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[RW]
value comes from list: transfer, fusion, speciation_or_duplication, other, mixed, unassigned
Public Instance Methods
confidence=(type, value)
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# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 333 def confidence=(type, value) @confidence = Confidence.new(type, value) end
duplications=(str)
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# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 341 def duplications=(str) @duplications = str.to_i end
losses=(str)
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# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 345 def losses=(str) @losses = str.to_i end
speciations=(str)
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# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 349 def speciations=(str) @speciations=str.to_i end
to_xml()
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Converts elements to xml representation. Called by PhyloXML::Writer class.
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 362 def to_xml #@todo add unit test events = LibXML::XML::Node.new('events') PhyloXML::Writer.generate_xml(events, self, [ [:simple, 'type', @type], [:simple, 'duplications', @duplications], [:simple, 'speciations', @speciations], [:simple, 'losses', @losses], [:complex, 'confidence', @confidence]]) return events end
type=(str)
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# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 353 def type=(str) @type = str #@todo add unit test for this if not ['transfer','fusion','speciation_or_duplication','other','mixed', 'unassigned'].include?(str) raise "Warning #{str} is not one of the allowed values" end end