[BioRuby-cvs] bioruby/lib/bio reference.rb,1.24.2.3,1.24.2.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv7295/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
Bio::References and backward-compatibility module (renamed to Bio::References::BackwardCompatibility) is moved to lib/bio/compat/references.rb


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24.2.3
retrieving revision 1.24.2.4
diff -C2 -d -r1.24.2.3 -r1.24.2.4
*** reference.rb	28 Feb 2008 05:51:03 -0000	1.24.2.3
--- reference.rb	4 Mar 2008 10:07:49 -0000	1.24.2.4
***************
*** 578,680 ****
    end
  
-   # = DESCRIPTION
-   #
-   # This class is OBSOLETED, and will soon be removed.
-   # Instead of this class, an array is to be used.
-   #
-   # 
-   # A container class for Bio::Reference objects.
-   #
-   # = USAGE
-   #
-   # This class should NOT be used.
-   #
-   #   refs = Bio::References.new
-   #   refs.append(Bio::Reference.new(hash))
-   #   refs.each do |reference|
-   #     ...
-   #   end
-   #
-   class References
- 
-     # module to keep backward compatibility with obsoleted Bio::References
-     module BackwardCompatibilityForBioReferences #:nodoc:
- 
-       # Backward compatibility with Bio::References#references.
-       # Now, references are stored in an array, and
-       # you should change your code not to use this method.
-       def references
-         warn 'Bio::References is obsoleted. Now, references are stored in an array.'
-         self
-       end
- 
-       # Backward compatibility with Bio::References#append.
-       # Now, references are stored in an array, and
-       # you should change your code not to use this method.
-       def append(reference)
-         warn 'Bio::References is obsoleted. Now, references are stored in an array.'
-         self.push(reference) if reference.is_a? Reference
-         self
-       end
-     end #module BackwardCompatibilityForBioReferences
- 
-     # This method should not be used.
-     # Only for backward compatibility of existing code.
-     #
-     # Since Bio::References is obsoleted,
-     # Bio::References.new not returns Bio::References object,
-     # but modifies given _ary_ and returns the _ary_.
-     #
-     # *Arguments*:
-     # * (optional) __: Array of Bio::Reference objects
-     # *Returns*:: the given array
-     def self.new(ary = [])
-       warn 'Bio::References is obsoleted. Some methods are added to given array to keep backward compatibility.'
-       ary.extend(BackwardCompatibilityForBioReferences)
-       ary
-     end
- 
-     # Array of Bio::Reference objects
-     attr_accessor :references
- 
-     # Create a new Bio::References object
-     # 
-     #   refs = Bio::References.new
-     # ---
-     # *Arguments*:
-     # * (optional) __: Array of Bio::Reference objects
-     # *Returns*:: Bio::References object
-     def initialize(ary = [])
-       @references = ary
-     end
- 
- 
-     # Add a Bio::Reference object to the container.
-     #
-     #   refs.append(reference)
-     # ---
-     # *Arguments*:
-     # * (required) _reference_: Bio::Reference object
-     # *Returns*:: current Bio::References object
-     def append(reference)
-       @references.push(reference) if reference.is_a? Reference
-       return self
-     end
- 
-     # Iterate through Bio::Reference objects.
-     #
-     #   refs.each do |reference|
-     #     ...
-     #   end
-     # ---
-     # *Block*:: yields each Bio::Reference object
-     def each
-       @references.each do |reference|
-         yield reference
-       end
-     end
- 
-   end
- 
  end
  
--- 578,581 ----