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();
}
