Class: Bio::PhyloXML::Tree

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

Overview

Object to hold one phylogeny element (and its subelements.) Extended version of Bio::Tree.

Constant Summary

Constants inherited from Tree

Tree::DEFAULT_OPTIONS

Instance Attribute Summary collapse

Attributes inherited from Tree

#options, #root

Instance Method Summary collapse

Methods inherited from Tree

#add_edge, #add_node, #adjacency_matrix, #adjacent_nodes, #ancestors, #children, #clear, #clear_node, #collect_edge!, #collect_node!, #concat, #descendents, #distance, #distance_matrix, #each_edge, #each_edge_in_path, #each_node, #each_out_edge, #edges, #get_edge, #get_edge_distance, #get_edge_distance_string, #get_edge_merged, #get_node_bootstrap, #get_node_bootstrap_string, #get_node_by_name, #get_node_name, #include?, #insert_node, #leaves, #lowest_common_ancestor, #nodes, #number_of_edges, #number_of_nodes, #out_degree, #out_edges, #output, #output_newick, #output_nhx, #output_phylip_distance_matrix, #parent, #path, #remove_edge, #remove_edge_if, #remove_node, #remove_node_if, #remove_nonsense_nodes, #subtree, #subtree_with_all_paths, #total_distance

Constructor Details

#initialize ⇒ Tree

Returns a new instance of Tree.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 154

def initialize
  super
  @sequence_relations = []
  @clade_relations = []
  @confidences = []
  @properties = []
  @other = []
end

Instance Attribute Details

#branch_length_unit ⇒ Object

String.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 142

def branch_length_unit
  @branch_length_unit
end

#clade_relations ⇒ Object

CladeRelation object. This is used to express a typed relationship between two clades. For example it could be used to describe multiple parents of a clade.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 133

def clade_relations
  @clade_relations
end

#confidences ⇒ Object

Array of confidence object



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 139

def confidences
  @confidences
end

#date ⇒ Object

String. Date



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 148

def date
  @date
end

#description ⇒ Object

String. Description of tree.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 121

def description
  @description
end

#name ⇒ Object

String. Name of tree (name subelement of phylogeny element).



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 115

def name
  @name
end

#other ⇒ Object

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 152

def other
  @other
end

#phylogeny_id ⇒ Object

Id object.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 118

def phylogeny_id
  @phylogeny_id
end

#properties ⇒ Object

Array of Property object. Allows for typed and referenced properties from external resources to be attached.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 130

def properties
  @properties
end

#rerootable ⇒ Object

Boolean. Can be used to indicate that the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent data, such as gene duplications).



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 124

def rerootable
  @rerootable
end

#rooted ⇒ Object

Boolean. Required element.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 127

def rooted
  @rooted
end

#sequence_relations ⇒ Object

SequenceRelation object. This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 136

def sequence_relations
  @sequence_relations
end

#type ⇒ Object

String. Indicate the type of phylogeny (i.e. ‘gene tree’).



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 145

def type
  @type
end