public void Equal_When_All_Fields_Are_Equal()
{
var x = new Composition
{
Code = 1,
GnEenh = 2,
GnGnK = 3,
GnHoev = 4,
GnStam = 5,
MutKod = MutKod.RecordNotChanged,
SrtCde = 6,
StAdd = true,
StEenh = 7,
StHoev = 8,
ThsrTc = 9,
TsGneH = 11,
TsStEh = 12
};
var y = new Composition
{
Code = 1,
GnEenh = 2,
GnGnK = 3,
GnHoev = 4,
GnStam = 5,
MutKod = MutKod.RecordNotChanged,
SrtCde = 6,
StAdd = true,
StEenh = 7,
StHoev = 8,
ThsrTc = 9,
TsGneH = 11,
TsStEh = 12
};
var comparer = new CompositionComparer();
Assert.IsTrue(comparer.Equals(x, y));
}
public ShaderSourceComparer()
{
compositionComparer = new CompositionComparer(this);
}
static void Main(string[] args)
{
if (args.Length < 2)
{
Console.WriteLine("Usage: ParseIsotopeAbundancesFromNIST <input_file. <output_file>");
Console.WriteLine(
"Assumes input file contains text produced by https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=all ");
Console.WriteLine("There should be an example checked in to the Inputs folder of this program's source code directory.");
Console.WriteLine("Output file will contain a code snippet suitable for updating /pwiz_tools/Shared/Common/Chemistry/IsotopeAbundances.cs");
Environment.Exit(1);
}
// Parse the report of entries like:
//
// Atomic Number = 1
// Atomic Symbol = H
// Mass Number = 1
// Relative Atomic Mass = 1.00782503223(9)
// Isotopic Composition = 0.999885(70)
// Standard Atomic Weight = [1.00784, 1.00811]
// Notes = m
//
//
// in order to build strings like:
// {"H",new []{1.007825035,0.999855,2.014101779,0.000145,}},
// Notes:
// Not all entries report Isoptopic Composition, and not all report a Standard Atomic Weight
// For most elements, at least one Isotopic Composition is reported, for those elements we discard any entries not reporting Isotopic Composition as being uncommon.
// For elements which report no Isotopic Composition, use the reported Standard Atomic Weight and claim isotopic composition 1.0 per Skyline custom
// For elements which report neither Isotopic Composition nor Standard Atomic Weight, use the middle reported mass value and claim isotopic composition 1.0 per Skyline custom
var comparer = new CompositionComparer();
var elementNumbers = new Dictionary <string, SortedList <string, string> >();
var elementNames = new Dictionary <string, string>();
var standardAtomicWeights = new Dictionary <string, string>();
var text = File.ReadAllLines(args[0]).ToList();
var indices = Enumerable.Range(0, text.Count).Where(t => text[t].StartsWith(@"Atomic Number =")).ToArray();
foreach (var index in indices)
{
var elementNumber = text[index].Split('=')[1].Trim();
if (!elementNames.ContainsKey(elementNumber)) // May find more than one name per number, as in H, D, T
{
elementNames.Add(elementNumber, text[index + 1].Split('=')[1].Trim());
}
var mass = text[index + 3].Split('=')[1].Trim().Split('(')[0];
var composition = text[index + 4].Split('=')[1].Trim().Split('(')[0];
var standardAtomicWeight = text[index + 5].Split('=')[1].Trim();
if (standardAtomicWeight.StartsWith(@"["))
{
standardAtomicWeight = standardAtomicWeight.Substring(1).Replace(@"]", @".0").Trim();
standardAtomicWeights[elementNumber] = standardAtomicWeight;
}
if (!elementNumbers.TryGetValue(elementNumber, out _))
{
elementNumbers.Add(elementNumber, new SortedList <string, string>(comparer));
}
elementNumbers[elementNumber].Add(mass, composition);
}
var output = new List <string>();
output.Add(" // " + text[0]); // Hopefuly it says something about source and date, like "These values obtained 3/25/2019 from https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some"
foreach (var elementNumber in elementNumbers)
{
var line = " {\"" + elementNames[elementNumber.Key] + "\", new[]{";
int nIsotopes = 0;
foreach (var pair in elementNumber.Value)
{
var composition = pair.Value;
if (!string.IsNullOrEmpty(composition) && double.Parse(composition, CultureInfo.InvariantCulture) > 0)
{
if (Equals("1", composition))
{
composition = "1.0";
}
line += pair.Key + "," + composition + ",";
nIsotopes++;
}
}
if (nIsotopes == 0)
{
// Nothing declared as stable, take the declared standard atomic weightm or failing that use the middle value in the list
var mass = standardAtomicWeights.TryGetValue(elementNumber.Key, out var stdWeight) ? stdWeight : elementNumber.Value.Keys.ToArray()[elementNumber.Value.Count / 2];
line += mass + "," + "1.0" + ",";
}
line += "}},";
Console.WriteLine(line);
output.Add(line);
}
File.WriteAllLines(args[1], output);
Console.WriteLine("code snippet written to " + args[1]);
}
public void Return_Correct_HashCode_From_Fields()
{
var composition = new Composition
{
Code = 1,
GnEenh = 2,
GnGnK = 3,
GnHoev = 4,
GnStam = 5,
MutKod = MutKod.RecordNotChanged,
SrtCde = 6,
StAdd = true,
StEenh = 7,
StHoev = 8,
ThsrTc = 9,
TsGneH = 11,
TsStEh = 12
};
int expectedHashCode = composition.Code ^ composition.GnEenh ^ composition.GnGnK ^
composition.GnHoev.GetHashCode() ^ composition.GnStam ^
(byte)composition.MutKod ^ composition.SrtCde ^ composition.StAdd.GetHashCode() ^
composition.StEenh ^ composition.StHoev.GetHashCode() ^
composition.ThsrTc ^ composition.TsGneH ^ composition.TsStEh;
var comparer = new CompositionComparer();
int result = comparer.GetHashCode(composition);
Assert.AreEqual(expectedHashCode, result);
}
public void Not_Equal_When_TsStEh_Is_Different()
{
var x = new Composition
{
Code = 1,
GnEenh = 2,
GnGnK = 3,
GnHoev = 4,
GnStam = 5,
MutKod = MutKod.RecordNotChanged,
SrtCde = 6,
StAdd = true,
StEenh = 7,
StHoev = 8,
ThsrTc = 9,
TsGneH = 11,
TsStEh = 12
};
var y = new Composition
{
Code = 1,
GnEenh = 2,
GnGnK = 3,
GnHoev = 4,
GnStam = 5,
MutKod = MutKod.RecordNotChanged,
SrtCde = 6,
StAdd = true,
StEenh = 7,
StHoev = 8,
ThsrTc = 9,
TsGneH = 11,
TsStEh = 13
};
var comparer = new CompositionComparer();
Assert.IsFalse(comparer.Equals(x, y));
}