Class: Bio::PhyloXML::Events

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/phyloxml/phyloxml_elements.rb

Overview

Description

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#confidenceObject

Confidence object


331
332
333
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 331

def confidence
  @confidence
end

#duplicationsObject

Integer


328
329
330
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 328

def duplications
  @duplications
end

#lossesObject

Integer


328
329
330
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 328

def losses
  @losses
end

#speciationsObject

Integer


328
329
330
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 328

def speciations
  @speciations
end

#typeObject

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


325
326
327
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 325

def type
  @type
end

Instance Method Details

#to_xmlObject

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


362
363
364
365
366
367
368
369
370
371
372
# 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