public static void DetectTranslatableControls(this LocalizationEngine engine, Application app) { // Get the type of ITranslatable var translatableControls = new List <Type>(); // Add ITranslatable types foreach (var type in Assembly.GetEntryAssembly().GetTypes().Where(x => x.GetInterfaces().Contains(typeof(ITranslatable)))) { if (typeof(Control).IsAssignableFrom(type)) { translatableControls.Add(type); } } // Translate every control foreach (var controlType in translatableControls) { // If the control type is a Window if (controlType.BaseType == typeof(Window)) { foreach (Window window in app.Windows) { if (window.GetType() == controlType) { } } } } }
static void Main(string[] args) { string url = string.Format(@"http://translate.google.com/translate_a/t?client=j&text={0}&hl=en&sl={1}&tl={2}", HttpUtility.UrlEncode("hello my dear"), "en", "es"); WebClient client = new WebClient(); client.Headers.Add(HttpRequestHeader.UserAgent, "Mozilla/5.0"); client.Headers.Add(HttpRequestHeader.AcceptCharset, "UTF-8"); client.Encoding = Encoding.UTF8; string result = client.DownloadString(url); LocalizationEngine.MakeNew(new PhysicalFileDecoder(Path.Combine(Directory.GetCurrentDirectory(), "langs"))); LocalizationEngine.Instance.DetectLanguages("fr"); Console.WriteLine("Installed languages:"); foreach (var lang in LocalizationEngine.Instance.GetInstalledLanguages()) { Console.WriteLine($"\t- {lang.ToString()}"); } Console.WriteLine($"Current language: {LocalizationEngine.Instance.CurrentLanguage.ToString()}"); LocalizationEngine.Instance.ChangeLanguage(""); string value = LocalizationEngine.Localizator["Titles.Principal"]; Console.WriteLine($"A value: {value}"); // Keep console opened Console.ReadLine(); }
public static void TestLocalization() { var protease = new Protease("Custom Protease", new List <string> { "K" }, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null); Protein parentProteinForMatch = new Protein("MEK", null); DigestionParams digestionParams = new DigestionParams { MinPeptideLength = 1, }; ModificationMotif.TryGetMotif("E", out ModificationMotif motif); List <ModificationWithMass> variableModifications = new List <ModificationWithMass> { new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943) }; List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList(); Assert.AreEqual(4, allPeptidesWithSetModifications.Count()); PeptideWithSetModifications ps = allPeptidesWithSetModifications.First(); List <ProductType> lp = new List <ProductType> { ProductType.BnoB1ions, ProductType.Y }; PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1]; IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> { pepWithSetModsForSpectrum }); Tolerance fragmentTolerance = new AbsoluteTolerance(0.01); Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.Last() as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >, pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null); PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan); Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>(); Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > { { ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> { ps } } }; newPsm.MatchToProteinLinkedPeptides(matching); LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> { newPsm }, lp, myMsDataFile, fragmentTolerance, new List <string>(), false); f.Run(); // Was single peak!!! Assert.AreEqual(0, newPsm.MatchedIonDictOnlyMatches[ProductType.BnoB1ions].Count(b => b > 0)); Assert.AreEqual(1, newPsm.MatchedIonDictOnlyMatches[ProductType.Y].Count(b => b > 0)); // If localizing, three match!!! Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4); }
public static void TestLocalization() { Protein parentProteinForMatch = new Protein("MEK", null); DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1); ModificationMotif.TryGetMotif("E", out ModificationMotif motif); List <ModificationWithMass> variableModifications = new List <ModificationWithMass> { new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943) }; List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList(); Assert.AreEqual(4, allPeptidesWithSetModifications.Count()); PeptideWithSetModifications ps = allPeptidesWithSetModifications.First(); List <ProductType> lp = new List <ProductType> { ProductType.BnoB1ions, ProductType.Y }; PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1]; MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> { pepWithSetModsForSpectrum }); Tolerance fragmentTolerance = new AbsoluteTolerance(0.01); Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null); PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan, digestionParams); Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>(); Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > { { ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> { ps } } }; newPsm.MatchToProteinLinkedPeptides(matching); CommonParameters commonParameters = new CommonParameters(productMassTolerance: fragmentTolerance); LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> { newPsm }, lp, myMsDataFile, commonParameters, new List <string>()); f.Run(); // Was single peak!!! Assert.AreEqual(0, newPsm.MatchedIonMassToChargeRatioDict[ProductType.BnoB1ions].Count(b => b > 0)); Assert.AreEqual(1, newPsm.MatchedIonMassToChargeRatioDict[ProductType.Y].Count(b => b > 0)); Assert.AreEqual(0, newPsm.MatchedIonIntensitiesDict[ProductType.BnoB1ions].Count(b => b > 0)); Assert.AreEqual(1, newPsm.MatchedIonIntensitiesDict[ProductType.Y].Count(b => b > 0)); // If localizing, three match!!! Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4); }
protected override void OnStartup(StartupEventArgs e) { base.OnStartup(e); // Make a new localization engine var m = LocalizationEngine.MakeNew(new PhysicalFileDecoder(Path.Combine(Directory.GetCurrentDirectory(), "langs"))); int foundLangs = LocalizationEngine.Instance.DetectLanguages(); // Detect the languages LocalizationEngine.Instance.AddOnlineLanguage(LocalizationEngine.Instance.GetLanguage("en-US"), CultureInfo.GetCultureInfo("de")); Console.WriteLine($"Loaded languages: {foundLangs} [{string.Join(",", LocalizationEngine.Instance.GetInstalledLanguages())}]"); }
public static void SingleEventArgsTest() { Protein parentProteinForMatch = new Protein("MEK", null); CommonParameters commonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 1)); var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>(); fsp.Add(("", commonParameters)); ModificationMotif.TryGetMotif("E", out ModificationMotif motif); List <Modification> variableModifications = new List <Modification> { new Modification(_originalId: "21", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943) }; List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(commonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList(); Assert.AreEqual(4, allPeptidesWithSetModifications.Count()); PeptideWithSetModifications ps = allPeptidesWithSetModifications.First(); PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1]; MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> { pepWithSetModsForSpectrum }); Tolerance fragmentTolerance = new AbsoluteTolerance(0.01); Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters()); var theoreticalProducts = new List <Product>(); ps.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalProducts); var matchedIons = MetaMorpheusEngine.MatchFragmentIons(scan, theoreticalProducts, new CommonParameters()); PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps, 0, 0, 2, scan, commonParameters, matchedIons); LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> { newPsm }, myMsDataFile, new CommonParameters(), fsp, new List <string>()); var singleEngine = new SingleEngineEventArgs(f); Assert.That(singleEngine.MyEngine.Equals(f)); var singleFile = new SingleFileEventArgs("", new List <string>()); Assert.That(singleFile.WrittenFile.Equals("")); var stringList = new StringListEventArgs(new List <string>()); var rr = (stringList.StringList.DefaultIfEmpty().First()); Assert.That(stringList.StringList.DefaultIfEmpty().First() == null); }
public static void TestLocalization() { Protein parentProteinForMatch = new Protein("MEK", null); CommonParameters commonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 1)); var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>(); fsp.Add(("", commonParameters)); ModificationMotif.TryGetMotif("E", out ModificationMotif motif); List <Modification> variableModifications = new List <Modification> { new Modification(_originalId: "21", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943) }; List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(commonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList(); Assert.AreEqual(4, allPeptidesWithSetModifications.Count()); PeptideWithSetModifications ps = allPeptidesWithSetModifications.First(); PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1]; MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> { pepWithSetModsForSpectrum }); Tolerance fragmentTolerance = new AbsoluteTolerance(0.01); Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters()); var theoreticalProducts = new List <Product>(); ps.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalProducts); var matchedIons = MetaMorpheusEngine.MatchFragmentIons(scan, theoreticalProducts, new CommonParameters()); PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps, 0, 0, 2, scan, commonParameters, matchedIons); newPsm.ResolveAllAmbiguities(); LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> { newPsm }, myMsDataFile, commonParameters, fsp, new List <string>()); f.Run(); // single peak matches Assert.AreEqual(1, newPsm.MatchedFragmentIons.Where(p => p.NeutralTheoreticalProduct.ProductType == ProductType.b).Count());//including b1 now Assert.AreEqual(1, newPsm.MatchedFragmentIons.Where(p => p.NeutralTheoreticalProduct.ProductType == ProductType.y).Count()); // when localizing, three peaks match Assert.IsTrue(newPsm.LocalizedScores[1] > 4 && newPsm.LocalizedScores[1] < 5);//we have another matched ion }
private (List <PeptideSpectralMatch>, DataPointAquisitionResults) GetDataAcquisitionResults(IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile, string currentDataFile, List <ModificationWithMass> variableModifications, List <ModificationWithMass> fixedModifications, List <Protein> proteinList, string taskId, ICommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol) { var fileNameWithoutExtension = Path.GetFileNameWithoutExtension(currentDataFile); MassDiffAcceptor searchMode; if (initPrecTol is PpmTolerance) { searchMode = new SinglePpmAroundZeroSearchMode(initPrecTol.Value); } else { searchMode = new SingleAbsoluteAroundZeroSearchMode(initPrecTol.Value); } FragmentTypes fragmentTypesForCalibration = FragmentTypes.None; if (combinedParameters.BIons) { fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.b; } if (combinedParameters.YIons) { fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.y; } if (combinedParameters.CIons) { fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.c; } if (combinedParameters.ZdotIons) { fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.zdot; } var listOfSortedms2Scans = GetMs2Scans(myMsDataFile, currentDataFile, combinedParameters.DoPrecursorDeconvolution, combinedParameters.UseProvidedPrecursorInfo, combinedParameters.DeconvolutionIntensityRatio, combinedParameters.DeconvolutionMaxAssumedChargeState, combinedParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray(); PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length]; List <ProductType> lp = new List <ProductType>(); if (combinedParameters.BIons) { lp.Add(ProductType.B); } if (combinedParameters.YIons) { lp.Add(ProductType.Y); } if (combinedParameters.CIons) { lp.Add(ProductType.C); } if (combinedParameters.ZdotIons) { lp.Add(ProductType.Zdot); } Log("Searching with searchMode: " + searchMode, new List <string> { taskId, "Individual Spectra Files", fileNameWithoutExtension }); Log("Searching with productMassTolerance: " + initProdTol, new List <string> { taskId, "Individual Spectra Files", fileNameWithoutExtension }); new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, lp, searchMode, false, combinedParameters, initProdTol, new List <string> { taskId, "Individual Spectra Files", fileNameWithoutExtension }).Run(); List <PeptideSpectralMatch> allPsms = allPsmsArray.ToList(); Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > compactPeptideToProteinPeptideMatching = ((SequencesToActualProteinPeptidesEngineResults) new SequencesToActualProteinPeptidesEngine(allPsms, proteinList, fixedModifications, variableModifications, lp, new List <IDigestionParams> { combinedParameters.DigestionParams }, combinedParameters.ReportAllAmbiguity, new List <string> { taskId, "Individual Spectra Files", fileNameWithoutExtension }).Run()).CompactPeptideToProteinPeptideMatching; foreach (var huh in allPsms) { if (huh != null) { huh.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching); } } allPsms = allPsms.Where(b => b != null).OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => (b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList(); new FdrAnalysisEngine(allPsms, searchMode.NumNotches, false, new List <string> { taskId, "Individual Spectra Files", fileNameWithoutExtension }).Run(); List <PeptideSpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.01 && !b.IsDecoy && b.FullSequence != null).ToList(); if (!goodIdentifications.Any()) { Warn("No PSMs below 1% FDR observed!"); return(new List <PeptideSpectralMatch>(), null); } var dissociationTypes = MetaMorpheusEngine.DetermineDissociationType(lp); foreach (var psm in allPsms) { var theScan = myMsDataFile.GetOneBasedScan(psm.ScanNumber); double thePrecursorMass = psm.ScanPrecursorMass; foreach (var huh in lp) { var ionMasses = psm.CompactPeptides.First().Key.ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> { huh }); Array.Sort(ionMasses); List <double> matchedIonMassesList = new List <double>(); List <double> productMassErrorDaList = new List <double>(); List <double> productMassErrorPpmList = new List <double>(); LocalizationEngine.MatchIons(theScan, initProdTol, ionMasses, matchedIonMassesList, productMassErrorDaList, productMassErrorPpmList, thePrecursorMass, dissociationTypes, false); double[] matchedIonMassesOnlyMatches = matchedIonMassesList.ToArray(); psm.MatchedIonDictOnlyMatches.Add(huh, matchedIonMassesOnlyMatches); psm.ProductMassErrorDa.Add(huh, productMassErrorDaList.ToArray()); psm.ProductMassErrorPpm.Add(huh, productMassErrorPpmList.ToArray()); } } DataPointAquisitionResults currentResult = (DataPointAquisitionResults) new DataPointAcquisitionEngine( goodIdentifications, myMsDataFile, initPrecTol, initProdTol, CalibrationParameters.NumFragmentsNeededForEveryIdentification, CalibrationParameters.MinMS1IsotopicPeaksNeededForConfirmedIdentification, CalibrationParameters.MinMS2IsotopicPeaksNeededForConfirmedIdentification, fragmentTypesForCalibration, new List <string> { taskId, "Individual Spectra Files", fileNameWithoutExtension }).Run(); return(goodIdentifications, currentResult); }