class Bio::PhyloXML::Events

Description

Events at the root node of a clade (e.g. one gene duplication).

Attributes

confidence[R]

Confidence object

duplications[R]

Integer

losses[R]

Integer

speciations[R]

Integer

type[R]

value comes from list: transfer, fusion, speciation_or_duplication, other, mixed, unassigned

Public Instance Methods

confidence=(conf) click to toggle source

Confidence object

    # File lib/bio-phyloxml/phyloxml_elements.rb
328 def confidence=(conf)
329   @confidence = conf
330 end
duplications=(str) click to toggle source

Integer

    # File lib/bio-phyloxml/phyloxml_elements.rb
333 def duplications=(str)
334   @duplications = str.to_i
335 end
losses=(str) click to toggle source

Integer

    # File lib/bio-phyloxml/phyloxml_elements.rb
338 def losses=(str)
339   @losses = str.to_i
340 end
speciations=(str) click to toggle source

Integer

    # File lib/bio-phyloxml/phyloxml_elements.rb
343 def speciations=(str)
344   @speciations=str.to_i
345 end
to_xml() click to toggle source

Converts elements to xml representation. Called by PhyloXML::Writer class.

    # File lib/bio-phyloxml/phyloxml_elements.rb
357 def to_xml
358   #@todo add unit test
359   events = LibXML::XML::Node.new('events')
360   PhyloXML::Writer.generate_xml(events, self, [
361     [:simple, 'type', (defined? @type) ? @type : nil],
362     [:simple, 'duplications', (defined? @duplications) ? @duplications : nil],
363     [:simple, 'speciations', (defined? @speciations) ? @speciations : nil],
364     [:simple, 'losses', (defined? @losses) ? @losses : nil],
365     [:complex, 'confidence', (defined? @confidence) ? @confidence : nil]])
366   return events
367 end
type=(str) click to toggle source

value comes from list: transfer, fusion, speciation_or_duplication, other, mixed, unassigned

    # File lib/bio-phyloxml/phyloxml_elements.rb
348 def type=(str)
349   @type = str
350   #@todo add unit test for this
351   if not ['transfer','fusion','speciation_or_duplication','other','mixed', 'unassigned'].include?(str)
352     raise "Warning #{str} is not one of the allowed values"
353   end
354 end