Contents

require File.join(File.dirname(__FILE__), '../../tap_test_helper.rb') 
require 'ms/in_silico/digest'

class Ms::InSilico::DigestTest < Test::Unit::TestCase
  include Ms::InSilico
  acts_as_tap_test
  acts_as_shell_test(
    :cmd_pattern => '% ',
    :env => {'TAP_GEMS' => ''}
  )
  
  attr_accessor :d
  
  def setup
    super
    @d = Digest.new
  end
  
  def test_digest_documentation
    sh_test %q{
% rap digest MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG --:i dump
MIVIGR
SIVHPYITNEYEPFAAEK
QQILSIMAG
}
  end
  
  #
  # process test
  #
  
  def test_process_returns_array_of_peptide_fragments
    assert_equal %w{
      MIVIGR
      SIVHPYITNEYEPFAAEK
      QQILSIMAG
    }, d.process("MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG")
  end
  
  def test_process_removes_whitespace_from_sequence
    assert_equal %w{
      MIVIGR
      SIVHPYITNEYEPFAAEK
      QQILSIMAG
    }, d.process("  MIVI\nGRSIVHP  YITNEYEPFA \n\r\nAEKQQILSIMAG\n")
  end
  
  def test_process_skips_header_of_fasta_entries
    assert_equal %w{
      MIVIGR
      SIVHPYITNEYEPFAAEK
      QQILSIMAG
    }, d.process(">header\nMIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG")
  end
  
  def test_process_filters_on_min_max_length
    d.min_length = 9
    d.max_length = 9
    assert_equal %w{
      QQILSIMAG
    }, d.process("MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG")
    
    d.min_length = 6
    d.max_length = 18
    assert_equal %w{
      MIVIGR
      SIVHPYITNEYEPFAAEK
      QQILSIMAG
    }, d.process("MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG")
  end
  
end

Version data entries

3 entries across 3 versions & 1 rubygems

Version	Path
ms-in_silico-0.4.2	test/ms/in_silico/digest_test.rb
ms-in_silico-0.4.1	test/ms/in_silico/digest_test.rb
ms-in_silico-0.4.0	test/ms/in_silico/digest_test.rb