/// <summary> /// Initializes a new instance of the <see cref="ChemicalProteoformHashGenerator" /> class. /// </summary> /// <param name="proFormaParser">The proForma parser.</param> /// <param name="proteoformGroupFactory">The proteoform group factory.</param> /// <param name="proteoformModificationLookup">The proteoform modification lookup.</param> /// <param name="mapper">The mapper.</param> public ChemicalProteoformHashGenerator(ProFormaParser proFormaParser, ProteoformGroupFactory proteoformGroupFactory, IProteoformModificationLookup proteoformModificationLookup, IAccessionMapper mapper) { _proFormaParser = proFormaParser; _proteoformGroupFactory = proteoformGroupFactory; _proteoformModificationLookup = proteoformModificationLookup; _mapper = mapper; }
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); }