Class Bio::FANTOM::MaXML::Annotations
In: lib/bio/db/fantom.rb  (CVS)
Parent: MaXML

Methods

Included Modules

Enumerable

Constants

Data_XPath = nil

Public Instance methods

[Source]

# File lib/bio/db/fantom.rb, line 304
        def [](*arg)
          if arg[0].is_a?(String) and arg.size == 1 then
            get_by_qualifier(arg[0])
          else
            to_a[*arg]
          end
        end

[Source]

# File lib/bio/db/fantom.rb, line 312
        def cds_start
          unless defined?(@cds_start)
            e = get_by_qualifier('cds_start')
            @cds_start = e ? e.anntext.to_i : nil
          end
          @cds_start
        end

[Source]

# File lib/bio/db/fantom.rb, line 320
        def cds_stop
          unless defined?(@cds_stop)
            e = get_by_qualifier('cds_stop')
            @cds_stop = e ? e.anntext.to_i : nil
          end
          @cds_stop
        end

[Source]

# File lib/bio/db/fantom.rb, line 336
        def data_source
          unless defined?(@data_source)
            e = get_by_qualifier('gene_name')
            @data_source = e ? e.datasrc[0] : nil
          end
          @data_source
        end

[Source]

# File lib/bio/db/fantom.rb, line 275
        def each
          to_a.each { |x| yield x }
        end

[Source]

# File lib/bio/db/fantom.rb, line 344
        def evidence
          unless defined?(@evidence)
            e = get_by_qualifier('gene_name')
            @evidence = e ? e.evidence : nil
          end
          @evidence
        end

[Source]

# File lib/bio/db/fantom.rb, line 328
        def gene_name
          unless defined?(@gene_name)
            e = get_by_qualifier('gene_name')
            @gene_name = e ? e.anntext : nil
          end
          @gene_name
        end

[Source]

# File lib/bio/db/fantom.rb, line 287
        def get_all_by_qualifier(qstr)
          unless defined?(@hash)
            @hash = {}
          end
          unless @hash.member?(qstr) then
            @hash[qstr] = self.find_all do |x|
              x.qualifier == qstr
            end
          end
          @hash[qstr]
        end

[Source]

# File lib/bio/db/fantom.rb, line 299
        def get_by_qualifier(qstr)
          a = get_all_by_qualifier(qstr)
          a ? a[0] : nil
        end

[Source]

# File lib/bio/db/fantom.rb, line 279
        def to_a
          unless defined?(@a)
            @a = @elem.get_elements('annotation')
            @a.collect! { |e| MaXML::Annotation.new(e) }
          end
          @a
        end

[Validate]