Class: Bio::PhyloXML::BinaryCharacters

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

Overview

Description

The names and/or counts of binary characters present, gained, and lost at the root of a clade.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ BinaryCharacters

Returns a new instance of BinaryCharacters.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1060

def initialize
  @gained = []
  @lost = []
  @present = []
  @absent = []
end

Instance Attribute Details

#absent ⇒ Object

Returns the value of attribute absent.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1041

def absent
  @absent
end

#absent_count ⇒ Object

Returns the value of attribute absent_count.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1042

def absent_count
  @absent_count
end

#bc_type ⇒ Object

Returns the value of attribute bc_type.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1041

def bc_type
  @bc_type
end

#gained ⇒ Object

Returns the value of attribute gained.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1041

def gained
  @gained
end

#gained_count ⇒ Object

Returns the value of attribute gained_count.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1042

def gained_count
  @gained_count
end

#lost ⇒ Object

Returns the value of attribute lost.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1041

def lost
  @lost
end

#lost_count ⇒ Object

Returns the value of attribute lost_count.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1042

def lost_count
  @lost_count
end

#present ⇒ Object

Returns the value of attribute present.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1041

def present
  @present
end

#present_count ⇒ Object

Returns the value of attribute present_count.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1042

def present_count
  @present_count
end

Instance Method Details

#to_xml ⇒ Object

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



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 1068

def to_xml
  bc = LibXML::XML::Node.new('binary_characters')
  bc['type'] = @bc_type
  PhyloXML::Writer.generate_xml(bc, self, [
      [:attr, 'gained_count'],
      [:attr, 'lost_count'],
      [:attr, 'present_count'],
      [:attr, 'absent_count']])

  if not @gained.empty?
    gained_xml = LibXML::XML::Node.new('gained')
    PhyloXML::Writer.generate_xml(gained_xml, self, [[:simplearr, 'bc', @gained]])
    bc << gained_xml
  end

  if not @lost.empty?
    lost_xml = LibXML::XML::Node.new('lost')
    PhyloXML::Writer.generate_xml(lost_xml, self, [[:simplearr, 'bc', @lost]])
    bc << lost_xml
  end

  if not @present.empty?
    present_xml = LibXML::XML::Node.new('present')
    PhyloXML::Writer.generate_xml(present_xml, self, [[:simplearr, 'bc', @present]])
    bc << present_xml
  end

  if not @absent.empty?
    absent_xml = LibXML::XML::Node.new('absent')
    PhyloXML::Writer.generate_xml(absent_xml, self, [[:simplearr, 'bc', @absent]])
    bc << absent_xml
  end

  return bc
end