public bool TestClient(PrositPredictionClient client) { var pingPep = new Peptide(@"PING"); var peptide = new PeptideDocNode(pingPep); var precursor = new TransitionGroupDocNode(new TransitionGroup(pingPep, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light), new TransitionDocNode[0]); var input = new PrositIntensityModel.PeptidePrecursorNCE(peptide, precursor, IsotopeLabelType.light, 32); var intensityModel = PrositIntensityModel.GetInstance(PrositIntensityModel.Models.First()); try { intensityModel.PredictSingle(client, SrmSettingsList.GetDefault(), input, CancellationToken.None); return(true); } catch (Exception) { return(false); } }
public PrositMS2Spectrum(SrmSettings settings, PrositIntensityModel.PeptidePrecursorNCE peptidePrecursorNCE, int precursorIndex, PrositIntensityModel.PrositIntensityOutput prositIntensityOutput, IsotopeLabelType labelTypeOverride = null) { PeptidePrecursorNCE = peptidePrecursorNCE; Settings = settings; var precursor = peptidePrecursorNCE.NodeGroup; var peptide = peptidePrecursorNCE.NodePep; var calc = settings.GetFragmentCalc(IsotopeLabelType.light, peptide.ExplicitMods); var ionTable = calc.GetFragmentIonMasses(peptide.Target); // TODO: get mods and pass them as explicit mods above? var ions = ionTable.GetLength(1); var mis = new List <SpectrumPeaksInfo.MI>(ions * PrositConstants.IONS_PER_RESIDUE); for (int i = 0; i < ions; ++i) { var intensities = prositIntensityOutput.OutputRows[precursorIndex].Intensities[i].Intensities .Select(ReLu).ToArray(); var yMIs = CalcMIs(ionTable[IonType.y, ions - i - 1], intensities, 0); var bMIs = CalcMIs(ionTable[IonType.b, i], intensities, PrositConstants.IONS_PER_RESIDUE / 2); mis.AddRange(yMIs); mis.AddRange(bMIs); } var maxIntensity = mis.Max(mi => mi.Intensity); // Max Norm for (int i = 0; i < mis.Count; ++i) { mis[i] = new SpectrumPeaksInfo.MI { Mz = mis[i].Mz, Intensity = mis[i].Intensity / maxIntensity } } ; SpectrumPeaks = new SpectrumPeaksInfo(mis.ToArray()); }
public ToolOptionsUI(SrmSettings settings) { InitializeComponent(); checkBoxShowWizard.Checked = Settings.Default.ShowStartupForm; powerOfTenCheckBox.Checked = Settings.Default.UsePowerOfTen; Icon = Resources.Skyline; _driverServers = new SettingsListBoxDriver <Server>(listboxServers, Settings.Default.ServerList); _driverServers.LoadList(); _driverRemoteAccounts = new SettingsListBoxDriver <RemoteAccount>(listBoxRemoteAccounts, Settings.Default.RemoteAccountList); _driverRemoteAccounts.LoadList(); _driverColorSchemes = new SettingsListComboDriver <ColorScheme>(comboColorScheme, Settings.Default.ColorSchemes, true); _driverColorSchemes.LoadList(Settings.Default.CurrentColorScheme); var pingPep = new Peptide(@"PING"); var peptide = new PeptideDocNode(pingPep); var precursor = new TransitionGroupDocNode(new TransitionGroup(pingPep, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light), new TransitionDocNode[0]); _pingInput = new PrositIntensityModel.PeptidePrecursorNCE(peptide, precursor, IsotopeLabelType.light, 32); _settingsNoMod = settings.ChangePeptideModifications( pm => new PeptideModifications(new StaticMod[0], new TypedModifications[0])); // Hide ability to turn off live reports //tabControl.TabPages.Remove(tabMisc); // Populate the languages list with the languages that Skyline has been localized to string defaultDisplayName = string.Format(Resources.ToolOptionsUI_ToolOptionsUI_Default___0__, CultureUtil.GetDisplayLanguage(CultureInfo.InstalledUICulture).DisplayName); listBoxLanguages.Items.Add(new DisplayLanguageItem(string.Empty, defaultDisplayName)); foreach (var culture in CultureUtil.AvailableDisplayLanguages()) { listBoxLanguages.Items.Add(new DisplayLanguageItem(culture.Name, culture.DisplayName)); } for (int i = 0; i < listBoxLanguages.Items.Count; i++) { var displayLanguageItem = (DisplayLanguageItem)listBoxLanguages.Items[i]; if (Equals(displayLanguageItem.Key, Settings.Default.DisplayLanguage)) { listBoxLanguages.SelectedIndex = i; } } comboCompactFormatOption.Items.AddRange(CompactFormatOption.ALL_VALUES.ToArray()); comboCompactFormatOption.SelectedItem = CompactFormatOption.FromSettings(); var iModels = PrositIntensityModel.Models.ToList(); iModels.Insert(0, string.Empty); var rtModels = PrositRetentionTimeModel.Models.ToList(); rtModels.Insert(0, string.Empty); tbxPrositServer.Text = PrositConfig.GetPrositConfig().Server; intensityModelCombo.Items.AddRange(iModels.ToArray()); iRTModelCombo.Items.AddRange(rtModels.ToArray()); prositServerStatusLabel.Text = string.Empty; if (iModels.Contains(Settings.Default.PrositIntensityModel)) { intensityModelCombo.SelectedItem = Settings.Default.PrositIntensityModel; } if (rtModels.Contains(Settings.Default.PrositRetentionTimeModel)) { iRTModelCombo.SelectedItem = Settings.Default.PrositRetentionTimeModel; } ceCombo.Items.AddRange( Enumerable.Range(PrositConstants.MIN_NCE, PrositConstants.MAX_NCE - PrositConstants.MIN_NCE + 1).Select(c => (object)c) .ToArray()); ceCombo.SelectedItem = Settings.Default.PrositNCE; }