Class: Bio::PhyloXML::Node

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

Overview

Description

Class to hold clade element of phyloXML.

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (Node) initialize

Returns a new instance of Node



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 221

def initialize
  @confidences = []
  @sequences = []
  @taxonomies = []
  @distributions = []
  @references = []
  @properties = []
  @other = []
end

Instance Attribute Details

- (Object) binary_characters

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



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 203

def binary_characters
  @binary_characters
end

- (Object) color

BranchColor object. Apply for the whole clade unless overwritten in sub-clade.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 194

def color
  @color
end

- (Object) confidences

Array of Confidence objects. Indicates the support for a clade/parent branch.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 191

def confidences
  @confidences
end

- (Object) date

Date object. A date associated with a clade/node.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 209

def date
  @date
end

- (Object) distributions

Array of Distribution objects. The geographic distribution of the items of a clade (species, sequences), intended for phylogeographic applications.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 206

def distributions
  @distributions
end

- (Object) events

Events at the root node of a clade (e.g. one gene duplication).



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 172

def events
  @events
end

- (Object) id_source

String. Used to link other elements to a clade (node) (on the xml-level).



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 175

def id_source
  @id_source
end

- (Object) name

String. Name of the node.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 178

def name
  @name
end

- (Object) node_id

Id object



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 197

def node_id
  @node_id
end

- (Object) other

Array of Other objects. Used to save additional information from other than PhyloXML namspace.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 219

def other
  @other
end

- (Object) properties

An array of Property objects, for example depth for sea animals.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 215

def properties
  @properties
end

- (Object) references

Array of Reference objects. A literature reference for a clade.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 212

def references
  @references
end

- (Object) sequences

Array of Sequence objects. Represents a molecular sequence (Protein, DNA, RNA) associated with a node.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 200

def sequences
  @sequences
end

- (Object) taxonomies

Array of Taxonomy objects. Describes taxonomic information for a clade.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 188

def taxonomies
  @taxonomies
end

- (Object) width

Float. Branch width for this node (including parent branch). Applies for the whole clade unless overwritten in sub-clades.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 181

def width
  @width
end

Instance Method Details

- (Object) extract_biosequence(seq_i = 0)

Extracts the relevant information from node (specifically taxonomy and sequence) to create Bio::Sequence object. Node can have several sequences, so parameter to this method is to specify which sequence to extract.


Returns

Bio::Sequence



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 269

def extract_biosequence(seq_i=0)

  seq = @sequences[seq_i].to_biosequence
  seq.classification = []
  @taxonomies.each do |t|
    seq.classification << t.scientific_name
    if t.rank == "species"
      seq.species = t.scientific_name
    end
  end

  #seq.division => .. http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_2
  # It doesn't seem there is anything in PhyloXML corresponding to this.

  return seq
end

- (Object) to_biotreenode

Converts to a Bio::Tree::Node object. If it contains several taxonomies Bio::Tree::Node#scientific name will get the scientific name of the first taxonomy.

If there are several confidence values, the first with bootstrap type will be returned as Bio::Tree::Node#bootstrap

tree = phyloxmlparser.next_tree

node = tree.get_node_by_name(“A”).to_biotreenode


Returns

Bio::Tree::Node



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 245

def to_biotreenode
  node = Bio::Tree::Node.new
  node.name = @name
  node.scientific_name = @taxonomies[0].scientific_name if not @taxonomies.empty?
  #@todo what if there are more?
  node.taxonomy_id = @taxonomies[0].taxononmy_id if @taxonomies[0] != nil

  if not @confidences.empty?
    @confidences.each do |confidence|
      if confidence.type == "bootstrap"
        node.bootstrap = confidence.value
        break
      end
    end
  end      
  return node
end

- (Object) to_xml(branch_length, write_branch_length_as_subelement)

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



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 287

def to_xml(branch_length,  write_branch_length_as_subelement)
  clade = LibXML::XML::Node.new('clade')
  
  PhyloXML::Writer.generate_xml(clade, self, [[:simple, 'name', @name]])

  if branch_length != nil       
    if write_branch_length_as_subelement
      clade << LibXML::XML::Node.new('branch_length', branch_length.to_s)
    else
      clade["branch_length"] = branch_length.to_s
    end
  end

  #generate all elements, except clade
  PhyloXML::Writer.generate_xml(clade, self, [
      [:attr, "id_source"],
      [:objarr, 'confidence', 'confidences'],
      [:simple, 'width', @width],
      [:complex, 'branch_color', @branch_color],
      [:simple, 'node_id', @node_id],
      [:objarr, 'taxonomy', 'taxonomies'],
      [:objarr, 'sequence', 'sequences'],
      [:complex, 'events', @events],
      [:complex, 'binary_characters', @binary_characters],          
      [:objarr, 'distribution', 'distributions'],
      [:complex, 'date', @date],          
      [:objarr, 'reference', 'references'],
      [:objarr, 'propery', 'properties']])
 
  return clade
end