[BioRuby-cvs] bioruby/lib/bio feature.rb,1.11,1.12

[Jan Aerts]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv19592

Modified Files:
	feature.rb 
Log Message:
Reverted to previous behaviour: new takes array of Bio::Feature::Qualifiers
instead of list of qualifier_key, qualifier_value pairs.


Index: feature.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/feature.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** feature.rb	26 Apr 2006 11:05:50 -0000	1.11
--- feature.rb	9 May 2006 11:52:30 -0000	1.12
***************
*** 23,27 ****
  #  #             /note="cytochrome P450 IID6; GOO-132-127"
  #  #             /number="1"
! #  feature = Bio::Feature.new('exon','1532..1799',['gene' => 'CYP2D6','note' => 'cytochrome P450 IID6; GOO-132-127','number' => '1'])
  #
  #  # Print the feature
--- 23,37 ----
  #  #             /note="cytochrome P450 IID6; GOO-132-127"
  #  #             /number="1"
! #  feature = Bio::Feature.new('exon','1532..1799')
! #  feature.append(Bio::Feature::Qualifier.new('gene', 'CYP2D6'))
! #  feature.append(Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6'))
! #  feature.append(Bio::Feature::Qualifier.new('number', '1'))
! #
! #  # or all in one go:
! #  feature2 = Bio::Feature.new('exon','1532..1799',
! #    [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
! #      Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6; GOO-132-127'),
! #      Bio::Feature::Qualifier.new('number', '1')
! #    ])
  #
  #  # Print the feature
***************
*** 38,54 ****
    # * (required) _feature_: type of feature (e.g. "exon")
    # * (required) _position_: position of feature (e.g. "complement(1532..1799)")
!   # * (optional) _qualifiers_: list of qualifiers (e.g. "['gene' => 'CYP2D6','number' => '1']")
    # *Returns*:: Bio::Feature object
    def initialize(feature = '', position = '', qualifiers = [])
!     @feature, @position = feature, position
!     @qualifiers = Array.new
!     if qualifiers.length.modulo(2) > 0
!       $stderr.puts "WARNING"
!     end
!     while qualifiers.length > 0
!       key = qualifiers.shift
!       value = qualifiers.shift || ''
!       self.append(Qualifier.new(key, value))
!     end
    end
  
--- 48,55 ----
    # * (required) _feature_: type of feature (e.g. "exon")
    # * (required) _position_: position of feature (e.g. "complement(1532..1799)")
!   # * (opt) _qualifiers_: list of Bio::Feature::Qualifier objects (default: [])
    # *Returns*:: Bio::Feature object
    def initialize(feature = '', position = '', qualifiers = [])
!     @feature, @position, @qualifiers = feature, position, qualifiers
    end
  
***************
*** 131,137 ****
      attr_reader :value
  
!   end
  
! end
  
  
--- 132,138 ----
      attr_reader :value
  
!   end #Qualifier
  
! end #Feature
  
  
***************
*** 141,148 ****
  # = USAGE
  #  # First, create some Bio::Feature objects
! #  feature1 = Bio::Feature.new('intron','3627..4059',['gene', 'CYP2D6', 'note', 'G00-132-127','number','4'])
! #  feature2 = Bio::Feature.new('exon','4060..4236',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
! #  feature3 = Bio::Feature.new('intron','4237..4426',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
! #  feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',['gene', 'CYP2D6','translation','MGXXTVMHLL...'])
  #
  #  # And create a container for them
--- 142,152 ----
  # = 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
***************
*** 217,257 ****
    end
  
! end
  
  end # Bio
  
- if __FILE__ == $0
-   puts "---TESTING Bio::Feature"
-   feature1 = Bio::Feature.new('exon','1532..1799',['gene','CYP2D6','note','cytochrome P450 IID6; GOO-132-127','number','1', 'note', 'a second note'])
- 
-   # Print the feature out
-   puts feature1.feature + "\t" + feature1.position
-   feature1.each do |qualifier|
-     puts "- " + qualifier.qualifier + ": " + qualifier.value
-   end
-   
-   feature2 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',['gene', 'CYP2D6','translation','MGXXTVMHLL...'])
- 
-   puts "---TESTING Bio::Features"
-   feature3 = Bio::Feature.new('intron','3627..4059',['gene', 'CYP2D6', 'note', 'G00-132-127','number','4'])
-   feature4 = Bio::Feature.new('exon','4060..4236',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
-   feature5 = Bio::Feature.new('intron','4237..4426',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
-   feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4, feature5 ])
-   feature_container.each do |feature|
-     puts "-NEXT FEATURE"
-     puts feature.feature + "\t" + feature.position
-     feature.each do |qualifier|
-       puts "- " + qualifier.qualifier + ": " + qualifier.value
-     end
-   end
- 
-   puts "---TESTING hash function"
-   feature_container.each('CDS') do |feature|
-     hash = feature.to_hash
-     name = hash["gene"] || hash["product"] || hash["note"] 
-     aaseq  = hash["translation"]
-     pos  = feature.position
-     puts ">#{name} #{feature.position}"
-     puts aaseq
-   end
- end
--- 221,226 ----
    end
  
! end # Features
  
  end # Bio