Class: BioDSL::Taxonomy::Search::TaxPath

Inherits:
Object
  • Object
show all
Defined in:
lib/BioDSL/taxonomy.rb

Overview

Class holding methods for manipulating tanomic paths.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(node_id, kmers_observed, kmers_total, tax_index) ⇒ TaxPath

Constructor method for TaxPath objects.



652
653
654
655
656
657
658
 
# File 'lib/BioDSL/taxonomy.rb', line 652

def initialize(node_id, kmers_observed, kmers_total, tax_index)
  @node_id        = node_id
  @kmers_observed = kmers_observed
  @kmers_total    = kmers_total
  @tax_index      = tax_index
  @nodes          = taxonomy_backtrack
end

Instance Attribute Details

#nodes ⇒ Object (readonly)

Returns the value of attribute nodes.



649
650
651
 
# File 'lib/BioDSL/taxonomy.rb', line 649

def nodes
  @nodes
end

Instance Method Details

#taxonomy_backtrack ⇒ Object

Method that returns a list of nodes for a given node_id and all parent ids up the taxonomy tree.



662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
 
# File 'lib/BioDSL/taxonomy.rb', line 662

def taxonomy_backtrack
  nodes = []

  node_id = @node_id

  while (node = @tax_index[node_id])
    nodes << node

    break if node.level == :r # At root level

    node_id = node.parent_id
  end

  nodes.reverse
end

#to_s ⇒ Object

Returns formatted taxonomy string.



679
680
681
682
683
684
685
686
687
 
# File 'lib/BioDSL/taxonomy.rb', line 679

def to_s
  levels = []

  @nodes[1..-1].each do |node|
    levels << "#{node.level.upcase}##{node.name}"
  end

  levels.join(';')
end