class Bio::FANTOM::MaXML::Annotations
Constants
- Data_XPath
Public Instance Methods
[](*arg)
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# File lib/bio/db/fantom.rb, line 302 def [](*arg) if arg[0].is_a?(String) and arg.size == 1 then get_by_qualifier(arg[0]) else to_a[*arg] end end
cds_start()
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# File lib/bio/db/fantom.rb, line 310 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
cds_stop()
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# File lib/bio/db/fantom.rb, line 318 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
data_source()
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# File lib/bio/db/fantom.rb, line 334 def data_source unless defined?(@data_source) e = get_by_qualifier('gene_name') @data_source = e ? e.datasrc[0] : nil end @data_source end
each() { |x| ... }
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# File lib/bio/db/fantom.rb, line 273 def each to_a.each { |x| yield x } end
evidence()
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# File lib/bio/db/fantom.rb, line 342 def evidence unless defined?(@evidence) e = get_by_qualifier('gene_name') @evidence = e ? e.evidence : nil end @evidence end
gene_name()
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# File lib/bio/db/fantom.rb, line 326 def gene_name unless defined?(@gene_name) e = get_by_qualifier('gene_name') @gene_name = e ? e.anntext : nil end @gene_name end
get_all_by_qualifier(qstr)
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# File lib/bio/db/fantom.rb, line 285 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
get_by_qualifier(qstr)
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# File lib/bio/db/fantom.rb, line 297 def get_by_qualifier(qstr) a = get_all_by_qualifier(qstr) a ? a[0] : nil end
to_a()
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# File lib/bio/db/fantom.rb, line 277 def to_a unless defined?(@a) @a = @elem.get_elements('annotation') @a.collect! { |e| MaXML::Annotation.new(e) } end @a end