/// <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();
}
}
public PeptidePrediction ValidateNewSettings(bool showMessages)
{
var helper = new MessageBoxHelper(ParentForm, showMessages);
bool useLibraryDriftTime = cbUseSpectralLibraryIonMobilityValues.Checked;
var libraryDriftTimeWindowWidthCalculator = IonMobilityWindowWidthCalculator.EMPTY;
if (useLibraryDriftTime)
{
double resolvingPower = 0;
double widthAtDt0 = 0;
double widthAtDtMax = 0;
IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType peakWidthType;
if (cbLinear.Checked)
{
if (!helper.ValidateDecimalTextBox(textSpectralLibraryIonMobilityWindowWidthAtDt0, out widthAtDt0))
{
return(null);
}
if (!helper.ValidateDecimalTextBox(textSpectralLibraryIonMobilityWindowWidthAtDtMax, out widthAtDtMax))
{
return(null);
}
var errmsg = EditDriftTimePredictorDlg.ValidateWidth(widthAtDt0);
if (errmsg != null)
{
helper.ShowTextBoxError(textSpectralLibraryIonMobilityWindowWidthAtDt0, errmsg);
return(null);
}
errmsg = EditDriftTimePredictorDlg.ValidateWidth(widthAtDtMax);
if (errmsg != null)
{
helper.ShowTextBoxError(textSpectralLibraryIonMobilityWindowWidthAtDtMax, errmsg);
return(null);
}
peakWidthType = IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType.linear_range;
}
else
{
if (!helper.ValidateDecimalTextBox(textSpectralLibraryIonMobilityValuesResolvingPower, out resolvingPower))
{
return(null);
}
var errmsg = EditDriftTimePredictorDlg.ValidateResolvingPower(resolvingPower);
if (errmsg != null)
{
helper.ShowTextBoxError(textSpectralLibraryIonMobilityValuesResolvingPower, errmsg);
return(null);
}
peakWidthType = IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType.resolving_power;
}
libraryDriftTimeWindowWidthCalculator = new IonMobilityWindowWidthCalculator(peakWidthType, resolvingPower, widthAtDt0, widthAtDtMax);
}
return(Prediction.ChangeLibraryDriftTimesWindowWidthCalculator(libraryDriftTimeWindowWidthCalculator).ChangeUseLibraryIonMobilityValues(useLibraryDriftTime));
}
public DriftTimePredictor(string name,
IDictionary <LibKey, IonMobilityAndCCS> measuredMobilityIons,
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType windowWidthMode,
double resolvingPower,
double widthAtIonMobilityZero, double widthAtIonMobilityMax,
double fixedPeakWidth)
: base(name)
{
_windowWidthCalculator = new IonMobilityWindowWidthCalculator(windowWidthMode,
resolvingPower, widthAtIonMobilityZero, widthAtIonMobilityMax, fixedPeakWidth);
MeasuredMobilityIons = measuredMobilityIons;
Validate();
}
private static double driftTimeMax = 13.799765403988133; // Known max drift time for this file - use to mimic resolving power logic for test purposes
private static SrmDocument InitWatersImsMseDocument(TestFilesDir testFilesDir,
IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType driftPeakWidthCalcType,
bool withDriftTimeFilter, bool withDriftTimePredictor,
out string docPath)
{
var skyFile = withDriftTimePredictor ? "single_with_driftinfo.sky" : "single_no_driftinfo.sky";
docPath = testFilesDir.GetTestPath(skyFile);
var cmdline = new CommandLine();
Assert.IsTrue(cmdline.OpenSkyFile(docPath)); // Handles any path shifts in database files, like our .imdb file
SrmDocument doc = cmdline.Document;
// Cause library load and subsequent document update
using (var docContainer = new ResultsTestDocumentContainer(null, docPath))
{
docContainer.SetDocument(doc, null, true);
docContainer.AssertComplete();
doc = docContainer.Document;
double resolvingPower = 100; // Test was originally written with resolving power 100
double widthAtDtMax = 2 * driftTimeMax / resolvingPower;
var driftTimeWindowWidthCalculator = new IonMobilityWindowWidthCalculator(driftPeakWidthCalcType, resolvingPower, 0, widthAtDtMax);
if (withDriftTimeFilter && !withDriftTimePredictor)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("waters-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesWindowWidthCalculator(driftTimeWindowWidthCalculator)).
ChangePeptidePrediction(p => p.ChangeUseLibraryIonMobilityValues(true))
);
}
else if (withDriftTimeFilter)
{
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideSettings(ps => ps.ChangePrediction(
ps.Prediction.ChangeDriftTimePredictor(ps.Prediction.IonMobilityPredictor.ChangeDriftTimeWindowWidthCalculator(driftTimeWindowWidthCalculator)))));
}
}
return(doc);
}
public override void ReadXml(XmlReader reader)
{
var name = reader.Name;
// Read start tag attributes
base.ReadXml(reader);
_windowWidthCalculator = new IonMobilityWindowWidthCalculator(reader, true, false);
// Consume start tag
reader.ReadStartElement();
// Skip over ion_mobility_library stuff that never saw the light of day, but appears in some older tests
while (reader.Name.Equals(@"ion_mobility_library") || reader.Name.Equals(@"regression_dt"))
{
reader.Read();
}
// Read all measured ion mobilities
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
while (reader.IsStartElement(EL.measured_dt)) // N.B. EL.measured_dt is a misnomer, this covers all IMS types
{
var im = MeasuredIonMobility.Deserialize(reader);
var key = new LibKey(im.Target, im.Charge);
if (!dict.ContainsKey(key))
{
dict.Add(key, im.IonMobilityInfo);
}
}
if (dict.Any())
{
MeasuredMobilityIons = dict;
}
if (reader.Name.Equals(name)) // Make sure we haven't stepped off the end
{
reader.ReadEndElement(); // Consume end tag
}
Validate();
}
public TransitionIonMobilityFiltering CreateTransitionIonMobilityFiltering(string dbDir)
{
// Create .imsdb library from MeasuredMobilityIons, for backward compatibility
var oldDict = MeasuredMobilityIons;
var dict = oldDict == null
? null
: oldDict.ToDictionary(kvp => kvp.Key,
kvp => new List <IonMobilityAndCCS>()
{
kvp.Value
});
if ((dict == null || dict.Count == 0) && IonMobilityWindowWidthCalculator.IsNullOrEmpty(_windowWidthCalculator))
{
return(TransitionIonMobilityFiltering.EMPTY);
}
var val = new TransitionIonMobilityFiltering(Name, dbDir, dict,
true,
_windowWidthCalculator);
return(val.ChangeLibrary(val.IonMobilityLibrary.Initialize(null)));
}
private TransitionIonMobilityFiltering ValidateIonMobilitySettings(MessageBoxHelper helper)
{
var IonMobilityLibrary = GetSelectedIonMobilityLibrary();
var useSpectralLibraryIonMobilities = cbUseSpectralLibraryIonMobilities.Checked;
var peakWidthType = ShowPeakWidthTypeControl ?
(IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType)comboBoxWindowType.SelectedIndex :
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.resolving_power;
double resolvingPower = 0;
double widthAtDt0 = 0;
double widthAtDtMax = 0;
double fixedPeakWidth = 0;
string errmsg;
switch (peakWidthType)
{
case IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.linear_range:
if (!helper.ValidateDecimalTextBox(textIonMobilityFilterWidthAtMobility0, out widthAtDt0))
{
return(null);
}
if (!helper.ValidateDecimalTextBox(textIonMobilityFilterWidthAtMobilityMax, out widthAtDtMax))
{
return(null);
}
errmsg = ValidateWidth(widthAtDt0);
if (errmsg != null)
{
helper.ShowTextBoxError(textIonMobilityFilterWidthAtMobility0, errmsg);
return(null);
}
errmsg = ValidateWidth(widthAtDtMax);
if (errmsg != null)
{
helper.ShowTextBoxError(textIonMobilityFilterWidthAtMobilityMax, errmsg);
return(null);
}
break;
case IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.resolving_power:
if (!helper.ValidateDecimalTextBox(textIonMobilityFilterResolvingPower, out resolvingPower))
{
return(null);
}
errmsg = ValidateResolvingPower(resolvingPower);
if (errmsg != null)
{
helper.ShowTextBoxError(textIonMobilityFilterResolvingPower, errmsg);
return(null);
}
break;
case IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width: // Fixed width
if (!helper.ValidateDecimalTextBox(textIonMobilityFilterFixedWidth, out fixedPeakWidth))
{
return(null);
}
errmsg = ValidateFixedWindow(fixedPeakWidth);
if (errmsg != null)
{
helper.ShowTextBoxError(textIonMobilityFilterFixedWidth, errmsg);
return(null);
}
break;
}
var ionMobilityWindowWidthCalculator =
new IonMobilityWindowWidthCalculator(peakWidthType, resolvingPower, widthAtDt0, widthAtDtMax, fixedPeakWidth);
return(new TransitionIonMobilityFiltering(IonMobilityLibrary, useSpectralLibraryIonMobilities, ionMobilityWindowWidthCalculator));
}
private void PerformTestMeasuredDriftValues(bool asSmallMolecules)
{
if (asSmallMolecules)
{
if (!RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
}
var testFilesDir = new TestFilesDir(TestContext, @"TestData\Results\BlibDriftTimeTest.zip"); // Re-used from BlibDriftTimeTest
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
// This was a malformed document, which caused problems after a fix to not recalculate
// document library settings on open. To avoid rewriting this test for the document
// which now contains 2 precursors, the first precursor is removed immediately.
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var pathFirstPeptide = docOriginal.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodeFirstPeptide = (DocNodeParent)docOriginal.FindNode(pathFirstPeptide);
docOriginal = (SrmDocument)docOriginal.RemoveChild(pathFirstPeptide, nodeFirstPeptide.Children[0]);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOriginal = refine.ConvertToSmallMolecules(docOriginal, testFilesDir.FullPath);
}
using (var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath))
{
var doc = docContainer.Document;
// Import an mz5 file that contains drift info
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714" + ExtensionTestContext.ExtMz5)), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
// Clear out any current settings
document = document.ChangeSettings(document.Settings.ChangeTransitionIonMobilityFiltering(s => TransitionIonMobilityFiltering.EMPTY));
// Verify ability to extract predictions from raw data
var libraryName0 = "test0";
var dbPath0 = testFilesDir.GetTestPath(libraryName0 + IonMobilityDb.EXT);
var newIMFiltering = document.Settings.TransitionSettings.IonMobilityFiltering.ChangeLibrary(
IonMobilityLibrary.CreateFromResults(
document, docContainer.DocumentFilePath, true,
libraryName0, dbPath0));
var result = newIMFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(1, result.Count);
var expectedDT = 4.0019;
var expectedOffset = .4829;
Assert.AreEqual(expectedDT, result.Values.First().First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result.Values.First().First().HighEnergyIonMobilityValueOffset ?? 0, .001);
// Check ability to update, and to preserve unchanged
var revised = new List <PrecursorIonMobilities>();
var libKey = result.Keys.First();
revised.Add(new PrecursorIonMobilities(libKey, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(expectedDT = 4, eIonMobilityUnits.drift_time_msec), null, expectedOffset = 0.234))); // N.B. CCS handling would require actual raw data in this test, it's covered in a perf test
var pepSequence = "DEADEELS";
var libKey2 = asSmallMolecules ?
new LibKey(SmallMoleculeLibraryAttributes.Create(pepSequence, "C12H5", null, null, null, null), Adduct.M_PLUS_2H) :
new LibKey(pepSequence, Adduct.DOUBLY_PROTONATED);
revised.Add(new PrecursorIonMobilities(libKey2, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, 0.123)));
var libraryName = "test";
var dbPath = testFilesDir.GetTestPath(libraryName + IonMobilityDb.EXT);
var imsdb = IonMobilityDb.CreateIonMobilityDb(dbPath, libraryName, false, revised);
var newLibIM = new IonMobilityLibrary(libraryName, dbPath, imsdb);
var ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.resolving_power, 40, 0, 0, 0);
var calculator = ionMobilityWindowWidthCalculator;
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(calculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width, 40, 0, 0, 100);
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(ionMobilityWindowWidthCalculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
}
}
