/// <summary>
/// Initializes a new instance of the <see cref="ProteoformGroupFactory"/> class.
/// </summary>
/// <param name="elementProvider">The element provider.</param>
/// <param name="residueProvider">The residue provider.</param>
public ProteoformGroupFactory(IElementProvider elementProvider, IResidueProvider residueProvider)
{
_elementProvider = elementProvider;
_residueProvider = residueProvider;
_water = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement(1), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement(8), 1),
});
}
public void Setup()
{
_elementProvider = new MockElementProvider();
_residueProvider = new IupacAminoAcidProvider(_elementProvider);
_factory = new ProteoformGroupFactory(_elementProvider, _residueProvider);
var parser = new ResidXmlParser();
var modifications = parser.Parse(ResidXmlParserTest.GetResidFilePath()).ToArray();
_residLookup = ResidModificationLookup.CreateFromModifications(modifications.Where(x => x.Id == "AA0038" || x.Id == "AA0074"),
_elementProvider);
}
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);
}