Class: Bio::PhyloXML::Annotation

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

Overview

Description

The annotation of a molecular sequence. It is recommended to annotate by using the optional 'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270', 'KEGG:Tetrachloroethene degradation',

'EC:1.1.1.1').

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (Annotation) initialize

A new instance of Annotation



715
716
717
718
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 715

def initialize
  #@todo add unit test for this, since didn't break anything when changed from property to properties
  @properties = []
end

Instance Attribute Details

- (Object) confidence

Confidence object. Type and value of support for a annotation.



708
709
710
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 708

def confidence
  @confidence
end

- (Object) desc

String. Free text description.



706
707
708
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 706

def desc
  @desc
end

- (Object) evidence

String. evidence for a annotation as free text (e.g. 'experimental')



702
703
704
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 702

def evidence
  @evidence
end

- (Object) properties

Array of Property objects. Allows for further, typed and referenced annotations from external resources



711
712
713
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 711

def properties
  @properties
end

- (Object) ref

String. For example, 'GO:0008270', 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'



698
699
700
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 698

def ref
  @ref
end

- (Object) source

String



700
701
702
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 700

def source
  @source
end

- (Object) type

String. Type of the annotation.



704
705
706
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 704

def type
  @type
end

- (Object) uri

Uri object.



713
714
715
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 713

def uri
  @uri
end

Instance Method Details

- (Object) to_xml

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



721
722
723
724
725
726
727
728
729
 
# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 721

def to_xml
  annot = LibXML::XML::Node.new('annotation')
  annot["ref"] = @ref if @ref != nil
  PhyloXML::Writer.generate_xml(annot, self, [[:simple, 'desc', @desc],
    [:complex, 'confidence', @confidence],
    [:objarr, 'property', 'properties'],
    [:complex, 'uri', @uri]])
  return annot
end