public void GetDriftTimesFromResults()
{
try
{
var driftTable = new MeasuredDriftTimeTable(gridMeasuredDriftTimes);
var tempDriftTimePredictor = new DriftTimePredictor("tmp", driftTable.GetTableMeasuredDriftTimes(cbOffsetHighEnergySpectra.Checked), null, null, 30); // Not L10N
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.EditDriftTimePredictorDlg_btnGenerateFromDocument_Click_Finding_drift_time_values_for_peaks,
Message = string.Empty,
ProgressValue = 0
})
{
longWaitDlg.PerformWork(this, 100, broker =>
{
tempDriftTimePredictor = tempDriftTimePredictor.ChangeMeasuredDriftTimesFromResults(Program.MainWindow.Document, Program.MainWindow.DocumentFilePath, broker);
});
if (!longWaitDlg.IsCanceled && tempDriftTimePredictor != null)
{
UpdateMeasuredDriftTimesControl(tempDriftTimePredictor);
}
}
}
catch (Exception ex)
{
MessageDlg.ShowException(this, ex);
}
}
private void UpdateMeasuredDriftTimesControl(DriftTimePredictor predictor)
{
// List any measured drift times
gridMeasuredDriftTimes.Rows.Clear();
if (predictor.MeasuredDriftTimePeptides != null)
{
bool hasHighEnergyOffsets =
predictor.MeasuredDriftTimePeptides.Any(p => p.Value.HighEnergyDriftTimeOffsetMsec != 0);
cbOffsetHighEnergySpectra.Checked = hasHighEnergyOffsets;
foreach (var p in predictor.MeasuredDriftTimePeptides)
{
if (hasHighEnergyOffsets)
{
gridMeasuredDriftTimes.Rows.Add(p.Key.Sequence,
p.Key.Charge.ToString(LocalizationHelper.CurrentCulture),
(p.Value.DriftTimeMsec(false) ?? 0).ToString(LocalizationHelper.CurrentCulture),
p.Value.HighEnergyDriftTimeOffsetMsec.ToString(LocalizationHelper.CurrentCulture)
);
}
else
{
gridMeasuredDriftTimes.Rows.Add(p.Key.Sequence,
p.Key.Charge.ToString(LocalizationHelper.CurrentCulture),
(p.Value.DriftTimeMsec(false) ?? 0).ToString(LocalizationHelper.CurrentCulture)
);
}
}
}
else
{
cbOffsetHighEnergySpectra.Checked = false;
}
}
/// <summary>
/// Write XML representation, possibly in backward compatible format using
/// old style in-document serialization
/// </summary>
public void WriteXml(XmlWriter writer, IonMobilityWindowWidthCalculator extraInfoForPre20_12)
{
if (extraInfoForPre20_12 == null)
{
WriteXml(writer);
return;
}
// Write the contents of the currently-in-use .imsdb to old style in-document serialization
var libKeyMap = GetIonMobilityLibKeyMap();
if (libKeyMap == null)
{
return;
}
var dict = libKeyMap.AsDictionary();
if (dict != null && dict.Any())
{
var oldDict =
dict.ToDictionary(kvp => kvp.Key,
kvp => kvp.Value.First()); // No multiple conformers in earlier formats
var dtp = new DriftTimePredictor(Name,
oldDict, extraInfoForPre20_12.WindowWidthMode, extraInfoForPre20_12.ResolvingPower,
extraInfoForPre20_12.PeakWidthAtIonMobilityValueZero,
extraInfoForPre20_12.PeakWidthAtIonMobilityValueMax,
extraInfoForPre20_12.FixedWindowWidth);
writer.WriteStartElement(DriftTimePredictor.EL.predict_drift_time); // N.B. EL.predict_drift_time is a misnomer, this covers all IMS types
dtp.WriteXml(writer);
writer.WriteEndElement();
}
}
/// <summary>
/// Finds drift times by examining loaded results in a document.
/// </summary>
/// <param name="document">The document to be inspected</param>
/// <param name="documentFilePath">Aids in locating the raw files</param>
/// <param name="existing">If non-null, will be examined for any existing drift time measurements (which may be overwritten) </param>
/// <param name="progressMonitor">Optional progress monitor for this potentially long operation</param>
public DriftTimeFinder(SrmDocument document, string documentFilePath, DriftTimePredictor existing, IProgressMonitor progressMonitor)
{
_document = document;
_documentFilePath = documentFilePath;
_existing = existing;
_currentDisplayedTransitionGroupDocNode = null;
_progressMonitor = progressMonitor;
}
/// <summary>
/// Finds drift times by examining loaded results in a document.
/// </summary>
/// <param name="document">The document to be inspected</param>
/// <param name="documentFilePath">Aids in locating the raw files</param>
/// <param name="existing">If non-null, will be examined for any existing drift time measurements (which may be overwritten) </param>
/// <param name="progressMonitor">Optional progress monitor for this potentially long operation</param>
public DriftTimeFinder(SrmDocument document, string documentFilePath, DriftTimePredictor existing, IProgressMonitor progressMonitor)
{
_document = document;
_documentFilePath = documentFilePath;
_existing = existing;
_currentDisplayedTransitionGroupDocNode = null;
_progressMonitor = progressMonitor;
}
private void IonMobilityLibraryChanged()
{
var calc = _driverIonMobilityLibraryListComboDriver.SelectedItem;
if (calc != null)
{
try
{
if (_predictor != null)
{
_predictor = _predictor.ChangeLibrary(calc);
}
}
catch (Exception e)
{
MessageDlg.ShowException(this, e);
}
}
UpdateControls();
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
var driftTable = new MeasuredDriftTimeTable(gridMeasuredDriftTimes);
var table = new ChargeRegressionTable(gridRegression);
string name;
if (!helper.ValidateNameTextBox(textName, out name))
{
return;
}
if (_existing.Contains(r => !ReferenceEquals(_predictor, r) && Equals(name, r.Name)))
{
if (MessageBox.Show(this,
TextUtil.LineSeparate(string.Format(Resources.EditDriftTimePredictorDlg_OkDialog_A_drift_time_predictor_with_the_name__0__already_exists_, name),
Resources.EditDriftTimePredictorDlg_OkDialog_Do_you_want_to_change_it_),
Program.Name, MessageBoxButtons.YesNo) != DialogResult.Yes)
{
return;
}
}
if (driftTable.GetTableMeasuredDriftTimes(cbOffsetHighEnergySpectra.Checked) == null) // Some error detected in the measured drift times table
{
return;
}
if (table.GetTableChargeRegressionLines() == null) // Some error detected in the charged regression lines table
{
return;
}
double resolvingPower;
if (!helper.ValidateDecimalTextBox(textResolvingPower, out resolvingPower))
{
return;
}
var errmsg = ValidateResolvingPower(resolvingPower);
if (errmsg != null)
{
helper.ShowTextBoxError(textResolvingPower, errmsg);
return;
}
if ((comboLibrary.SelectedIndex > 0) && (comboLibrary.SelectedItem.ToString().Length == 0))
{
MessageBox.Show(this, Resources.EditDriftTimePredictorDlg_OkDialog_Drift_time_prediction_requires_an_ion_mobility_library_,
Program.Name);
comboLibrary.Focus();
return;
}
var ionMobilityLibrary = _driverIonMobilityLibraryListComboDriver.SelectedItem;
DriftTimePredictor predictor =
new DriftTimePredictor(name, driftTable.GetTableMeasuredDriftTimes(cbOffsetHighEnergySpectra.Checked),
ionMobilityLibrary, table.GetTableChargeRegressionLines(), resolvingPower);
_predictor = predictor;
DialogResult = DialogResult.OK;
}
public PeptidePrediction ChangeDriftTimePredictor(DriftTimePredictor prop)
{
return ChangeProp(ImClone(this), im => im.DriftTimePredictor = prop);
}
public PeptidePrediction(RetentionTimeRegression retentionTime, DriftTimePredictor driftTimePredictor, bool useMeasuredRTs, double? measuredRTWindow,
bool useLibraryDriftTimes, double? libraryDriftTimesResolvingPower)
{
RetentionTime = retentionTime;
DriftTimePredictor = driftTimePredictor;
UseMeasuredRTs = useMeasuredRTs;
MeasuredRTWindow = measuredRTWindow;
UseLibraryDriftTimes = useLibraryDriftTimes;
LibraryDriftTimesResolvingPower = libraryDriftTimesResolvingPower;
DoValidate();
}
public PeptidePrediction(RetentionTimeRegression retentionTime, DriftTimePredictor driftTimePredictor = null)
: this(retentionTime, driftTimePredictor, true, DEFAULT_MEASURED_RT_WINDOW, false, null)
{
}
