Class Bio::PhyloXML::Events
In: lib/bio/db/phyloxml/phyloxml_elements.rb
Parent: Object

Description

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

Methods

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

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 333
333:     def confidence=(type, value)
334:       @confidence = Confidence.new(type, value)
335:     end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 337
337:     def confidence=(conf)
338:       @confidence = conf
339:     end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 341
341:     def duplications=(str)
342:       @duplications = str.to_i
343:     end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 345
345:     def losses=(str)
346:       @losses = str.to_i
347:     end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 349
349:     def speciations=(str)
350:       @speciations=str.to_i
351:     end

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

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 362
362:     def to_xml
363:       #@todo add unit test
364:       events = LibXML::XML::Node.new('events')
365:       PhyloXML::Writer.generate_xml(events, self, [
366:         [:simple, 'type', @type],
367:         [:simple, 'duplications', @duplications],
368:         [:simple, 'speciations', @speciations],
369:         [:simple, 'losses', @losses],
370:         [:complex, 'confidence', @confidence]])
371:       return events
372:     end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 353
353:     def type=(str)
354:       @type = str
355:       #@todo add unit test for this
356:       if not ['transfer','fusion','speciation_or_duplication','other','mixed', 'unassigned'].include?(str)
357:         raise "Warning #{str} is not one of the allowed values"
358:       end
359:     end

[Validate]