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

#initialize ⇒ Annotation

Returns a new instance of Annotation.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 724

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

Instance Attribute Details

#confidence ⇒ Object

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



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

def confidence
  @confidence
end

#desc ⇒ Object

String. Free text description.



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

def desc
  @desc
end

#evidence ⇒ Object

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



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

def evidence
  @evidence
end

#properties ⇒ Object

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



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 720

def properties
  @properties
end

#ref ⇒ Object

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



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

def ref
  @ref
end

#source ⇒ Object

String



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

def source
  @source
end

#type ⇒ Object

String. Type of the annotation.



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

def type
  @type
end

#uri ⇒ Object

Uri object.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 722

def uri
  @uri
end

Instance Method Details

#to_xml ⇒ Object

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



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 730

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