public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo,
IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false)
{
_fullScan = document.Settings.TransitionSettings.FullScan;
_instrument = document.Settings.TransitionSettings.Instrument;
_acquisitionMethod = _fullScan.AcquisitionMethod;
if (instrumentInfo != null)
{
_isWatersFile = instrumentInfo.IsWatersFile;
}
IsFirstPass = firstPass;
var comparer = PrecursorTextId.PrecursorTextIdComparerInstance;
var dictPrecursorMzToFilter = new SortedDictionary <PrecursorTextId, SpectrumFilterPair>(comparer);
if (EnabledMs || EnabledMsMs)
{
if (EnabledMs)
{
_isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (!firstPass)
{
var key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.summed); // TIC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.base_peak); // BPC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
}
}
if (EnabledMsMs)
{
_isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA &&
_fullScan.IsolationScheme.IsAllIons)
{
if (instrumentInfo != null)
{
_isWatersMse = _isWatersFile;
_isAgilentMse = instrumentInfo.IsAgilentFile;
}
_mseLevel = 1;
}
}
Func <double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow;
Func <double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow;
_minTime = _instrument.MinTime;
_maxTime = _instrument.MaxTime;
bool canSchedule = CanSchedule(document, retentionTimePredictor);
// TODO: Figure out a way to turn off time sharing on first SIM scan so that
// times can be shared for MS1 without SIM scans
_isSharedTime = !canSchedule;
// If we're using bare measured drift times from spectral libraries, go get those now
var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes
? document.Settings.GetIonMobilities(msDataFileUri)
: null;
foreach (var nodePep in document.Molecules)
{
if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep))
{
continue;
}
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (nodeGroup.Children.Count == 0)
{
continue;
}
double? minTime = _minTime, maxTime = _maxTime;
double? startDriftTimeMsec = null, endDriftTimeMsec = null;
double windowDT;
double highEnergyDriftTimeOffsetMsec = 0;
DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT);
if (centerDriftTime.DriftTimeMsec(false).HasValue)
{
startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time
endDriftTimeMsec = startDriftTimeMsec + windowDT;
highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec;
}
if (canSchedule)
{
if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType)
{
double?centerTime = null;
double windowRT = 0;
if (retentionTimePredictor != null)
{
centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep);
}
else
{
var prediction = document.Settings.PeptideSettings.Prediction;
if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated)
{
centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport(
document, nodePep, nodeGroup, out windowRT);
}
}
// Force the center time to be at least zero
if (centerTime.HasValue && centerTime.Value < 0)
{
centerTime = 0;
}
if (_fullScan.RetentionTimeFilterLength != 0)
{
windowRT = _fullScan.RetentionTimeFilterLength * 2;
}
if (centerTime != null)
{
double startTime = centerTime.Value - windowRT / 2;
double endTime = startTime + windowRT;
minTime = Math.Max(minTime ?? 0, startTime);
maxTime = Math.Min(maxTime ?? double.MaxValue, endTime);
}
}
else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType)
{
var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri);
if (times.Length > 0)
{
minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength);
maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength);
}
}
}
SpectrumFilterPair filter;
string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions
var mz = new SignedMz(nodeGroup.PrecursorMz, nodeGroup.PrecursorCharge < 0);
var key = new PrecursorTextId(mz, textId, ChromExtractor.summed);
if (!dictPrecursorMzToFilter.TryGetValue(key, out filter))
{
filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime,
startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec,
_isHighAccMsFilter, _isHighAccProductFilter);
dictPrecursorMzToFilter.Add(key, filter);
}
if (!EnabledMs)
{
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
select nodeTran.Mz, calcWindowsQ3);
}
else if (!EnabledMsMs)
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
}
else
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
where !nodeTran.IsMs1
select nodeTran.Mz, calcWindowsQ3);
}
}
}
_filterMzValues = dictPrecursorMzToFilter.Values.ToArray();
var listChromKeyFilterIds = new List <ChromKey>();
foreach (var spectrumFilterPair in _filterMzValues)
{
spectrumFilterPair.AddChromKeys(listChromKeyFilterIds);
}
_productChromKeys = listChromKeyFilterIds.ToArray();
// Sort a copy of the filter pairs by maximum retention time so that we can detect when
// filters are no longer active.
_filterRTValues = new SpectrumFilterPair[_filterMzValues.Length];
Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length);
Array.Sort(_filterRTValues, CompareByRT);
}
InitRTLimits();
}
protected override void DoTest()
{
using (var testFilesDir = new TestFilesDir(TestContext, TestFilesZip))
{
const double HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC = -.1;
// do a few unit tests on the UI error handlers
TestGetIonMobilityDBErrorHandling(testFilesDir);
TestImportIonMobilityFromSpectralLibraryErrorHandling();
TestEditIonMobilityLibraryDlgErrorHandling();
TestEditDriftTimePredictorDlgErrorHandling();
// Now exercise the UI
var goodPeptide = new ValidatingIonMobilityPeptide("SISIVGSYVGNR", 133.3210342, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC);
Assert.IsNull(goodPeptide.Validate());
var badPeptides = new[]
{
new ValidatingIonMobilityPeptide("@#$!", 133.3210342, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("SISIVGSYVGNR", 0, 0),
new ValidatingIonMobilityPeptide("SISIVGSYVGNR", -133.3210342, -HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
};
foreach (var badPeptide in badPeptides)
{
Assert.IsNotNull(badPeptide.Validate());
}
var ionMobilityPeptides = new[]
{
new ValidatingIonMobilityPeptide("SISIVGSYVGNR", 133.3210342, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), // These are made-up values
new ValidatingIonMobilityPeptide("SISIVGSYVGNR", 133.3210342, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("CCSDVFNQVVK", 131.2405487, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("CCSDVFNQVVK", 131.2405487, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("ANELLINVK", 119.2825783, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("ANELLINVK", 119.2825783, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("EALDFFAR", 110.6867676, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("EALDFFAR", 110.6867676, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("GVIFYESHGK", 123.7844632, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("GVIFYESHGK", 123.7844632, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("EKDIVGAVLK", 124.3414249, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("EKDIVGAVLK", 124.3414249, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("VVGLSTLPEIYEK", 149.857687, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("VVGLSTLPEIYEK", 149.857687, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("VVGLSTLPEIYEK", 149.857687, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("ANGTTVLVGMPAGAK", 144.7461979, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("ANGTTVLVGMPAGAK", 144.7461979, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("IGDYAGIK", 102.2694763, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("IGDYAGIK", 102.2694763, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("GDYAGIK", 91.09155861, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("GDYAGIK", 91.09155861, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("IFYESHGK", 111.2756406, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
new ValidatingIonMobilityPeptide("EALDFFAR", 110.6867676, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC),
};
List <ValidatingIonMobilityPeptide> minimalSet;
var message = EditIonMobilityLibraryDlg.ValidateUniqueChargedPeptides(ionMobilityPeptides, out minimalSet); // Check for conflicts, strip out dupes
Assert.IsNull(message, "known good data set failed import");
Assert.AreEqual(11, minimalSet.Count, "known good data imported but with wrong result count");
var save = ionMobilityPeptides[0].CollisionalCrossSection;
ionMobilityPeptides[0].CollisionalCrossSection += 1.0; // Same sequence and charge, different cross section
message = EditIonMobilityLibraryDlg.ValidateUniqueChargedPeptides(ionMobilityPeptides, out minimalSet); // Check for conflicts, strip out dupes
Assert.IsNotNull(message, message);
Assert.IsNull(minimalSet, "bad inputs to drift time library paste should be rejected wholesale");
ionMobilityPeptides[0].CollisionalCrossSection = save; // restore
// Present the Prediction tab of the peptide settings dialog
var peptideSettingsDlg1 = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate picking "Add..." from the Ion Mobility Libraries button context menu
var ionMobilityLibDlg1 = ShowDialog <EditIonMobilityLibraryDlg>(peptideSettingsDlg1.AddIonMobilityLibrary);
// Simulate user pasting in collisional cross section data to create a new drift time library
const string testlibName = "testlib";
string databasePath = testFilesDir.GetTestPath(testlibName + IonMobilityDb.EXT);
RunUI(() =>
{
string libraryText = BuildPasteLibraryText(ionMobilityPeptides, seq => seq.Substring(0, seq.Length - 1));
ionMobilityLibDlg1.LibraryName = testlibName;
ionMobilityLibDlg1.CreateDatabase(databasePath);
SetClipboardText(libraryText);
ionMobilityLibDlg1.DoPasteLibrary();
ionMobilityLibDlg1.OkDialog();
});
WaitForClosedForm(ionMobilityLibDlg1);
RunUI(peptideSettingsDlg1.OkDialog);
WaitForClosedForm(peptideSettingsDlg1);
// Use that drift time database in a differently named library
const string testlibName2 = "testlib2";
var peptideSettingsDlg2 = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate user picking Add... from the Drift Time Predictor combo control
var driftTimePredictorDlg = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg2.AddDriftTimePredictor);
// ... and reopening an existing drift time database
var ionMobility = ShowDialog <EditIonMobilityLibraryDlg>(driftTimePredictorDlg.AddIonMobilityLibrary);
RunUI(() =>
{
ionMobility.LibraryName = testlibName2;
ionMobility.OpenDatabase(databasePath);
ionMobility.OkDialog();
});
WaitForClosedForm(ionMobility);
// Set other parameters - name, resolving power, per-charge slope+intercept
const string predictorName = "test";
const double resolvingPower = 123.4;
RunUI(() =>
{
driftTimePredictorDlg.SetResolvingPower(resolvingPower);
driftTimePredictorDlg.SetPredictorName(predictorName);
SetClipboardText("1\t2\t3\n2\t4\t5"); // Silly values: z=1 s=2 i=3, z=2 s=4 i=5
driftTimePredictorDlg.PasteRegressionValues();
});
var olddoc = SkylineWindow.Document;
RunUI(() =>
{
// Go back to the first library we created
driftTimePredictorDlg.ChooseIonMobilityLibrary(testlibName);
driftTimePredictorDlg.OkDialog();
var docUI = SkylineWindow.DocumentUI;
if (docUI != null)
{
SetUiDocument(docUI.ChangeSettings(docUI.Settings.ChangePeptideSettings(
docUI.Settings.PeptideSettings.ChangePrediction(
docUI.Settings.PeptideSettings.Prediction.ChangeDriftTimePredictor(driftTimePredictorDlg.Predictor)))));
}
});
WaitForClosedForm(driftTimePredictorDlg);
RunUI(peptideSettingsDlg2.OkDialog);
/*
* Check that the database was created successfully
* Check that it has the correct number peptides
*/
IonMobilityDb db = IonMobilityDb.GetIonMobilityDb(databasePath, null);
Assert.AreEqual(11, db.GetPeptides().Count());
WaitForDocumentChange(olddoc);
// Check serialization and background loader
WaitForDocumentLoaded();
RunUI(() =>
{
SkylineWindow.SaveDocument(TestContext.GetTestPath("test.sky"));
SkylineWindow.NewDocument();
SkylineWindow.OpenFile(TestContext.GetTestPath("test.sky"));
});
var doc = WaitForDocumentLoaded();
// Verify that the schema has been updated to include these new settings
AssertEx.ValidatesAgainstSchema(doc);
// Do some DT calculations
double windowDT;
DriftTimeInfo centerDriftTime = doc.Settings.PeptideSettings.Prediction.GetDriftTimeHelper(
new LibKey("ANELLINV", 2), null, out windowDT);
Assert.AreEqual((4 * (119.2825783)) + 5, centerDriftTime.DriftTimeMsec(false));
Assert.AreEqual(2 * ((4 * (119.2825783)) + 5) / resolvingPower, windowDT);
Assert.AreEqual((4 * (119.2825783)) + 5 + HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, centerDriftTime.DriftTimeMsec(true));
//
// Test importing collisional cross sections from a spectral lib that has drift times but no high energy offset info
//
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
const string libname = "libIMS";
var blibPath = TestContext.GetTestPath("IonMobilityTest\\mse-mobility.filtered-scaled.blib");
var editListUI =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI.EditLibraryList);
RunDlg <EditLibraryDlg>(editListUI.AddItem, editLibraryDlg =>
{
editLibraryDlg.LibrarySpec = new BiblioSpecLibSpec(libname, blibPath);
editLibraryDlg.OkDialog();
});
OkDialog(editListUI, editListUI.OkDialog);
RunUI(() => peptideSettingsUI.PickedLibraries = new[] { libname });
// Check error cases for resolving power (caused unexpected excption)
RunUI(() =>
{
peptideSettingsUI.IsUseSpectralLibraryDriftTimes = true;
peptideSettingsUI.SpectralLibraryDriftTimeResolvingPower = null;
});
RunDlg <MessageDlg>(peptideSettingsUI.OkDialog, dlg =>
{
AssertEx.AreComparableStrings(Resources.MessageBoxHelper_ValidateDecimalTextBox__0__must_contain_a_decimal_value, dlg.Message);
dlg.OkDialog();
});
RunUI(() => peptideSettingsUI.SpectralLibraryDriftTimeResolvingPower = 0);
RunDlg <MessageDlg>(peptideSettingsUI.OkDialog, dlg =>
{
Assert.AreEqual(Resources.EditDriftTimePredictorDlg_ValidateResolvingPower_Resolving_power_must_be_greater_than_0_, dlg.Message);
dlg.OkDialog();
});
RunUI(() => peptideSettingsUI.IsUseSpectralLibraryDriftTimes = false);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
WaitForDocumentLoaded(); // Let that library load
// In this lib: ANGTTVLVGMPAGAK at z=2, with drift time 4.99820623749102
// and, a single CCS value, for ANELLINVK, which is 3.8612432898618
// Present the Prediction tab of the peptide settings dialog
var peptideSettingsDlg3 = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate picking "Add..." from the Drift Time Predictor combo control
var driftTimePredictorDlg3 = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg3.AddDriftTimePredictor);
const double deadeelsDT = 3.456;
const double deadeelsDTHighEnergyOffset = -0.1;
var threeCols = "DEADEELS\t5\t" + deadeelsDT.ToString(CultureInfo.CurrentCulture);
var fourCols = "DEADEELS\t5\t" + deadeelsDT.ToString(CultureInfo.CurrentCulture) + "\t" +
deadeelsDTHighEnergyOffset.ToString(CultureInfo.CurrentCulture);
RunUI(() =>
{
driftTimePredictorDlg3.SetResolvingPower(resolvingPower);
driftTimePredictorDlg3.SetPredictorName("test3");
SetClipboardText("1\t2\t3\n2\t4\t5"); // Silly values: z=1 s=2 i=3, z=2 s=4 i=5
driftTimePredictorDlg3.PasteRegressionValues();
// Simulate user pasting in some measured drift time info without high energy offset, even though its enabled - should not throw
driftTimePredictorDlg3.SetOffsetHighEnergySpectraCheckbox(true);
SetClipboardText(threeCols);
driftTimePredictorDlg3.PasteMeasuredDriftTimes();
// Simulate user pasting in some measured drift time info with high energy offset
SetClipboardText(fourCols);
driftTimePredictorDlg3.PasteMeasuredDriftTimes();
// Now turn off the high energy column and paste in four columns - should fail
driftTimePredictorDlg3.SetOffsetHighEnergySpectraCheckbox(false);
SetClipboardText(fourCols);
});
// An error will appear because the column count is wrong
ShowDialog <MessageDlg>(driftTimePredictorDlg3.PasteMeasuredDriftTimes);
var errorDlg = WaitForOpenForm <MessageDlg>();
Assert.AreEqual(string.Format(Resources.SettingsUIUtil_DoPasteText_Incorrect_number_of_columns__0__found_on_line__1__, 4, 1), errorDlg.Message);
errorDlg.OkDialog();
RunUI(() =>
{
// And now paste in three columns, should be OK
SetClipboardText(threeCols);
driftTimePredictorDlg3.PasteMeasuredDriftTimes();
// Finally turn the high energy column back on, and put in a value
driftTimePredictorDlg3.SetOffsetHighEnergySpectraCheckbox(true);
SetClipboardText(fourCols);
driftTimePredictorDlg3.PasteMeasuredDriftTimes();
});
// Simulate picking "Add..." from the Ion Mobility Library combo control
var ionMobilityLibDlg3 = ShowDialog <EditIonMobilityLibraryDlg>(driftTimePredictorDlg3.AddIonMobilityLibrary);
const string testlibName3 = "testlib3";
string databasePath3 = testFilesDir.GetTestPath(testlibName3 + IonMobilityDb.EXT);
RunUI(() =>
{
ionMobilityLibDlg3.LibraryName = testlibName3;
ionMobilityLibDlg3.CreateDatabase(databasePath3);
});
// Simulate pressing "Import" button from the Edit Ion Mobility Library dialog
var importSpectralLibDlg =
ShowDialog <ImportIonMobilityFromSpectralLibraryDlg>(ionMobilityLibDlg3.ImportFromSpectralLibrary);
RunUI(() =>
{
// Set up to fail - don't provide z=2 info
importSpectralLibDlg.Source = SpectralLibrarySource.settings; // Simulate user selecting 1st radio button
SetClipboardText("1\t1\t0"); // This will fail - no z=2 information
importSpectralLibDlg.PasteRegressionValues();
});
importSpectralLibDlg.BeginInvoke(new Action(importSpectralLibDlg.OkDialog)); // User clicks OK - we expect an error dialog to follow
WaitForOpenForm <MessageDlg>().OkDialog(); // Dismiss the error message, we'll be dropped back into the dialog
RunUI(() =>
{
importSpectralLibDlg.Source = SpectralLibrarySource.file; // Simulate user selecting 2nd radio button
importSpectralLibDlg.FilePath = blibPath; // Simulate user entering filename
SetClipboardText("1\t1\t0\n2\t2\t2"); // Note non-unity slope and charge for z=2, for test purposes
importSpectralLibDlg.PasteRegressionValues();
importSpectralLibDlg.OkDialog();
});
WaitForClosedForm(importSpectralLibDlg);
WaitForCondition(() => ionMobilityLibDlg3.LibraryPeptideCount > 8); // Let that library load
RunUI(ionMobilityLibDlg3.OkDialog);
WaitForClosedForm(ionMobilityLibDlg3);
RunUI(driftTimePredictorDlg3.OkDialog);
WaitForClosedForm(driftTimePredictorDlg3);
RunUI(peptideSettingsDlg3.OkDialog);
WaitForClosedForm(peptideSettingsDlg3);
doc = WaitForDocumentChangeLoaded(doc); // Let that library load
// Do some DT calculations with this new library
centerDriftTime = doc.Settings.PeptideSettings.Prediction.GetDriftTimeHelper(
new LibKey("ANELLINVK", 2), null, out windowDT);
double ccs = 3.8612432898618; // should have imported CCS without any transformation
Assert.AreEqual((4 * (ccs)) + 5, centerDriftTime.DriftTimeMsec(false) ?? ccs, .000001);
Assert.AreEqual(2 * ((4 * (ccs)) + 5) / resolvingPower, windowDT, .000001);
centerDriftTime = doc.Settings.PeptideSettings.Prediction.GetDriftTimeHelper(
new LibKey("ANGTTVLVGMPAGAK", 2), null, out windowDT);
ccs = (4.99820623749102 - 2) / 2; // should have imported CCS as a converted drift time
Assert.AreEqual((4 * (ccs)) + 5, centerDriftTime.DriftTimeMsec(false) ?? ccs, .000001);
Assert.AreEqual(2 * ((4 * (ccs)) + 5) / resolvingPower, windowDT, .000001);
// Do some DT calculations with the measured drift time
centerDriftTime = doc.Settings.PeptideSettings.Prediction.GetDriftTimeHelper(
new LibKey("DEADEELS", 3), null, out windowDT); // Should fail
Assert.AreEqual(windowDT, 0);
Assert.IsFalse(centerDriftTime.DriftTimeMsec(false).HasValue);
centerDriftTime = doc.Settings.PeptideSettings.Prediction.GetDriftTimeHelper(
new LibKey("DEADEELS", 5), null, out windowDT);
Assert.AreEqual(deadeelsDT, centerDriftTime.DriftTimeMsec(false) ?? -1, .000001);
Assert.AreEqual(deadeelsDT + deadeelsDTHighEnergyOffset, centerDriftTime.DriftTimeMsec(true) ?? -1, .000001);
Assert.AreEqual(2 * (deadeelsDT / resolvingPower), windowDT, .0001); // Directly measured, should match
// Now check handling of scenario where user pastes in high energy offsets then unchecks the "Use High Energy Offsets" box
var peptideSettingsDlg4 = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate picking "Edit Current..." from the Drift Time Predictor combo control
var driftTimePredictorDlg4 = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg4.EditDriftTimePredictor);
RunUI(() =>
{
Assert.IsTrue(driftTimePredictorDlg4.GetOffsetHighEnergySpectraCheckbox()); // Should start out enabled if we have offsets
driftTimePredictorDlg4.SetOffsetHighEnergySpectraCheckbox(false); // Turn off the high energy offset column
driftTimePredictorDlg4.SetPredictorName("test4");
});
RunUI(driftTimePredictorDlg4.OkDialog);
WaitForClosedForm(driftTimePredictorDlg4);
RunUI(peptideSettingsDlg4.OkDialog);
WaitForClosedForm(peptideSettingsDlg4);
doc = WaitForDocumentChangeLoaded(doc);
centerDriftTime = doc.Settings.PeptideSettings.Prediction.GetDriftTimeHelper(
new LibKey("DEADEELS", 5), null, out windowDT);
Assert.AreEqual(deadeelsDT, centerDriftTime.DriftTimeMsec(false) ?? -1, .000001);
Assert.AreEqual(deadeelsDT, centerDriftTime.DriftTimeMsec(true) ?? -1, .000001); // High energy value should now be same as low energy value
Assert.AreEqual(2 * (deadeelsDT / resolvingPower), windowDT, .0001); // Directly measured, should match
// Now make sure that high energy checkbox initial state is as we expect
var peptideSettingsDlg5 = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate picking "Edit Current..." from the Drift Time Predictor combo control
var driftTimePredictorDlg5 = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg5.EditDriftTimePredictor);
RunUI(() => Assert.IsFalse(driftTimePredictorDlg5.GetOffsetHighEnergySpectraCheckbox()));
RunUI(driftTimePredictorDlg5.CancelDialog);
WaitForClosedForm(driftTimePredictorDlg5);
RunUI(peptideSettingsDlg5.OkDialog);
WaitForClosedForm(peptideSettingsDlg5);
}
TestMeasuredDriftTimes();
}
public Dictionary <LibKey, DriftTimeInfo> FindDriftTimePeaks()
{
// Overwrite any existing measurements with newly derived ones
var measured = new Dictionary <LibKey, DriftTimeInfo>();
if (_existing != null && _existing.MeasuredDriftTimePeptides != null)
{
foreach (var existingPair in _existing.MeasuredDriftTimePeptides)
{
measured.Add(existingPair.Key, existingPair.Value);
}
}
var filepaths = _document.Settings.MeasuredResults.MSDataFilePaths.ToArray();
_totalSteps = filepaths.Length * _document.MoleculeTransitionGroupCount;
if (_totalSteps == 0)
{
return(measured);
}
using (_msDataFileScanHelper = new MsDataFileScanHelper(SetScans, HandleLoadScanException))
{
//
// Avoid opening and re-opening raw files - make these the outer loop
//
_ms1DriftTimes = new Dictionary <LibKey, List <DriftTimeIntensityPair> >();
_ms2DriftTimes = new Dictionary <LibKey, List <DriftTimeIntensityPair> >();
var twopercent = (int)Math.Ceiling(_totalSteps * 0.02);
_totalSteps += twopercent;
_currentStep = twopercent;
if (_progressMonitor != null)
{
_progressStatus = new ProgressStatus(filepaths.First().GetFileName());
_progressStatus = _progressStatus.UpdatePercentCompleteProgress(_progressMonitor, _currentStep, _totalSteps); // Make that inital lag seem less dismal to the user
}
foreach (var fp in filepaths)
{
if (!ProcessFile(fp))
{
return(null); // User cancelled
}
}
// Find drift times based on MS1 data
foreach (var dt in _ms1DriftTimes)
{
// Choose the drift time which gave the largest signal
var ms1DriftTime = dt.Value.OrderByDescending(p => p.Intensity).First().DriftTime;
// Check for MS2 data to use for high energy offset
List <DriftTimeIntensityPair> listDt;
var ms2DriftTime = _ms2DriftTimes.TryGetValue(dt.Key, out listDt)
? listDt.OrderByDescending(p => p.Intensity).First().DriftTime
: (ms1DriftTime ?? 0);
var value = new DriftTimeInfo(ms1DriftTime, ms2DriftTime - ms1DriftTime ?? 0);
if (!measured.ContainsKey(dt.Key))
{
measured.Add(dt.Key, value);
}
else
{
measured[dt.Key] = value;
}
}
// Check for data for which we have only MS2 to go on
foreach (var dt in _ms2DriftTimes)
{
if (!_ms1DriftTimes.ContainsKey(dt.Key))
{
// Only MS2 drift times found, use that
var value = new DriftTimeInfo(dt.Value.OrderByDescending(p => p.Intensity).First().DriftTime, 0);
if (!measured.ContainsKey(dt.Key))
{
measured.Add(dt.Key, value);
}
else
{
measured[dt.Key] = value;
}
}
}
}
return(measured);
}
public Dictionary<LibKey, DriftTimeInfo> FindDriftTimePeaks()
{
// Overwrite any existing measurements with newly derived ones
var measured = new Dictionary<LibKey, DriftTimeInfo>();
if (_existing != null && _existing.MeasuredDriftTimePeptides != null)
{
foreach (var existingPair in _existing.MeasuredDriftTimePeptides)
measured.Add(existingPair.Key, existingPair.Value);
}
var filepaths = _document.Settings.MeasuredResults.MSDataFilePaths.ToArray();
_totalSteps = filepaths.Length * _document.MoleculeTransitionGroupCount;
if (_totalSteps == 0)
return measured;
using (_msDataFileScanHelper = new MsDataFileScanHelper(SetScans, HandleLoadScanException))
{
//
// Avoid opening and re-opening raw files - make these the outer loop
//
_ms1DriftTimes = new Dictionary<LibKey, List<DriftTimeIntensityPair>>();
_ms2DriftTimes = new Dictionary<LibKey, List<DriftTimeIntensityPair>>();
var twopercent = (int) Math.Ceiling(_totalSteps*0.02);
_totalSteps += twopercent;
_currentStep = twopercent;
if (_progressMonitor != null)
{
_progressStatus = new ProgressStatus(filepaths.First().GetFileName());
_progressStatus = _progressStatus.UpdatePercentCompleteProgress(_progressMonitor, _currentStep, _totalSteps); // Make that inital lag seem less dismal to the user
}
foreach (var fp in filepaths)
{
if (!ProcessFile(fp))
return null; // User cancelled
}
// Find drift times based on MS1 data
foreach (var dt in _ms1DriftTimes)
{
// Choose the drift time which gave the largest signal
var ms1DriftTime = dt.Value.OrderByDescending(p => p.Intensity).First().DriftTime;
// Check for MS2 data to use for high energy offset
List<DriftTimeIntensityPair> listDt;
var ms2DriftTime = _ms2DriftTimes.TryGetValue(dt.Key, out listDt)
? listDt.OrderByDescending(p => p.Intensity).First().DriftTime
: (ms1DriftTime ?? 0);
var value = new DriftTimeInfo(ms1DriftTime, ms2DriftTime - ms1DriftTime ?? 0);
if (!measured.ContainsKey(dt.Key))
measured.Add(dt.Key, value);
else
measured[dt.Key] = value;
}
// Check for data for which we have only MS2 to go on
foreach (var dt in _ms2DriftTimes)
{
if (!_ms1DriftTimes.ContainsKey(dt.Key))
{
// Only MS2 drift times found, use that
var value = new DriftTimeInfo(dt.Value.OrderByDescending(p => p.Intensity).First().DriftTime, 0);
if (!measured.ContainsKey(dt.Key))
measured.Add(dt.Key, value);
else
measured[dt.Key] = value;
}
}
}
return measured;
}
/// <summary>
/// Get drift time for the charged peptide from explicitly set values, or our drift time predictor, or,
/// failing that, from the provided spectral library if it has bare drift times.
/// If no drift info is available, returns a new zero'd out drift time info object.
/// </summary>
public DriftTimeInfo GetDriftTime(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
LibraryIonMobilityInfo libraryIonMobilityInfo, out double windowDtMsec)
{
if (nodeGroup.ExplicitValues.DriftTimeMsec.HasValue)
{
// Use the explicitly specified value
var result = new DriftTimeInfo(nodeGroup.ExplicitValues.DriftTimeMsec,
nodeGroup.ExplicitValues.DriftTimeHighEnergyOffsetMsec ?? 0);
// Now get the resolving power
if (DriftTimePredictor != null)
{
windowDtMsec = DriftTimePredictor.InverseResolvingPowerTimesTwo*result.DriftTimeMsec(false).Value;
}
else if (LibraryDriftTimesResolvingPower.HasValue)
{
windowDtMsec = 2.0 * result.DriftTimeMsec(false).Value / LibraryDriftTimesResolvingPower.Value;
}
else
{
windowDtMsec = 0;
}
return result;
}
else
{
return GetDriftTimeHelper(
new LibKey(nodePep.RawTextId, nodeGroup.TransitionGroup.PrecursorCharge), libraryIonMobilityInfo,
out windowDtMsec);
}
}
