Class: Bio::PhyloXML::Node

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

Overview

Description

Class to hold clade element of phyloXML.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Node

Returns a new instance of Node.



209
210
211
212
213
214
215
216
217
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 209

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

Instance Attribute Details

#binary_characters ⇒ Object

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



191
192
193
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 191

def binary_characters
  @binary_characters
end

#color ⇒ Object

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



182
183
184
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 182

def color
  @color
end

#confidences ⇒ Object

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



179
180
181
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 179

def confidences
  @confidences
end

#date ⇒ Object

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



197
198
199
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 197

def date
  @date
end

#distributions ⇒ Object

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



194
195
196
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 194

def distributions
  @distributions
end

#events ⇒ Object

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



160
161
162
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 160

def events
  @events
end

#id_source ⇒ Object

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



163
164
165
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 163

def id_source
  @id_source
end

#name ⇒ Object

String. Name of the node.



166
167
168
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 166

def name
  @name
end

#node_id ⇒ Object

Id object



185
186
187
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 185

def node_id
  @node_id
end

#other ⇒ Object

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



207
208
209
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 207

def other
  @other
end

#properties ⇒ Object

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



203
204
205
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 203

def properties
  @properties
end

#references ⇒ Object

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



200
201
202
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 200

def references
  @references
end

#sequences ⇒ Object

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



188
189
190
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 188

def sequences
  @sequences
end

#taxonomies ⇒ Object

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



176
177
178
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 176

def taxonomies
  @taxonomies
end

#width ⇒ Object

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



169
170
171
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 169

def width
  @width
end

Instance Method Details

#extract_biosequence(seq_i = 0) ⇒ Object

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



257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 257

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

#to_biotreenode ⇒ Object

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



233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 233

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

#to_xml(branch_length, write_branch_length_as_subelement) ⇒ Object

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



275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
 
# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 275

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

  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', (defined? @width) ? @width : nil],
      [:complex, 'branch_color', (defined? @branch_color) ? @branch_color : nil],
      [:simple, 'node_id', (defined? @node_id) ? @node_id : nil],
      [:objarr, 'taxonomy', 'taxonomies'],
      [:objarr, 'sequence', 'sequences'],
      [:complex, 'events', (defined? @events) ? @events : nil],
      [:complex, 'binary_characters', (defined? @binary_characters) ? @binary_characters : nil],
      [:objarr, 'distribution', 'distributions'],
      [:complex, 'date', (defined? @date) ? @date : nil],
      [:objarr, 'reference', 'references'],
      [:objarr, 'propery', 'properties']])
 
  return clade
end