public void Setup()
{
//_elementProvider = new MockElementProvider();
NistElementParser parser = new NistElementParser();
IElement[] elements = parser.ParseFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "elements.dat")).ToArray();
_elementProvider = new InMemoryElementProvider(elements);
this.SetupUnimod();
this.SetupResid();
this.SetupPsiMod();
this.SetupUniProt();
this.SetupFormula();
}
public void LoadEntireFile()
{
var parser = new NistElementParser();
var elements = parser.ParseFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "elements.dat"));
Assert.IsNotNull(elements);
Assert.AreEqual(84, elements.Count); // Only count elements with isotope abundances
var h = elements.Single(x => x.AtomicNumber == 1);
Assert.AreEqual("H", h.Symbol);
Assert.AreEqual(2, h.Isotopes.Count);
var h1 = h.Isotopes.Single(x => x.AtomicMass < 2);
Assert.AreEqual(1.00782503223, h1.AtomicMass);
Assert.AreEqual(0.999885, h1.RelativeAbundance);
var h2 = h.Isotopes.Single(x => x.AtomicMass > 2);
Assert.AreEqual(2.01410177812, h2.AtomicMass);
Assert.AreEqual(0.000115, h2.RelativeAbundance);
var c = elements.Single(x => x.AtomicNumber == 6);
var c12 = c.Isotopes.Single(x => Math.Round(x.AtomicMass) == 12);
Assert.AreEqual(6, c12.NeutronCount);
var c13 = c.Isotopes.Single(x => Math.Round(x.AtomicMass) == 13);
Assert.AreEqual(7, c13.NeutronCount);
var ru = elements.Single(x => x.AtomicNumber == 44);
Assert.AreEqual("Ru", ru.Symbol);
Assert.AreEqual(7, ru.Isotopes.Count);
var xe = elements.Single(x => x.AtomicNumber == 54);
Assert.AreEqual("Xe", xe.Symbol);
Assert.AreEqual(9, xe.Isotopes.Count);
var u = elements.Single(x => x.AtomicNumber == 92);
Assert.AreEqual("U", u.Symbol);
Assert.AreEqual(3, u.Isotopes.Count);
}
public void Setup()
{
var unimodOboParser = new UnimodOboParser();
UnimodModification[] modifications = unimodOboParser.Parse(UnimodTest.GetUnimodFilePath()).ToArray();
NistElementParser nistParser = new NistElementParser();
IElement[] elements = nistParser.ParseFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "elements.dat")).ToArray();
_elementProvider = new InMemoryElementProvider(elements);
_residueProvider = new IupacAminoAcidProvider(_elementProvider);
var atomProvider = new UnimodHardCodedAtomProvider(_elementProvider);
_lookup = new CompositeModificationLookup(new IProteoformModificationLookup[]
{
UnimodModificationLookup.CreateFromModifications(modifications, atomProvider),
new FormulaLookup(_elementProvider),
new MassLookup(),
new BrnoModificationLookup(_elementProvider),
new IgnoreKeyModificationLookup(ProFormaKey.Info),
});
ProFormaParser proFormaParser = new ProFormaParser();
ProteoformGroupFactory proteoformGroupFactory = new ProteoformGroupFactory(_elementProvider, _residueProvider);
var mapper = new RelayAccessionMapper(d =>
{
if (d == "B:ac")
{
return(Tuple.Create(ProFormaEvidenceType.PsiMod, "MOD:00394")); // acetylated residue
}
return(Tuple.Create(ProFormaEvidenceType.None, d));
});
var parser = new UniProtPtmListParser();
var entries = parser.Parse(File.ReadAllText(UniProtTests.GetPtmListPath())).ToList();
_chemicalProteoformHashGenerator = new ChemicalProteoformHashGenerator(proFormaParser, proteoformGroupFactory, _lookup, mapper);
}
