Method: Bio::AAindex1#index

Defined in:
lib/bio/db/aaindex.rb

#index(type = :float) ⇒ Object

Returns the index (Array) in the I line.

an argument: :string, :float, :zscore or :integer



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# File 'lib/bio/db/aaindex.rb', line 214

def index(type = :float)
  aa = %w( A R N D C Q E G H I L K M F P S T W Y V )
  values = field_fetch('I', 1).split(' ')

  if values.size != 20
    raise "Invalid format in #{entry_id} : #{values.inspect}"
  end

  if type == :zscore and values.size > 0
    sum = 0.0
    values.each do |a|
      sum += a.to_f
    end
    mean = sum / values.size # / 20
    var = 0.0
    values.each do |a|
      var += (a.to_f - mean) ** 2
    end
    sd = Math.sqrt(var)
  end

  if type == :integer
    figure = 0
    values.each do |a|
      figure = [ figure, a[/\..*/].length - 1 ].max
    end
  end

  hash = {}

  aa.each_with_index do |a, i|
    case type
    when :string
      hash[a] = values[i]
    when :float
      hash[a] = values[i].to_f
    when :zscore
      hash[a] = (values[i].to_f - mean) / sd
    when :integer
      hash[a] = (values[i].to_f * 10 ** figure).to_i
    end
  end
  return hash
end