class BioDSL::Taxonomy::Search::TaxPath
Class holding methods for manipulating tanomic paths.
Attributes
nodes[R]
Public Class Methods
new(node_id, kmers_observed, kmers_total, tax_index)
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Constructor method for TaxPath
objects.
# 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
Public Instance Methods
taxonomy_backtrack()
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Method that returns a list of nodes for a given node_id and all parent ids up the taxonomy tree.
# 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()
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Returns formatted taxonomy string.
# 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