Class: Bio::PhyloXML::Date

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

Overview

Description

A date associated with a clade/node. Its value can be numerical by using the 'value' element and/or free text with the 'desc' element' (e.g. 'Silurian'). If a numerical value is used, it is recommended to employ the 'unit' attribute to indicate the type of the numerical value (e.g. 'mya' for 'million years ago').

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#descObject

Free text description of the date.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 807

def desc
  @desc
end

#maximumObject

Integer. Minimum and maximum of the value.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 810

def maximum
  @maximum
end

#minimumObject

Integer. Minimum and maximum of the value.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 810

def minimum
  @minimum
end

#unitObject

String. Units in which value is stored.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 804

def unit
  @unit
end

#valueObject

Integer. Value of the date.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 813

def value
  @value
end

Instance Method Details

#to_sObject

Returns value + unit, for exampe “7 mya”


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 828

def to_s
  return "#{value} #{unit}"
end

#to_xmlObject

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


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 833

def to_xml
  date = LibXML::XML::Node.new('date')
  PhyloXML::Writer.generate_xml(date, self, [
      [:attr, 'unit'],
      [:simple, 'desc', (defined? @desc) ? @desc : nil],
      [:simple, 'value', (defined? @value) ? @value : nil],
      [:simple, 'minimum', (defined? @minimum) ? @minimum : nil],
      [:simple, 'maximum', (defined? @maximum) ? @maximum : nil]])
  return date
end