Class: MiGA::TaxIndex

Inherits:
MiGA
  • Object
show all
Defined in:
lib/miga/tax_index.rb

Overview

Indexing methods based on taxonomy.

Constant Summary

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from Common::Path

#root_path, #script_path

Methods included from Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from Common::Net

#download_file_ftp, #known_hosts, #remote_connection

Methods included from Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

#initialize ⇒ TaxIndex

Initialize an empty MiGA::TaxIndex



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# File 'lib/miga/tax_index.rb', line 19

def initialize
  @root = MiGA::TaxIndexTaxon.new(:root, 'biota')
  @datasets = []
end

Instance Attribute Details

#datasets ⇒ Object (readonly)

Datasets in the index.



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# File 'lib/miga/tax_index.rb', line 13

def datasets
  @datasets
end

#root ⇒ Object (readonly)

Taxonomy root.



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# File 'lib/miga/tax_index.rb', line 15

def root
  @root
end

Instance Method Details

#<<(dataset) ⇒ Object

Index dataset, a MiGA::Dataset object.



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# File 'lib/miga/tax_index.rb', line 26

def <<(dataset)
  return nil if dataset.metadata[:tax].nil?

  taxon = @root
  MiGA::Taxonomy.KNOWN_RANKS.each do |rank|
    next if rank == :ns

    taxon = taxon.add_child(rank, dataset.metadata[:tax][rank])
  end
  taxon.add_dataset dataset
  @datasets << dataset
end

#taxa_by_rank(rank) ⇒ Object

Finds all the taxa in the collection at the rank taxonomic rank



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# File 'lib/miga/tax_index.rb', line 41

def taxa_by_rank(rank)
  rank = MiGA::Taxonomy.normalize_rank(rank)
  taxa = [@root]
  select = []
  loop do
    new_taxa = []
    taxa.map(&:children).flatten.each do |ch|
      if ch.rank == rank
        select << ch
      elsif !ch.children.empty?
        new_taxa << ch
      end
    end
    taxa = new_taxa
    break if taxa.empty?
  end
  select
end

#to_json ⇒ Object

Generate JSON String for the index.



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# File 'lib/miga/tax_index.rb', line 62

def to_json
  MiGA::Json.generate(
    root: root.to_hash,
    datasets: datasets.map(&:name)
  )
end

#to_tab(unknown = false) ⇒ Object

Generate tabular String for the index.



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# File 'lib/miga/tax_index.rb', line 71

def to_tab(unknown = false)
  root.to_tab(unknown)
end