constants 0.1.0

data/test/constants/constant_test.rb

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+require File.join(File.dirname(__FILE__), '../constants_test_helper.rb') 
+require 'constants/constant'
+
+class ConstantTest < Test::Unit::TestCase
+  include Constants
+  
+  #
+  # parse test
+  #
+  
+  def test_parse_documentation
+    assert_equal [1.0, 0.2], Constant.parse("1.0(2)").to_a
+    assert_equal [1.0078250321, 1/2500000000], Constant.parse("1.007 825 032 1(4)").to_a
+    assert_equal [6.62606896, nil], Constant.parse("6.626 068 96").to_a
+  end
+  
+  def test_parse
+    assert_equal [1.0, nil], Constant.parse("1.0").to_a
+    assert_equal [1.0, 0], Constant.parse("1.0(0)").to_a
+    assert_equal [1.0, 0.1], Constant.parse("1.0(1)").to_a
+    assert_equal [100, 1], Constant.parse("100(1)").to_a
+    assert_equal [100, 11], Constant.parse("100(11)").to_a
+    assert_equal [1234.54789, 0.00011], Constant.parse("1234.54789(11)").to_a
+    assert_equal [1234.54789, 0.00011], Constant.parse("1234.547 89 (11)").to_a
+    assert_equal [1000, 100], Constant.parse("1.0(1)e3").to_a
+    assert_equal [0.001, 0.0001], Constant.parse("1.0(1)e-3").to_a
+  end
+  
+  #
+  # == test
+  #
+  
+  def test_equal_compares_Numerics_with_value
+    c = Constant.new(1.23)
+    assert c == 1.23
+    assert c != 1.24
+    
+    assert_equal 1.23, c
+    assert_not_equal 1.24, c
+  end
+  
+  def test_equal_compares_non_Numerics_directly
+    c1 = Constant.new(1.23)
+    c2 = Constant.new(1.23)
+    c3 = Constant.new(1.24)
+    
+    assert c1 == c2
+    assert c1 != c3
+  end
+  
+  #
+  # <=> test
+  #
+  
+  def test_compare_compares_on_value
+    c1 = Constant.new(1.23)
+    c2 = Constant.new(1.23)
+    c3 = Constant.new(1.24)
+    
+    assert_equal 0, c1 <=> c2
+    assert_equal -1, c1 <=> c3
+    assert_equal 1, c3 <=> c1
+  end
+  
+  #
+  # to_a test
+  #
+  
+  def test_to_a_returns_value_uncertainty_array
+    c = Constant.new(1.23)
+    assert_equal [1.23, nil], c.to_a
+    
+    c = Constant.new(1.23, nil, 0.03)
+    assert_equal [1.23, 0.03], c.to_a
+  end
+ 
+end

data/test/constants/libraries/element_test.rb

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+require File.join(File.dirname(__FILE__), '../../constants_test_helper.rb') 
+require 'constants/libraries/element'
+
+class ElementTest < Test::Unit::TestCase
+  include Constants::Libraries
+  
+  #
+  # documentation test
+  #
+  
+  def test_documentation
+    e = Element::He
+    assert_equal "Helium", e.name
+    assert_equal "He", e.symbol
+    assert_equal 2, e.atomic_number
+    assert_equal 4.0026032497, e.mass
+    assert_equal [3, 4], e.isotopes
+    assert_equal [0.000137, 99.999863], e.abundances
+  end
+  
+  #
+  # initialize test
+  #
+  
+  def test_initialize
+    c = Element::C
+    
+    assert_equal "C", c.symbol
+    assert_equal "Carbon", c.name
+    assert_equal 6, c.atomic_number
+    assert_equal [12, 13], c.isotopes
+    assert_equal [[12.0, 0], [13.0033548378, 0.000000001]], c.masses.collect {|m| m.to_a}
+    assert_equal [[98.93, 0.08], [1.07, 0.08]], c.abundances.collect {|m| m.to_a}
+    assert_equal 0, c.index_max_abundance
+  end
+  
+  #
+  # lookup test
+  #
+  
+  def test_lookup
+    c = Element::C
+    assert_equal c, Element['C']
+    assert_equal c, Element['Carbon']
+    assert_equal c, Element[6]
+  end
+  
+  def test_lookup_is_nil_for_undefined_elements
+    assert_nil Element['Q']
+    assert_nil Element["Madeupium"]
+    assert_nil Element[102]
+  end
+  
+  #
+  # methods test
+  #
+  
+  def test_has_isotope?
+    assert Element::C.has_isotope?(12)
+    assert Element::C.has_isotope?(13)
+    assert !Element::C.has_isotope?(8)
+  end
+
+  def test_index_isotope
+    assert_equal 0, Element::C.index_isotope(12)
+    assert_equal 1, Element::C.index_isotope(13)
+    assert_equal nil, Element::C.index_isotope(8)
+  end
+  
+  def test_mass
+    assert_equal 12, Element::C.mass
+    assert_equal 12, Element::C.mass(12)
+    assert_equal 13.0033548378, Element::C.mass(13)
+    assert_equal nil, Element::C.mass(8)
+  end
+  
+  def test_abundance
+    assert_equal 98.93, Element::C.abundance
+    assert_equal 98.93, Element::C.abundance(12)
+    assert_equal 1.07, Element::C.abundance(13)
+    assert_equal nil, Element::C.abundance(8)
+  end
+  
+  # vs the Proteome Commons Atom Reference, 2008-01-11
+  # http://www.proteomecommons.org/archive/1129086318745/docs/atom-reference.html
+  #
+  # The website states 'These values are taken from the NIST's list, http://physics.nist.gov'
+  def test_mass_values_vs_proteome_commons
+    str = %Q{
+H 1.0078250321  0.999885
+H2  2.014101778 1.15E-4
+O 15.9949146221 0.9975700000000001
+O17 16.9991315  3.7999999999999997E-4
+O18 17.9991604  0.0020499999999999997
+N14 14.0030740052 0.9963200000000001
+N15 15.0001088984 0.00368
+C12 12.0  0.9893000000000001
+C13 13.0033548378 0.010700000000000001
+P31 30.97376151 1.0
+S32 31.97207069 0.9493
+S33 32.9714585  0.0076
+S34 33.96786683 0.0429
+S36 35.96708088 2.0E-4}
+
+    atoms = str.split(/\n/)
+    atoms.each do |atom_str|
+      next if atom_str.empty?
+      
+      name, mass, abundance = atom_str.split(/\s+/)
+      name =~ /(\w)(\d*)/
+      symbol = $1
+      isotope = $2.empty? ? nil : $2.to_i
+      mass = mass.to_f
+      abundance = abundance.to_f * 100
+      
+      element = Element[symbol]
+      assert_not_nil element, atom_str
+      assert element.has_isotope?(isotope), atom_str unless isotope == nil
+      
+      assert_in_delta mass, element.mass(isotope), delta_mass, atom_str 
+      assert_in_delta abundance, element.abundance(isotope), delta_abundance, atom_str 
+    end
+  end
+  
+  # vs the Unimod Symbols and Mass Values, 2008-01-11
+  # http://www.unimod.org/masses.html
+  #
+  # The website states 'All mass values in Unimod are calculated 
+  # from the IUPAC atomic weights and isotopic abundances 
+  # tabulated by WebElements'
+  #
+  def test_mass_values_vs_unimod
+    str = %Q{
+H Hydrogen  1.007825035 1.00794
+2H  Deuterium 2.014101779 2.014101779
+Li  Lithium 7.016003  6.941
+C Carbon  12  12.0107
+13C Carbon13  13.00335483 13.00335483
+N Nitrogen  14.003074 14.0067
+15N Nitrogen15  15.00010897 15.00010897
+O Oxygen  15.99491463 15.9994
+18O Oxygen18  17.9991603  17.9991603
+F Fluorine  18.99840322 18.9984032
+Na  Sodium  22.9897677  22.98977
+P Phosphorous 30.973762 30.973761
+S Sulfur  31.9720707  32.065
+Cl  Chlorine  34.96885272 35.453
+K Potassium 38.9637074  39.0983
+Ca  Calcium 39.9625906  40.078
+Fe  Iron  55.9349393  55.845
+Ni  Nickel  57.9353462  58.6934
+Cu  Copper  62.9295989  63.546
+Zn  Zinc  63.9291448  65.409
+Br  Bromine 78.9183361  79.904
+Se  Selenium  79.9165196  78.96
+Mo  Molybdenum  97.9054073  95.94
+Ag  Silver  106.905092  107.8682
+I Iodine  126.904473  126.90447
+Au  Gold  196.966543  196.96655
+Hg  Mercury 201.970617  200.59}
+
+    atoms = str.split(/\n/)
+    atoms.each do |atom_str|
+      next if atom_str.empty?
+      
+      symbol, name, monoisotopic, average = atom_str.split(/\s+/)
+      symbol =~ /(\d*)(\w+)/
+      isotope = $1.empty? ? nil : $1.to_i
+      symbol = $2
+      monoisotopic = monoisotopic.to_f
+      average = average.to_f
+      
+      element = Element[symbol]
+      assert_not_nil element, atom_str
+      assert element.has_isotope?(isotope), atom_str unless isotope == nil
+
+      assert_in_delta monoisotopic, element.mass(isotope), delta_mass, atom_str 
+      # TODO -- check average mass
+    end
+  end
+
+  # vs the VG Analytical Organic Mass Spectrometry reference, reference date unknown (prior to 2005)
+  # the data from the data sheet was copied manually to doc/VG Analytical DataSheet.txt
+  def test_mass_values_vs_vg_analytical
+    str = %Q{
+H 1.0078250 1.00794
+C 12 12.011
+N 14.0030740 14.0067
+O 15.9949146 15.9994
+S 31.9720718 32.06}
+
+    atoms = str.split(/\n/)
+    atoms.each do |atom_str|
+      next if atom_str.empty?
+      
+      symbol, monoisotopic, average = atom_str.split(/\s+/)
+      monoisotopic = monoisotopic.to_f
+      average = average.to_f
+      
+      element = Element[symbol]
+      assert_not_nil element, atom_str
+      assert_in_delta monoisotopic, element.mass, delta_mass, atom_str 
+      # TODO -- check average mass
+    end    
+  end
+  
+end

data/test/constants/libraries/particle_test.rb

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+require File.join(File.dirname(__FILE__), '../../constants_test_helper.rb') 
+require 'constants/libraries/particle'
+
+class ParticleTest < Test::Unit::TestCase
+  include Constants::Libraries
+  
+  #
+  # initialize test
+  #
+  
+  def test_initialize
+    c = Particle::CHARM
+
+    assert_equal "Charm", c.name
+    assert_equal "Fermion", c.family
+    assert_equal "Quark", c.group
+    assert_equal "Second", c.generation
+    assert_equal 2.0/3, c.charge
+    assert_equal 0.5, c.spin
+
+    t = Particle::ANTITAU
+
+    assert_equal "Anti-Tau", t.name
+    assert_equal "Fermion", t.family
+    assert_equal "Lepton", t.group
+    assert_equal "Third", t.generation
+    assert_equal -1, t.charge
+    assert_equal 0.5, t.spin
+  end
+  
+  #
+  # lookup test
+  #
+  
+  def test_lookup
+    c = Particle::CHARM
+    assert_equal c, Particle['Charm']
+  end
+  
+  def test_lookup_is_nil_for_undefined_particles
+    assert_nil Particle['Blop']
+  end
+end

data/test/constants/libraries/physical_test.rb

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+require File.join(File.dirname(__FILE__), '../../constants_test_helper.rb') 
+require 'constants/libraries/physical'
+
+class PhysicalTest < Test::Unit::TestCase
+  include Constants::Libraries
+  
+  #
+  # initialize test
+  #
+  
+  def test_initialize
+    c = Physical::SPEED_OF_LIGHT_IN_VACUUM
+    
+    assert_equal "speed of light in vacuum", c.name
+    assert_equal 299792458, c.value
+    assert_equal 0, c.uncertainty
+    assert_equal Unit.new("m/s"), c.unit
+  end
+  
+  #
+  # lookup test
+  #
+  
+  def test_lookup
+    c = Physical::SPEED_OF_LIGHT_IN_VACUUM
+    assert_equal c, Physical["speed of light in vacuum"]
+  end
+  
+  def test_lookup_is_nil_for_undefined_constants
+    assert_nil Physical["made up blah in a blah"]
+  end
+end

data/test/constants/library_test.rb

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+require File.join(File.dirname(__FILE__), '../constants_test_helper.rb') 
+require 'constants/library'
+
+class Constants::LibraryTest < Test::Unit::TestCase
+  include Constants
+  
+  #
+  # documentation test
+  #
+
+  module Color
+    RED = 'red'
+    GREEN = 'green'
+    BLUE = 'blue'
+    GREY = 'grey'
+
+    include Constants::Library
+    library.index_by('name') {|c| c }
+  end
+
+  def test_documentation 
+    ###
+    assert_equal({
+      'red' => Color::RED,
+      'blue' => Color::BLUE,
+      'green' => Color::GREEN,
+      'grey' => Color::GREY},
+    Color.index('name'))
+
+    assert_equal Color::RED, Color['red']
+
+    ###
+    Color.library.index_by_attribute 'length'
+    const_ordered_assert_equal({
+      3 => Color::RED,
+      4 => [Color::BLUE, Color::GREY],
+      5 => Color::GREEN},
+    Color.index('length'))
+
+    const_ordered_assert_equal [Color::BLUE, Color::GREY], Color[4]
+    
+    ###
+    Color.library.collect('gstar') {|c| c =~ /^g/ ? c : nil }
+    const_ordered_assert_equal [Color::GREEN, Color::GREY], Color.collection('gstar')
+
+    Color.library.collect_attribute 'length'
+    const_ordered_assert_equal [3,5,4,4], Color.collection('length')
+
+    ###
+    Color.library.add('yellow')
+    const_ordered_assert_equal({
+      3 => Color::RED,
+      4 => [Color::BLUE, Color::GREY],
+      5 => Color::GREEN,
+      6 => 'yellow'},
+    Color.index('length'))
+
+    Color.module_eval %Q{
+      ORANGE = 'orange'
+      reset_library
+    }
+
+    const_ordered_assert_equal({
+      3 => Color::RED,
+      4 => [Color::BLUE, Color::GREY],
+      5 => Color::GREEN,
+      6 => Color::ORANGE},
+    Color.index('length'))
+  end
+
+  #
+  # extend test 
+  #
+  
+  module ExtendModule
+  end
+  
+  def test_extend_initializes_library
+    ExtendModule.extend Library
+    assert ExtendModule.respond_to?(:library)
+    assert ExtendModule.library.kind_of?(ConstantLibrary)
+  end
+  
+  #
+  # include test 
+  #
+  
+  module IncludeModule
+    include Constants::Library
+  end
+  
+  def test_include_initializes_library
+    assert IncludeModule.respond_to?(:library)
+    assert IncludeModule.library.kind_of?(ConstantLibrary)
+  end
+  
+  #
+  # benchmark tests
+  #
+  
+  module BenchmarkModule
+    include Constants::Library
+    A = 'A'
+    
+    library.index_by("name") {|value| value}
+    reset_library
+  end
+
+  def test_access_speed
+    benchmark_test(24) do |x|
+      n = 100
+      x.report("#{n}k BenchmarkModule::A") do 
+        (n*10**3).times { BenchmarkModule::A }
+      end
+  
+      x.report("#{n}k ['A']") do 
+        (n*10**3).times { BenchmarkModule['A'] }
+      end
+      
+      x.report("#{n}k index('name')['A']") do 
+        (n*10**3).times { BenchmarkModule.index('name')['A'] }
+      end
+    end
+  end
+end