Class: Bio::PhyloXML::Events

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-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

#confidence ⇒ Object

Confidence object



319
320
321
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 319

def confidence
  @confidence
end

#duplications ⇒ Object

Integer



316
317
318
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 316

def duplications
  @duplications
end

#losses ⇒ Object

Integer



316
317
318
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 316

def losses
  @losses
end

#speciations ⇒ Object

Integer



316
317
318
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 316

def speciations
  @speciations
end

#type ⇒ Object

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



313
314
315
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 313

def type
  @type
end

Instance Method Details

#to_xml ⇒ Object

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



357
358
359
360
361
362
363
364
365
366
367
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 357

def to_xml
  #@todo add unit test
  events = LibXML::XML::Node.new('events')
  PhyloXML::Writer.generate_xml(events, self, [
    [:simple, 'type', (defined? @type) ? @type : nil],
    [:simple, 'duplications', (defined? @duplications) ? @duplications : nil],
    [:simple, 'speciations', (defined? @speciations) ? @speciations : nil],
    [:simple, 'losses', (defined? @losses) ? @losses : nil],
    [:complex, 'confidence', (defined? @confidence) ? @confidence : nil]])
  return events
end