Class: Bio::NeXML::Trees

Inherits:

Object

• Object
• Bio::NeXML::Trees

show all

Includes:

Mapper

Defined in:

lib/bio/db/nexml/trees.rb

Constant Summary

@@writer =

Bio::NeXML::Writer.new

Instance Attribute Summary (collapse)

• - (Object) id

  Returns the value of attribute id.

• - (Object) label

  Returns the value of attribute label.

Instance Method Summary (collapse)

• - (Object) <<(object)

  Add a tree or a network to self.

• - (Object) [](id)

  Fetch a tree or a network by id.

• - (Object) add_network
• - (Object) add_tree
• - (Object) count (also: #length)

  Returns total number of trees and networks.

• - (Object) create_network(int = false, options = {})
• - (Object) create_tree(int = false, options = {})
• - (Object) delete_network
• - (Object) delete_tree
• - (Object) each(&block)

  Iterate over each element.

• - (Object) each_network(&block)
• - (Object) each_network_with_id(&block)
• - (Object) each_tree(&block)
• - (Object) each_tree_with_id(&block)
• - (Object) get_network_by_id
• - (Object) get_tree_by_id
• - (Boolean) has_network?(tree)
• - (Boolean) has_tree?(tree)
• - (Boolean) include?(object) (also: #has?)
• - (Trees) initialize(id = nil, options = {}, &block) constructor

  Create a trees object.

• - (Object) number_of_networks
• - (Object) number_of_trees
• - (Object) to_xml

Methods included from Mapper

#properties

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# File 'lib/bio/db/nexml/trees.rb', line 578

def initialize( id = nil, options = {}, &block )
  @id = id
  properties( options ) unless options.empty?
  block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
end

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# File 'lib/bio/db/nexml/trees.rb', line 565

def id
  @id
end

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# File 'lib/bio/db/nexml/trees.rb', line 566

def label
  @label
end

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# File 'lib/bio/db/nexml/trees.rb', line 591

def <<( object )
  case object
  when Network
    add_network( object )
  when Tree
    add_tree( object )
  end
  self
end

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# File 'lib/bio/db/nexml/trees.rb', line 614

def []( id )
  get_tree_by_id( id ) ||
    get_network_by_id( id )
end

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# File 'lib/bio/db/nexml/trees.rb', line 588

def add_network; end

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# File 'lib/bio/db/nexml/trees.rb', line 585

def add_tree; end

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# File 'lib/bio/db/nexml/trees.rb', line 638

def count
  number_of_trees + number_of_networks
end

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# File 'lib/bio/db/nexml/trees.rb', line 558

def create_network( int = false, options = {} )
  type = int ? Bio::NeXML::IntNetwork : Bio::NeXML::FloatNetwork
  network = type.new( Bio::NeXML.generate_id( type ), options )
  self << network
  network
end

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# File 'lib/bio/db/nexml/trees.rb', line 551

def create_tree( int = false, options = {} )
  type = int ? Bio::NeXML::IntTree : Bio::NeXML::FloatTree
  tree = type.new( Bio::NeXML.generate_id( type ), options )
  self << tree
  tree
end

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# File 'lib/bio/db/nexml/trees.rb', line 605

def delete_network; end

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# File 'lib/bio/db/nexml/trees.rb', line 602

def delete_tree; end

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# File 'lib/bio/db/nexml/trees.rb', line 658

def each( &block )
  @trees.merge( @networks ).each( &block )
end

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# File 'lib/bio/db/nexml/trees.rb', line 651

def each_network( &block ); end

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# File 'lib/bio/db/nexml/trees.rb', line 655

def each_network_with_id( &block ); end

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# File 'lib/bio/db/nexml/trees.rb', line 644

def each_tree( &block ); end

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# File 'lib/bio/db/nexml/trees.rb', line 648

def each_tree_with_id( &block ); end

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# File 'lib/bio/db/nexml/trees.rb', line 611

def get_network_by_id; end

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# File 'lib/bio/db/nexml/trees.rb', line 608

def get_tree_by_id; end

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# File 'lib/bio/db/nexml/trees.rb', line 623

def has_network?( tree ); end

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# File 'lib/bio/db/nexml/trees.rb', line 620

def has_tree?( tree ); end

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# File 'lib/bio/db/nexml/trees.rb', line 625

def include?( object )
  has_tree?( object ) ||
    has_network?( object )
end

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# File 'lib/bio/db/nexml/trees.rb', line 635

def number_of_networks; end

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# File 'lib/bio/db/nexml/trees.rb', line 632

def number_of_trees; end

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# File 'lib/bio/db/nexml/trees.rb', line 537

def to_xml
  node = @@writer.create_node( "trees", @@writer.attributes( self, :id, :label, :otus ) )

  self.each_tree do |tree|
    node << tree.to_xml
  end

  self.each_network do |network|
    node << network.to_xml
  end

  node
end