public PermuteIsotopeModificationsDlg(SkylineWindow skylineWindow)
{
InitializeComponent();
SkylineWindow = skylineWindow;
_driverIsotopeModification = new SettingsListComboDriver <StaticMod>(comboIsotopeModification, Settings.Default.HeavyModList);
_driverIsotopeModification.LoadList(null);
}
public EditDriftTimePredictorDlg(IEnumerable <IonMobilityPredictor> existing)
{
_existing = existing;
_showRegressions = true;
InitializeComponent();
foreach (eIonMobilityUnits units in Enum.GetValues(typeof(eIonMobilityUnits)))
{
if (units != eIonMobilityUnits.none) // Don't present "none" as an option
{
comboBoxIonMobilityUnits.Items.Add(IonMobilityFilter.IonMobilityUnitsL10NString(units));
}
}
_smallMoleculeUI = Program.MainWindow.Document.HasSmallMolecules || Program.MainWindow.ModeUI != SrmDocument.DOCUMENT_TYPE.proteomic;
if (_smallMoleculeUI)
{
gridMeasuredDriftTimes.Columns[COLUMN_SEQUENCE].HeaderText = Resources.EditDriftTimePredictorDlg_EditDriftTimePredictorDlg_Molecule;
gridMeasuredDriftTimes.Columns[COLUMN_CHARGE].HeaderText = Resources.EditDriftTimePredictorDlg_EditDriftTimePredictorDlg_Adduct;
}
var targetResolver = TargetResolver.MakeTargetResolver(Program.ActiveDocumentUI);
MeasuredDriftTimeSequence.TargetResolver = targetResolver;
// TODO: ion mobility libraries are more complex than initially thought - leave these conversions to the mass spec vendors for now
labelIonMobilityLibrary.Visible = comboLibrary.Visible = false;
Icon = Resources.Skyline;
_driverIonMobilityLibraryListComboDriver = new SettingsListComboDriver <IonMobilityLibrarySpec>(comboLibrary, Settings.Default.IonMobilityLibraryList);
_driverIonMobilityLibraryListComboDriver.LoadList(null);
UpdateControls();
}
public ReintegrateDlg(SrmDocument document)
{
InitializeComponent();
Icon = Resources.Skyline;
Document = document;
_scoreAnnotation = false;
_driverPeakScoringModel = new SettingsListComboDriver<PeakScoringModelSpec>(comboBoxScoringModel, Settings.Default.PeakScoringModelList);
var peakScoringModel = document.Settings.PeptideSettings.Integration.PeakScoringModel;
_driverPeakScoringModel.LoadList(peakScoringModel != null ? peakScoringModel.Name : null);
}
public ReintegrateDlg(SrmDocument document)
{
InitializeComponent();
Icon = Resources.Skyline;
Document = document;
_scoreAnnotation = false;
_driverPeakScoringModel = new SettingsListComboDriver <PeakScoringModelSpec>(comboBoxScoringModel, Settings.Default.PeakScoringModelList);
var peakScoringModel = document.Settings.PeptideSettings.Integration.PeakScoringModel;
_driverPeakScoringModel.LoadList(peakScoringModel != null ? peakScoringModel.Name : null);
}
public AddPeakCompareDlg(SrmDocument document, IEnumerable <ComparePeakBoundaries> existing)
{
InitializeComponent();
Document = document;
_existing = existing;
_driverPeakScoringModel = new SettingsListComboDriver <PeakScoringModelSpec>(comboBoxModel, Settings.Default.PeakScoringModelList);
var peakScoringModel = document.Settings.PeptideSettings.Integration.PeakScoringModel;
_driverPeakScoringModel.LoadList(peakScoringModel != null ? peakScoringModel.Name : null);
UpdateSelection(true);
}
public ComboBoxDriverWrapper(IContainer container, ComboBox comboBox)
{
container.Add(this);
Settings.Default.PersistedViews.Changed += ViewSettingsOnSettingsChange;
// Initialize the report comboBox.
// CONSIDER: Settings list editing is currently disabled, because
// it had problems with the empty element added to the list.
// Also, for live reports, would need to add code to take the
// modified list and persist it in ViewSettings.
// Might be nice to allow report spec editing in this form
// some day, though.
_liveReportDriver = new SettingsListComboDriver <ReportOrViewSpec>(comboBox, new ReportOrViewSpecList(), false);
RepopulateLiveReportList();
}
public ImportFastaControl(SkylineWindow skylineWindow)
{
SkylineWindow = skylineWindow;
InitializeComponent();
ImportFastaHelper = new ImportFastaHelper(tbxFasta, tbxError, panelError);
tbxFastaHeightDifference = Height - tbxFasta.Height;
_driverEnzyme = new SettingsListComboDriver<Enzyme>(comboEnzyme, Settings.Default.EnzymeList);
_driverEnzyme.LoadList(SkylineWindow.Document.Settings.PeptideSettings.Enzyme.GetKey());
MaxMissedCleavages = skylineWindow.Document.Settings.PeptideSettings.DigestSettings.MaxMissedCleavages;
}
public ImportFastaControl(SkylineWindow skylineWindow)
{
SkylineWindow = skylineWindow;
InitializeComponent();
ImportFastaHelper = new ImportFastaHelper(tbxFasta, tbxError, panelError);
tbxFastaHeightDifference = Height - tbxFasta.Height;
_driverEnzyme = new SettingsListComboDriver <Enzyme>(comboEnzyme, Settings.Default.EnzymeList);
_driverEnzyme.LoadList(SkylineWindow.Document.Settings.PeptideSettings.Enzyme.GetKey());
MaxMissedCleavages = skylineWindow.Document.Settings.PeptideSettings.DigestSettings.MaxMissedCleavages;
}
public EditDriftTimePredictorDlg(IEnumerable <DriftTimePredictor> existing)
{
_existing = existing;
_showRegressions = true;
InitializeComponent();
// TODO: ion mobility libraries are more complex than initially thought - put this off until after summer 2014 release
labelIonMobilityLibrary.Visible = comboLibrary.Visible = false;
Icon = Resources.Skyline;
_driverIonMobilityLibraryListComboDriver = new SettingsListComboDriver <IonMobilityLibrarySpec>(comboLibrary, Settings.Default.IonMobilityLibraryList);
_driverIonMobilityLibraryListComboDriver.LoadList(null);
UpdateControls();
}
public BuildPeptideSearchLibraryControl(IModifyDocumentContainer documentContainer, ImportPeptideSearch importPeptideSearch, LibraryManager libraryManager)
{
DocumentContainer = documentContainer;
ImportPeptideSearch = importPeptideSearch;
LibraryManager = libraryManager;
InitializeComponent();
textCutoff.Text = ImportPeptideSearch.CutoffScore.ToString(LocalizationHelper.CurrentCulture);
if (DocumentContainer.Document.PeptideCount == 0)
{
cbFilterForDocumentPeptides.Hide();
}
_driverStandards = new SettingsListComboDriver <IrtStandard>(comboStandards, Settings.Default.IrtStandardList);
_driverStandards.LoadList(IrtStandard.EMPTY.GetKey());
}
public ImportFastaControl(SkylineWindow skylineWindow)
{
SkylineWindow = skylineWindow;
InitializeComponent();
ImportFastaHelper = new ImportFastaHelper(tbxFasta, tbxError, panelError, helpTipFasta);
tbxFastaHeightDifference = Height - tbxFasta.Height;
_driverEnzyme = new SettingsListComboDriver <Enzyme>(comboEnzyme, Settings.Default.EnzymeList);
_driverEnzyme.LoadList(SkylineWindow.Document.Settings.PeptideSettings.Enzyme.GetKey());
MaxMissedCleavages = skylineWindow.Document.Settings.PeptideSettings.DigestSettings.MaxMissedCleavages;
cbDecoyMethod.Items.Add(string.Empty);
cbDecoyMethod.Items.Add(DecoyGeneration.SHUFFLE_SEQUENCE);
cbDecoyMethod.Items.Add(DecoyGeneration.REVERSE_SEQUENCE);
cbDecoyMethod.SelectedIndex = 0;
}
public void InitializeSettings(IModifyDocumentContainer documentContainer, bool?defaultState = null)
{
_ionMobilityFiltering = documentContainer.Document.Settings.TransitionSettings.IonMobilityFiltering;
var imsWindowCalc = _ionMobilityFiltering.FilterWindowWidthCalculator;
var hasLibIMS = _ionMobilityFiltering.IonMobilityLibrary != null && !_ionMobilityFiltering.IonMobilityLibrary.IsNone;
var useSpectralLibraryIonMobilityValues = defaultState ?? _ionMobilityFiltering.UseSpectralLibraryIonMobilityValues;
var hasIonMobilityFiltering = useSpectralLibraryIonMobilityValues || hasLibIMS;
// Resolving power is most commonly used window size type, give that a reasonable starting value if none provided
var resolvingPower = imsWindowCalc?.ResolvingPower ?? 0;
if (hasIonMobilityFiltering && resolvingPower == 0)
{
resolvingPower = 30; // Arbitrarily chosen non-zero value
}
if (imsWindowCalc != null)
{
comboBoxWindowType.SelectedIndex = (int)imsWindowCalc.WindowWidthMode;
textIonMobilityFilterResolvingPower.Text = resolvingPower.ToString(LocalizationHelper.CurrentCulture);
textIonMobilityFilterWidthAtMobility0.Text = imsWindowCalc.PeakWidthAtIonMobilityValueZero.ToString(LocalizationHelper.CurrentCulture);
textIonMobilityFilterWidthAtMobilityMax.Text = imsWindowCalc.PeakWidthAtIonMobilityValueMax.ToString(LocalizationHelper.CurrentCulture);
textIonMobilityFilterFixedWidth.Text = imsWindowCalc.FixedWindowWidth.ToString(LocalizationHelper.CurrentCulture);
}
else
{
comboBoxWindowType.SelectedIndex = (int)IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.none;
}
UpdateIonMobilityFilterWindowWidthControls();
_driverIonMobilityLib = new SettingsListComboDriver <IonMobilityLibrary>(comboIonMobilityLibrary, Settings.Default.IonMobilityLibraryList);
var libName = (_ionMobilityFiltering.IonMobilityLibrary == null ? null : _ionMobilityFiltering.IonMobilityLibrary.Name);
_driverIonMobilityLib.LoadList(libName);
cbUseSpectralLibraryIonMobilities.Checked = useSpectralLibraryIonMobilityValues;
}
public ToolOptionsUI()
{
InitializeComponent();
checkBoxShowWizard.Checked = Settings.Default.ShowStartupForm;
powerOfTenCheckBox.Checked = Settings.Default.UsePowerOfTen;
Icon = Resources.Skyline;
_driverServers = new SettingsListBoxDriver <Server>(listboxServers, Settings.Default.ServerList);
_driverServers.LoadList();
_driverChorusAccounts = new SettingsListBoxDriver <RemoteAccount>(listBoxRemoteAccounts, Settings.Default.RemoteAccountList);
_driverChorusAccounts.LoadList();
_driverColorSchemes = new SettingsListComboDriver <ColorScheme>(comboColorScheme, Settings.Default.ColorSchemes, true);
_driverColorSchemes.LoadList(Settings.Default.CurrentColorScheme);
// 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();
}
public EditDriftTimePredictorDlg(IEnumerable <IonMobilityPredictor> existing)
{
_existing = existing;
_showRegressions = true;
InitializeComponent();
foreach (MsDataFileImpl.eIonMobilityUnits units in Enum.GetValues(typeof(MsDataFileImpl.eIonMobilityUnits)))
{
if (units != MsDataFileImpl.eIonMobilityUnits.none) // Don't present "none" as an option
{
comboBoxIonMobilityUnits.Items.Add(IonMobilityFilter.IonMobilityUnitsL10NString(units));
}
}
// TODO: ion mobility libraries are more complex than initially thought - leave these conversions to the mass spec vendors for now
labelIonMobilityLibrary.Visible = comboLibrary.Visible = false;
Icon = Resources.Skyline;
_driverIonMobilityLibraryListComboDriver = new SettingsListComboDriver <IonMobilityLibrarySpec>(comboLibrary, Settings.Default.IonMobilityLibraryList);
_driverIonMobilityLibraryListComboDriver.LoadList(null);
UpdateControls();
}
public ComboBoxDriverWrapper(IContainer container, ComboBox comboBox)
{
container.Add(this);
Settings.Default.PersistedViews.Changed += ViewSettingsOnSettingsChange;
// Initialize the report comboBox.
// CONSIDER: Settings list editing is currently disabled, because
// it had problems with the empty element added to the list.
// Also, for live reports, would need to add code to take the
// modified list and persist it in ViewSettings.
// Might be nice to allow report spec editing in this form
// some day, though.
_liveReportDriver = new SettingsListComboDriver<ReportOrViewSpec>(comboBox, new ReportOrViewSpecList(), false);
RepopulateLiveReportList();
}
private void InitializeMs1FilterUI()
{
_driverEnrichments = new SettingsListComboDriver<IsotopeEnrichments>(comboEnrichments,
Settings.Default.IsotopeEnrichmentsList);
var sel = (FullScan.IsotopeEnrichments != null ? FullScan.IsotopeEnrichments.Name : null);
_driverEnrichments.LoadList(sel);
comboPrecursorIsotopes.Items.AddRange(
new object[]
{
FullScanPrecursorIsotopes.None.GetLocalizedString(),
FullScanPrecursorIsotopes.Count.GetLocalizedString(),
FullScanPrecursorIsotopes.Percent.GetLocalizedString()
});
comboPrecursorAnalyzerType.Items.AddRange(TransitionFullScan.MASS_ANALYZERS.Cast<object>().ToArray());
comboPrecursorIsotopes.SelectedItem = FullScan.PrecursorIsotopes.GetLocalizedString();
// Update the precursor analyzer type in case the SelectedIndex is still -1
UpdatePrecursorAnalyzerType();
}
private void InitializeMsMsFilterUI()
{
_driverIsolationScheme = new SettingsListComboDriver<IsolationScheme>(comboIsolationScheme,
Settings.Default.IsolationSchemeList);
string sel = (FullScan.IsolationScheme != null ? FullScan.IsolationScheme.Name : null);
_driverIsolationScheme.LoadList(sel);
comboAcquisitionMethod.Items.AddRange(
new object[]
{
FullScanAcquisitionMethod.None.GetLocalizedString(),
FullScanAcquisitionMethod.Targeted.GetLocalizedString(),
FullScanAcquisitionMethod.DIA.GetLocalizedString()
});
comboProductAnalyzerType.Items.AddRange(TransitionFullScan.MASS_ANALYZERS.Cast<object>().ToArray());
comboAcquisitionMethod.SelectedItem = FullScan.AcquisitionMethod.GetLocalizedString();
// Update the product analyzer type in case the SelectedIndex is still -1
UpdateProductAnalyzerType();
}
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;
}
private void comboBoxScoringModel_EditItem(object sender, SettingsListComboDriver <PeakScoringModelSpec> .EditItemEventArgs e)
{
e.Tag = this;
}
public TransitionSettingsUI(SkylineWindow parent)
{
InitializeComponent();
// Populate the fragment finder combo boxes
foreach (string item in TransitionFilter.GetStartFragmentFinderLabels())
comboRangeFrom.Items.Add(item);
foreach (string item in TransitionFilter.GetEndFragmentFinderLabels())
comboRangeTo.Items.Add(item);
_parent = parent;
_transitionSettings = _parent.DocumentUI.Settings.TransitionSettings;
// Initialize prediction settings
comboPrecursorMass.SelectedItem = Prediction.PrecursorMassType.GetLocalizedString();
comboIonMass.SelectedItem = Prediction.FragmentMassType.GetLocalizedString();
_driverCE = new SettingsListComboDriver<CollisionEnergyRegression>(comboCollisionEnergy,
Settings.Default.CollisionEnergyList);
string sel = (Prediction.CollisionEnergy == null ? null : Prediction.CollisionEnergy.Name);
_driverCE.LoadList(sel);
_driverDP = new SettingsListComboDriver<DeclusteringPotentialRegression>(comboDeclusterPotential,
Settings.Default.DeclusterPotentialList);
sel = (Prediction.DeclusteringPotential == null ? null : Prediction.DeclusteringPotential.Name);
_driverDP.LoadList(sel);
_driverCoV = new SettingsListComboDriver<CompensationVoltageParameters>(comboCompensationVoltage,
Settings.Default.CompensationVoltageList);
_driverCoV.LoadList(Prediction.CompensationVoltage == null ? null : Prediction.CompensationVoltage.Name);
_driverOptimizationLibrary = new SettingsListComboDriver<OptimizationLibrary>(comboOptimizationLibrary,
Settings.Default.OptimizationLibraryList);
_driverOptimizationLibrary.LoadList(Prediction.OptimizedLibrary == null ? null : Prediction.OptimizedLibrary.Name);
if (Prediction.OptimizedMethodType == OptimizedMethodType.None)
comboOptimizeType.SelectedIndex = 0;
else
{
cbUseOptimized.Checked = true;
comboOptimizeType.SelectedItem = Prediction.OptimizedMethodType.GetLocalizedString();
}
// Initialize filter settings
textPrecursorCharges.Text = Filter.PrecursorCharges.ToArray().ToString(", "); // Not L10N? Internationalization of comma?
textIonCharges.Text = Filter.ProductCharges.ToArray().ToString(", "); // Not L10N? Internationalization of comma?
textIonTypes.Text = TransitionFilter.ToStringIonTypes(Filter.IonTypes, true);
comboRangeFrom.SelectedItem = Filter.FragmentRangeFirst.Label;
comboRangeTo.SelectedItem = Filter.FragmentRangeLast.Label;
textExclusionWindow.Text = Filter.PrecursorMzWindow != 0
? Filter.PrecursorMzWindow.ToString(LocalizationHelper.CurrentCulture)
: string.Empty;
cbExclusionUseDIAWindow.Checked = Filter.ExclusionUseDIAWindow;
cbAutoSelect.Checked = Filter.AutoSelect;
_driverIons = new MeasuredIonListBoxDriver(listAlwaysAdd, Settings.Default.MeasuredIonList);
_driverIons.LoadList(Filter.MeasuredIons);
// Initialize library settings
cbLibraryPick.Checked = (Libraries.Pick != TransitionLibraryPick.none);
panelPick.Visible = cbLibraryPick.Checked;
textTolerance.Text = Libraries.IonMatchTolerance.ToString(LocalizationHelper.CurrentCulture);
textIonCount.Text = Libraries.IonCount.ToString(LocalizationHelper.CurrentCulture);
if (Libraries.Pick == TransitionLibraryPick.filter)
radioFiltered.Checked = true;
else if (Libraries.Pick == TransitionLibraryPick.all_plus)
radioAllAndFiltered.Checked = true;
// Initialize instrument settings
textMinMz.Text = Instrument.MinMz.ToString(LocalizationHelper.CurrentCulture);
textMaxMz.Text = Instrument.MaxMz.ToString(LocalizationHelper.CurrentCulture);
cbDynamicMinimum.Checked = Instrument.IsDynamicMin;
textMzMatchTolerance.Text = Instrument.MzMatchTolerance.ToString(LocalizationHelper.CurrentCulture);
if (Instrument.MaxTransitions.HasValue)
textMaxTrans.Text = Instrument.MaxTransitions.Value.ToString(LocalizationHelper.CurrentCulture);
if (Instrument.MaxInclusions.HasValue)
textMaxInclusions.Text = Instrument.MaxInclusions.Value.ToString(LocalizationHelper.CurrentCulture);
if (Instrument.MinTime.HasValue)
textMinTime.Text = Instrument.MinTime.Value.ToString(LocalizationHelper.CurrentCulture);
if (Instrument.MaxTime.HasValue)
textMaxTime.Text = Instrument.MaxTime.Value.ToString(LocalizationHelper.CurrentCulture);
// Initialize full-scan settings
FullScanSettingsControl = new FullScanSettingsControl(_parent)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Left),
Location = new Point(0, 0),
Size = new Size(363, 491)
};
FullScanSettingsControl.IsolationSchemeChangedEvent += IsolationSchemeChanged;
tabFullScan.Controls.Add(FullScanSettingsControl);
// VISUAL:
// - Store the distance between the cbExclusionDIAWindow and the lower end of the box (to use as margin later)
// - Shift the cbExclusionDIAWindow down (it is only higher in the designer for better manipulation)
_lower_margin = groupBox1.Height - textExclusionWindow.Location.Y - textExclusionWindow.Height;
int pixelShift = cbExclusionUseDIAWindow.Location.Y - lbPrecursorMzWindow.Location.Y;
cbExclusionUseDIAWindow.Location = new Point(cbExclusionUseDIAWindow.Location.X, cbExclusionUseDIAWindow.Location.Y - pixelShift);
DoIsolationSchemeChanged();
}
public PeptideSettingsUI(SkylineWindow parent, LibraryManager libraryManager)
{
InitializeComponent();
btnUpdateIonMobilityLibraries.Visible = false; // TODO: ion mobility libraries are more complex than initially thought - put this off until after summer 2014 release
_parent = parent;
_libraryManager = libraryManager;
_peptideSettings = parent.DocumentUI.Settings.PeptideSettings;
// Initialize digestion settings
_driverEnzyme = new SettingsListComboDriver<Enzyme>(comboEnzyme, Settings.Default.EnzymeList);
_driverEnzyme.LoadList(_peptideSettings.Enzyme.GetKey());
for (int i = DigestSettings.MIN_MISSED_CLEAVAGES; i <= DigestSettings.MAX_MISSED_CLEAVAGES; i++)
comboMissedCleavages.Items.Add(i.ToString(CultureInfo.InvariantCulture));
comboMissedCleavages.SelectedItem = Digest.MaxMissedCleavages.ToString(LocalizationHelper.CurrentCulture);
if (comboMissedCleavages.SelectedIndex < 0)
comboMissedCleavages.SelectedIndex = 0;
cbRaggedEnds.Checked = Digest.ExcludeRaggedEnds;
// Initialize prediction settings
_driverRT = new SettingsListComboDriver<RetentionTimeRegression>(comboRetentionTime, Settings.Default.RetentionTimeList);
string sel = (Prediction.RetentionTime == null ? null : Prediction.RetentionTime.Name);
_driverRT.LoadList(sel);
cbUseMeasuredRT.Checked = textMeasureRTWindow.Enabled = Prediction.UseMeasuredRTs;
if (Prediction.MeasuredRTWindow.HasValue)
textMeasureRTWindow.Text = Prediction.MeasuredRTWindow.Value.ToString(LocalizationHelper.CurrentCulture);
_driverDT = new SettingsListComboDriver<DriftTimePredictor>(comboDriftTimePredictor, Settings.Default.DriftTimePredictorList);
string selDT = (Prediction.DriftTimePredictor == null ? null : Prediction.DriftTimePredictor.Name);
_driverDT.LoadList(selDT);
cbUseSpectralLibraryDriftTimes.Checked = textSpectralLibraryDriftTimesResolvingPower.Enabled = Prediction.UseLibraryDriftTimes;
if (Prediction.LibraryDriftTimesResolvingPower.HasValue)
textSpectralLibraryDriftTimesResolvingPower.Text = Prediction.LibraryDriftTimesResolvingPower.Value.ToString(LocalizationHelper.CurrentCulture);
// Initialize filter settings
_driverExclusion = new SettingsListBoxDriver<PeptideExcludeRegex>(listboxExclusions, Settings.Default.PeptideExcludeList);
_driverExclusion.LoadList(null, Filter.Exclusions);
textExcludeAAs.Text = Filter.ExcludeNTermAAs.ToString(LocalizationHelper.CurrentCulture);
textMaxLength.Text = Filter.MaxPeptideLength.ToString(LocalizationHelper.CurrentCulture);
textMinLength.Text = Filter.MinPeptideLength.ToString(LocalizationHelper.CurrentCulture);
cbAutoSelect.Checked = Filter.AutoSelect;
// Initialize spectral library settings
_driverLibrary = new SettingsListBoxDriver<LibrarySpec>(listLibraries, Settings.Default.SpectralLibraryList);
IList<LibrarySpec> listLibrarySpecs = Libraries.LibrarySpecs;
_driverLibrary.LoadList(null, listLibrarySpecs);
_driverBackgroundProteome = new SettingsListComboDriver<BackgroundProteomeSpec>(comboBackgroundProteome, Settings.Default.BackgroundProteomeList);
_driverBackgroundProteome.LoadList(_peptideSettings.BackgroundProteome.Name);
panelPick.Visible = listLibrarySpecs.Count > 0;
btnExplore.Enabled = listLibraries.Items.Count > 0;
comboMatching.SelectedIndex = (int) Libraries.Pick;
_lastRankId = Libraries.RankId;
_lastPeptideCount = Libraries.PeptideCount.HasValue
? Libraries.PeptideCount.Value.ToString(LocalizationHelper.CurrentCulture)
: null;
UpdateRanks(null);
// Initialize modification settings
_driverStaticMod = new SettingsListBoxDriver<StaticMod>(listStaticMods, Settings.Default.StaticModList);
_driverStaticMod.LoadList(null, Modifications.StaticModifications);
_driverHeavyMod = new SettingsListBoxDriver<StaticMod>(listHeavyMods, Settings.Default.HeavyModList);
_driverLabelType = new LabelTypeComboDriver(comboLabelType, Modifications, _driverHeavyMod,
labelStandardType, comboStandardType, listStandardTypes);
textMaxVariableMods.Text = Modifications.MaxVariableMods.ToString(LocalizationHelper.CurrentCulture);
textMaxNeutralLosses.Text = Modifications.MaxNeutralLosses.ToString(LocalizationHelper.CurrentCulture);
// Initialize peak scoring settings.
_driverPeakScoringModel = new SettingsListComboDriver<PeakScoringModelSpec>(comboPeakScoringModel, Settings.Default.PeakScoringModelList);
var peakScoringModel = _peptideSettings.Integration.PeakScoringModel;
_driverPeakScoringModel.LoadList(peakScoringModel != null ? peakScoringModel.Name : null);
IsShowLibraryExplorer = false;
tabControl1.TabPages.Remove(tabIntegration);
comboNormalizationMethod.Items.AddRange(
NormalizationMethod.ListNormalizationMethods(parent.DocumentUI).ToArray());
comboNormalizationMethod.SelectedItem = _peptideSettings.Quantification.NormalizationMethod;
comboWeighting.Items.AddRange(RegressionWeighting.All.Cast<object>().ToArray());
comboWeighting.SelectedItem = _peptideSettings.Quantification.RegressionWeighting;
comboRegressionFit.Items.AddRange(RegressionFit.All.Cast<object>().ToArray());
comboRegressionFit.SelectedItem = _peptideSettings.Quantification.RegressionFit;
comboQuantMsLevel.SelectedIndex = Math.Max(0, _quantMsLevels.IndexOf(_peptideSettings.Quantification.MsLevel));
tbxQuantUnits.Text = _peptideSettings.Quantification.Units;
}
