Class | Bio::PhyloXML::Events |
In: |
lib/bio/db/phyloxml/phyloxml_elements.rb
|
Parent: | Object |
Events at the root node of a clade (e.g. one gene duplication).
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 |
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 333 333: def confidence=(type, value) 334: @confidence = Confidence.new(type, value) 335: end
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 337 337: def confidence=(conf) 338: @confidence = conf 339: end
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 341 341: def duplications=(str) 342: @duplications = str.to_i 343: end
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 345 345: def losses=(str) 346: @losses = str.to_i 347: end
# 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.
# 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
# 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