[BioRuby-cvs] bioruby/lib/bio feature.rb,1.13,1.13.2.1

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv7351/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	feature.rb 
Log Message:
Bio::Features is moved to lib/bio/compat/features.rb, and a module to 
keep backward compatibility (Bio::Features::BackwardCompatibility) is added.


Index: feature.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/feature.rb,v
retrieving revision 1.13
retrieving revision 1.13.2.1
diff -C2 -d -r1.13 -r1.13.2.1
*** feature.rb	5 Apr 2007 23:35:39 -0000	1.13
--- feature.rb	4 Mar 2008 10:12:22 -0000	1.13.2.1
***************
*** 136,226 ****
  end #Feature
  
- 
- # = DESCRIPTION
- # Container for a list of Feature objects.
- #
- # = USAGE
- #  # First, create some Bio::Feature objects
- #  feature1 = Bio::Feature.new('intron','3627..4059')
- #  feature2 = Bio::Feature.new('exon','4060..4236')
- #  feature3 = Bio::Feature.new('intron','4237..4426')
- #  feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',
- #                   [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
- #                     Bio::Feature::Qualifier.new('translation','MGXXTVMHLL...')
- #                   ])
- #
- #  # And create a container for them
- #  feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])
- #
- #  # Iterate over all features and print
- #  feature_container.each do |feature|
- #    puts feature.feature + "\t" + feature.position
- #    feature.each do |qualifier|
- #      puts "- " + qualifier.qualifier + ": " + qualifier.value
- #    end
- #  end
- #
- #  # Iterate only over CDS features and extract translated amino acid sequences
- #  features.each("CDS") do |feature|
- #    hash = feature.to_hash
- #    name = hash["gene"] || hash["product"] || hash["note"] 
- #    aaseq  = hash["translation"]
- #    pos  = feature.position
- #    if name and seq
- #      puts ">#{gene} #{feature.position}"
- #      puts aaseq
- #    end
- #  end
- class Features
-   # Create a new Bio::Features object.
-   #
-   # *Arguments*:
-   # * (optional) _list of features_: list of Bio::Feature objects
-   # *Returns*:: Bio::Features object
-   def initialize(ary = [])
-     @features = ary
-   end
- 
-   # Returns an Array of Feature objects.
-   attr_accessor :features
- 
-   # Appends a Feature object to Features.
-   # 
-   # *Arguments*:
-   # * (required) _feature_: Bio::Feature object
-   # *Returns*:: Bio::Features object
-   def append(a)
-     @features.push(a) if a.is_a? Feature
-     return self
-   end
- 
-   # Iterates on each feature object.
-   #
-   # *Arguments*:
-   # * (optional) _key_: if specified, only iterates over features with this key
-   def each(arg = nil)
-     @features.each do |x|
-       next if arg and x.feature != arg
-       yield x
-     end
-   end
- 
-   # Short cut for the Features#features[n]
-   def [](*arg)
-     @features[*arg]
-   end
- 
-   # Short cut for the Features#features.first
-   def first
-     @features.first
-   end
- 
-   # Short cut for the Features#features.last
-   def last
-     @features.last
-   end
- 
- end # Features
- 
  end # Bio
  
--- 136,139 ----