class Ulla::JoyTem

Attributes

entries[R]
file[R]

Public Class Methods

new(file) click to toggle source
# File lib/ulla/joy_tem.rb, line 6
def initialize(file)
  @file     = file
  io        = File.exist?(file) ? File.open(file, 'r') : StringIO.new(file)
  @entries  = {}
  ent_code  = nil
  ent_desc  = nil
  ent_data  = nil
  parse_tag = nil

  io.each_with_index do |line, li|
    line.chomp!
    if    line =~ /^#/ || line =~ /^\s*$/
      next
    elsif line =~ /^>\S+;(\S+)/
      parse_tag = :desc
      ent_code  = $1
      @entries[ent_code] = {} unless @entries.has_key?(ent_code)
    elsif line =~ /^(\S+.*)/ && parse_tag == :desc
      parse_tag = :data
      ent_desc  = $1.strip
      @entries[ent_code][ent_desc]  = ''
    elsif line =~ /^\s*(\S+.*)/ && parse_tag == :data
      ent_data = $1.strip.gsub('*', '')
      @entries[ent_code][ent_desc] += ent_data
    else
      $logger.error "Cannot parse line #{li+1}: #{line}"
      exit 1
    end
  end
end

Public Instance Methods

alignment_length() click to toggle source
# File lib/ulla/joy_tem.rb, line 45
def alignment_length
  @entries[entry_codes[0]][entry_descriptions[0]].length
end
entry_codes() click to toggle source
# File lib/ulla/joy_tem.rb, line 37
def entry_codes
  @entries.keys
end
entry_descriptions() click to toggle source
# File lib/ulla/joy_tem.rb, line 41
def entry_descriptions
  @entries[entry_codes[0]].keys
end
sequences() click to toggle source
# File lib/ulla/joy_tem.rb, line 49
def sequences
  seqs = []
  @entries.keys.each do |code|
    if @entries[code].has_key?('sequence')
      seqs << Sequence.new(@entries[code]['sequence'], code)
    else
      $logger.error "Cannot find 'sequence' data for #{code} in JOY template: #{@file}"
      exit 1
    end
  end
  seqs
end