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;
}
