Method: Bio::Abif#initialize

Defined in:
lib/bio/db/sanger_chromatogram/abif.rb

#initialize(string) ⇒ Abif

see SangerChromatogram class for how to create an Abif object and its usage



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# File 'lib/bio/db/sanger_chromatogram/abif.rb', line 37

def initialize(string)
  header = string.slice(0,128)
  # read in header info
  @chromatogram_type, @version, @directory_tag_name, @directory_tag_number, @directory_element_type, @directory_element_size, @directory_number_of_elements, @directory_data_size, @directory_data_offset, @directory_data_handle= header.unpack("a4 n a4 N n n N N N N")
  @version = @version/100.to_f
  get_directory_entries(string)
  # get sequence
  @sequence = @directory_entries["PBAS"][1].data.map{|char| char.chr.downcase}.join("")
  #get peak indices
  @peak_indices = @directory_entries["PLOC"][1].data
  #get qualities
  @qualities = @directory_entries["PCON"][1].data
  # get sample title
  @sample_title = @directory_entries["SMPL"][1].data
  @directory_entries["PDMF"].size > 2 ? @dye_mobility = @directory_entries["PDMF"][2].data : @dye_mobility = @directory_entries["PDMF"][1].data
  #get trace data
  @chemistry = @directory_entries["phCH"][1].data
  base_order = @directory_entries["FWO_"][1].data.map{|char| char.chr.downcase}
  (9..12).each do |data_index|
    self.instance_variable_set("@#{base_order[data_index-9]}trace", @directory_entries["DATA"][data_index].data)
  end

end