public MatchModificationsControl(IModifyDocumentContainer documentContainer, ImportPeptideSearch importPeptideSearch) { DocumentContainer = documentContainer; ImportPeptideSearch = importPeptideSearch; InitializeComponent(); }
public void InitializeSettings(IModifyDocumentContainer documentContainer, bool?defaultState = null) { Prediction = documentContainer.Document.Settings.PeptideSettings.Prediction; var imsWindowCalc = Prediction.LibraryIonMobilityWindowWidthCalculator; var resolvingPower = imsWindowCalc?.ResolvingPower ?? 0; if ((defaultState ?? Prediction.UseLibraryIonMobilityValues) && resolvingPower == 0) { resolvingPower = 30; // Arbitrarily chosen non-zero value } cbUseSpectralLibraryIonMobilityValues.Checked = textSpectralLibraryIonMobilityValuesResolvingPower.Enabled = defaultState ?? Prediction.UseLibraryIonMobilityValues; if (imsWindowCalc != null) { cbLinear.Checked = imsWindowCalc.PeakWidthMode == IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType.linear_range; if (cbLinear.Checked) { textSpectralLibraryIonMobilityValuesResolvingPower.Text = string.Empty; textSpectralLibraryIonMobilityWindowWidthAtDt0.Text = imsWindowCalc.PeakWidthAtIonMobilityValueZero.ToString(LocalizationHelper.CurrentCulture); textSpectralLibraryIonMobilityWindowWidthAtDtMax.Text = imsWindowCalc.PeakWidthAtIonMobilityValueMax.ToString(LocalizationHelper.CurrentCulture); } else { textSpectralLibraryIonMobilityValuesResolvingPower.Text = resolvingPower != 0 ? resolvingPower.ToString(LocalizationHelper.CurrentCulture) : string.Empty; textSpectralLibraryIonMobilityWindowWidthAtDt0.Text = string.Empty; textSpectralLibraryIonMobilityWindowWidthAtDtMax.Text = string.Empty; } } UpdateLibraryDriftPeakWidthControls(); }
public TransitionSettingsControl(IModifyDocumentContainer documentContainer) { _documentContainer = documentContainer; InitializeComponent(); SetFields(_documentContainer.Document.Settings.TransitionSettings); PeptideIonTypes = PeptideIonTypes.Union(new[] { IonType.precursor, IonType.y }).ToArray(); // Add p, y if not already set }
public SearchSettingsControl(IModifyDocumentContainer documentContainer, ImportPeptideSearch importPeptideSearch) { InitializeComponent(); ImportPeptideSearch = importPeptideSearch; _documentContainer = documentContainer; txtMS1Tolerance.LostFocus += txtMS1Tolerance_LostFocus; txtMS2Tolerance.LostFocus += txtMS2Tolerance_LostFocus; }
public ImportResultsDIAControl(IModifyDocumentContainer documentContainer) { DocumentContainer = documentContainer; InitializeComponent(); _foundResultsFiles = new BindingList <ImportPeptideSearch.FoundResultsFile>(); listResultsFiles.DataSource = _foundResultsFiles; listResultsFiles.DisplayMember = "Name"; // Not L10N SimultaneousFiles = Settings.Default.ImportResultsSimultaneousFiles; DoAutoRetry = Settings.Default.ImportResultsDoAutoRetry; }
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 TransitionSettingsControl(IModifyDocumentContainer documentContainer) { _documentContainer = documentContainer; InitializeComponent(); foreach (string item in TransitionFilter.GetStartFragmentFinderLabels()) { comboRangeFrom.Items.Add(item); } foreach (string item in TransitionFilter.GetEndFragmentFinderLabels()) { comboRangeTo.Items.Add(item); } SetFields(_documentContainer.Document.Settings.TransitionSettings); PeptideIonTypes = PeptideIonTypes.Union(new[] { IonType.precursor, IonType.y }).ToArray(); // Add p, y if not already set InitialPeptideIonTypes = PeptideIonTypes.ToArray(); }
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(); } foreach (var standard in IrtStandard.ALL) { comboStandards.Items.Add(standard); } }
public ImportFastaControl(IModifyDocumentContainer documentContainer, SequenceTree sequenceTree) { DocumentContainer = documentContainer; _sequenceTree = sequenceTree; InitializeComponent(); ImportFastaHelper = new ImportFastaHelper(tbxFasta, tbxError, panelError, helpTipFasta); tbxFastaHeightDifference = Height - tbxFasta.Height; _driverEnzyme = new SettingsListComboDriver <Enzyme>(comboEnzyme, Settings.Default.EnzymeList); _driverEnzyme.LoadList(DocumentContainer.Document.Settings.PeptideSettings.Enzyme.GetKey()); MaxMissedCleavages = documentContainer.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 FullScanSettingsControl(IModifyDocumentContainer documentContainer) { _documentContainer = documentContainer; InitializeComponent(); InitializeMs1FilterUI(); InitializeMsMsFilterUI(); InitializeRetentionTimeFilterUI(); // Update the precursor analyzer type in case the SelectedIndex is still -1 UpdatePrecursorAnalyzerType(); UpdateProductAnalyzerType(); PrecursorIsotopesCurrent = FullScan.PrecursorIsotopes; PrecursorMassAnalyzer = FullScan.PrecursorMassAnalyzer; cbHighSelectivity.Checked = FullScan.UseSelectiveExtraction; _prevval_comboIsolationScheme = IsolationScheme; // initialize previous value to initial value }
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 FullScanSettingsControl(IModifyDocumentContainer documentContainer) { _documentContainer = documentContainer; Initialize(); }