a +Hash+ with the key ":max_permutations" to specificy how many permutations are allowed - a value of 0 indicates no permutations are allowed.
    # *Returns*:: +Hash+ Keys are a permutation ID, values are SequenceRange objects that have cuts applied.
+   # _also_ may return the +Symbol+ ':sequence_empty', ':no_cuts_found', or ':too_many_permutations'
    def cut_and_return_by_permutations( sequence, *args )
      my_hash = {}
+     maximum_permutations = nil
+ 
+     hashes_in_args = args.select { |i| i.class == Hash }
+     args.delete_if { |i| i.class == Hash }
+     hashes_in_args.each do |hsh|
+       hsh.each do |key, value|
+         case key
+         when :max_permutations, 'max_permutations', :maximum_permutations, 'maximum_permutations'
+           maximum_permutations = value.to_i unless value == nil
+         else
+           raise ArgumentError, "Received key #{key.inspect} in argument - I only know the key ':max_permutations' currently.  Hash passed: #{hsh.inspect}"
+         end
+       end
+     end
      
!     if !sequence.kind_of?(String) or sequence.empty?
!       logger.warn "The supplied sequence is empty." if defined?(logger)
!       return :sequence_empty
!     end
      sequence = Bio::Sequence::NA.new( sequence )
      
      enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args )
! 
!     if enzyme_actions.empty? and initial_cuts.empty?
!       logger.warn "This enzyme does not make any cuts on this sequence." if defined?(logger)
!       return :no_cuts_found
!     end
! 
!     # * When enzyme_actions.size is equal to '1' that means there are no permutations.
!     # * If enzyme_actions.size is equal to '2' there is one
!     #   permutation ("[0, 1]")
!     # * If enzyme_actions.size is equal to '3' there are two
!     #   permutations ("[0, 1, 2]")
!     # * and so on..
!     if maximum_permutations and enzyme_actions.size > 1
!       if (enzyme_actions.size - 1) > maximum_permutations.to_i
!         logger.warn "More permutations than maximum, skipping.  Found: #{enzyme_actions.size-1}  Max: #{maximum_permutations.to_i}" if defined?(logger)
!         return :too_many_permutations
!       end
!     end
      
      if enzyme_actions.size > 1