/// <summary>
/// Saves the database to a new directory with only the charged peptides used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which charged peptides are to be kept</param>
/// <param name="smallMoleculeConversionMap">Used for changing charge,modifedSeq to adduct,molecule in small molecule conversion</param>
/// <returns>The full path to the file saved</returns>
public override string PersistMinimized(string pathDestDir,
SrmDocument document, IDictionary <LibKey, LibKey> smallMoleculeConversionMap)
{
RequireUsable();
var fname = Path.GetFileName(PersistencePath);
if (smallMoleculeConversionMap != null && fname != null &&
!fname.Contains(BiblioSpecLiteSpec.DotConvertedToSmallMolecules))
{
fname = fname.Replace(IonMobilityDb.EXT, BiblioSpecLiteSpec.DotConvertedToSmallMolecules + IonMobilityDb.EXT);
}
string persistPath = Path.Combine(pathDestDir, fname ?? String.Empty);
using (var fs = new FileSaver(persistPath))
{
var ionMobilityDbMinimal = IonMobilityDb.CreateIonMobilityDb(fs.SafeName);
// Calculate the minimal set of peptides needed for this document
var dbPeptides = _database.GetPeptides().ToList();
var persistPeptides = new List <ValidatingIonMobilityPeptide>();
var dictPeptides = dbPeptides.ToDictionary(pep => pep.GetLibKey());
foreach (var pair in document.MoleculePrecursorPairs)
{
var test =
new ValidatingIonMobilityPeptide(pair.NodePep.ModifiedTarget, pair.NodeGroup.PrecursorAdduct, 0, 0);
var key = test.GetLibKey();
DbIonMobilityPeptide dbPeptide;
if (dictPeptides.TryGetValue(key, out dbPeptide))
{
if (smallMoleculeConversionMap != null)
{
// We are in the midst of converting a document to small molecules for test purposes
LibKey smallMolInfo;
if (smallMoleculeConversionMap.TryGetValue(new LibKey(pair.NodePep.ModifiedSequence, pair.NodeGroup.PrecursorCharge), out smallMolInfo))
{
var precursorAdduct = smallMolInfo.Adduct;
var smallMoleculeAttributes = smallMolInfo.SmallMoleculeLibraryAttributes;
dbPeptide = new DbIonMobilityPeptide(smallMoleculeAttributes, precursorAdduct, dbPeptide.CollisionalCrossSection, dbPeptide.HighEnergyDriftTimeOffsetMsec);
}
else
{
// Not being converted
Assume.IsTrue(pair.NodeGroup.Peptide.IsDecoy);
continue;
}
}
persistPeptides.Add(new ValidatingIonMobilityPeptide(dbPeptide));
// Only add once
dictPeptides.Remove(key);
}
}
ionMobilityDbMinimal.UpdatePeptides(persistPeptides, new ValidatingIonMobilityPeptide[0]);
fs.Commit();
}
return(persistPath);
}
/// <summary>
/// Test various error conditions in EditDriftTimePredictorDlg.cs
/// </summary>
public void TestEditDriftTimePredictorDlgErrorHandling()
{
AssertEx.Contains(EditDriftTimePredictorDlg.ValidateResolvingPower(0), Resources.EditDriftTimePredictorDlg_ValidateResolvingPower_Resolving_power_must_be_greater_than_0_);
AssertEx.Contains(EditDriftTimePredictorDlg.ValidateResolvingPower(-1), Resources.EditDriftTimePredictorDlg_ValidateResolvingPower_Resolving_power_must_be_greater_than_0_);
Assert.IsNull(EditDriftTimePredictorDlg.ValidateResolvingPower(1));
AssertEx.Contains(MeasuredDriftTimeTable.ValidateCharge(0),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
0, TransitionGroup.MAX_PRECURSOR_CHARGE));
AssertEx.Contains(MeasuredDriftTimeTable.ValidateCharge(99),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
99, TransitionGroup.MAX_PRECURSOR_CHARGE));
string[] dtValues = { null, null, null, null };
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(new[] { "", "" }),
Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_pasted_text_must_have_three_columns_);
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_A_modified_peptide_sequence_is_required_for_each_entry_);
dtValues[0] = "$%$%!";
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
String.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_sequence__0__is_not_a_valid_modified_peptide_sequence_, dtValues[0]));
dtValues[0] = "JKLM";
dtValues[1] = "dog";
dtValues[2] = "-0.2"; // HighEnergyDriftTimeOffsetMsec
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
String.Format(Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
dtValues[EditDriftTimePredictorDlg.COLUMN_CHARGE].Trim(), TransitionGroup.MAX_PRECURSOR_CHARGE));
dtValues[2] = (17.9).ToString(CultureInfo.CurrentCulture);
dtValues[1] = "2";
Assert.IsNull(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
string.Format("unexpected error {0}", MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues)));
dtValues[2] = "fish";
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
String.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_value__0__is_not_a_valid_drift_time_, dtValues[EditDriftTimePredictorDlg.COLUMN_DRIFT_TIME_MSEC].Trim()));
AssertEx.Contains(ChargeRegressionTable.ValidateCharge(0),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
0, TransitionGroup.MAX_PRECURSOR_CHARGE));
AssertEx.Contains(ChargeRegressionTable.ValidateCharge(99),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
99, TransitionGroup.MAX_PRECURSOR_CHARGE));
Assert.IsNull(ChargeRegressionTable.ValidateCharge(1));
Assert.IsNull(ChargeRegressionTable.ValidateCharge(TransitionGroup.MAX_PRECURSOR_CHARGE));
string[] values = { "", "", "" };
AssertEx.Contains(ChargeRegressionTable.ValidateRegressionCellValues(values),
string.Format(
Resources.EditDriftTimePredictorDlg_ValidateRegressionCellValues_the_value__0__is_not_a_valid_charge__Charges_must_be_integer_values_between_1_and__1__,
values[0], TransitionGroup.MAX_PRECURSOR_CHARGE));
values[0] = "1";
AssertEx.Contains(ChargeRegressionTable.ValidateRegressionCellValues(values),
string.Format(Resources.EditDriftTimePredictorDlg_ValidateRegressionCellValues_the_value__0__is_not_a_valid_slope_, values[1]));
values[1] = "1";
AssertEx.Contains(ChargeRegressionTable.ValidateRegressionCellValues(values),
string.Format(Resources.EditDriftTimePredictorDlg_ValidateRegressionCellValues_the_value__0__is_not_a_valid_intercept_, values[2]));
values[2] = "1";
Assert.IsNull(ChargeRegressionTable.ValidateRegressionCellValues(values));
object[] column = { "1" };
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(column, 1),
Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_The_pasted_text_must_have_at_least_two_columns_);
object[] columns = { "", "", "" };
const int lineNumber = 1;
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Missing_peptide_sequence_on_line__0__, lineNumber));
columns[0] = "@#%!";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_The_text__0__is_not_a_valid_peptide_sequence_on_line__1__, columns[0], lineNumber));
columns[0] = "JKLM";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Missing_collisional_cross_section_value_on_line__0__, lineNumber));
columns[1] = "fish";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Invalid_number_format__0__for_collisional_cross_section_on_line__1__,
columns[1], lineNumber));
columns[1] = "0";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_The_collisional_cross_section__0__must_be_greater_than_zero_on_line__1__,
columns[1], lineNumber));
columns[1] = "1";
Assert.IsNull(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber));
columns[2] = "zeke"; // HighEnergyDriftTimeOffsetMsec
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Invalid_number_format__0__for_high_energy_drift_time_offset_on_line__1__,
columns[2], lineNumber));
columns[2] = ""; // HighEnergyDriftTimeOffsetMsec
Assert.IsNull(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber));
columns[2] = "1"; // HighEnergyDriftTimeOffsetMsec (usually negative, but we don't demand it)
Assert.IsNull(CollisionalCrossSectionGridViewDriverBase<ValidatingIonMobilityPeptide>.ValidateRow(columns, lineNumber));
var pep = new ValidatingIonMobilityPeptide(null, 0, 0);
AssertEx.Contains(pep.Validate(), Resources.ValidatingIonMobilityPeptide_ValidateSequence_A_modified_peptide_sequence_is_required_for_each_entry_);
const string seq = "@#%!";
pep = new ValidatingIonMobilityPeptide(seq, 0, 0);
AssertEx.Contains(pep.Validate(), string.Format(
Resources.ValidatingIonMobilityPeptide_ValidateSequence_The_sequence__0__is_not_a_valid_modified_peptide_sequence_, seq));
pep = new ValidatingIonMobilityPeptide("JLKM", 0, 0);
AssertEx.Contains(pep.Validate(),
Resources.ValidatingIonMobilityPeptide_ValidateCollisionalCrossSection_Measured_collisional_cross_section_values_must_be_valid_decimal_numbers_greater_than_zero_);
pep = new ValidatingIonMobilityPeptide("JLKM", 1, 0);
Assert.IsNull(pep.Validate());
}
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();
}
/// <summary>
/// Test various error conditions in EditDriftTimePredictorDlg.cs
/// </summary>
public void TestEditDriftTimePredictorDlgErrorHandling()
{
AssertEx.Contains(EditDriftTimePredictorDlg.ValidateResolvingPower(0), Resources.EditDriftTimePredictorDlg_ValidateResolvingPower_Resolving_power_must_be_greater_than_0_);
AssertEx.Contains(EditDriftTimePredictorDlg.ValidateResolvingPower(-1), Resources.EditDriftTimePredictorDlg_ValidateResolvingPower_Resolving_power_must_be_greater_than_0_);
Assert.IsNull(EditDriftTimePredictorDlg.ValidateResolvingPower(1));
AssertEx.Contains(MeasuredDriftTimeTable.ValidateCharge(0),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
0, TransitionGroup.MAX_PRECURSOR_CHARGE));
AssertEx.Contains(MeasuredDriftTimeTable.ValidateCharge(99),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
99, TransitionGroup.MAX_PRECURSOR_CHARGE));
string[] dtValues = { null, null, null, null };
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(new[] { "", "" }),
Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_pasted_text_must_have_three_columns_);
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_A_modified_peptide_sequence_is_required_for_each_entry_);
dtValues[0] = "$%$%!";
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
String.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_sequence__0__is_not_a_valid_modified_peptide_sequence_, dtValues[0]));
dtValues[0] = "JKLM";
dtValues[1] = "dog";
dtValues[2] = "-0.2"; // HighEnergyDriftTimeOffsetMsec
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
String.Format(Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
dtValues[EditDriftTimePredictorDlg.COLUMN_CHARGE].Trim(), TransitionGroup.MAX_PRECURSOR_CHARGE));
dtValues[2] = (17.9).ToString(CultureInfo.CurrentCulture);
dtValues[1] = "2";
Assert.IsNull(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
string.Format("unexpected error {0}", MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues)));
dtValues[2] = "fish";
AssertEx.Contains(MeasuredDriftTimeTable.ValidateMeasuredDriftTimeCellValues(dtValues),
String.Format(Resources.MeasuredDriftTimeTable_ValidateMeasuredDriftTimeCellValues_The_value__0__is_not_a_valid_drift_time_, dtValues[EditDriftTimePredictorDlg.COLUMN_DRIFT_TIME_MSEC].Trim()));
AssertEx.Contains(ChargeRegressionTable.ValidateCharge(0),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
0, TransitionGroup.MAX_PRECURSOR_CHARGE));
AssertEx.Contains(ChargeRegressionTable.ValidateCharge(99),
String.Format(
Resources.EditDriftTimePredictorDlg_ValidateCharge_The_entry__0__is_not_a_valid_charge__Precursor_charges_must_be_integer_values_between_1_and__1__,
99, TransitionGroup.MAX_PRECURSOR_CHARGE));
Assert.IsNull(ChargeRegressionTable.ValidateCharge(1));
Assert.IsNull(ChargeRegressionTable.ValidateCharge(TransitionGroup.MAX_PRECURSOR_CHARGE));
string[] values = { "", "", "" };
AssertEx.Contains(ChargeRegressionTable.ValidateRegressionCellValues(values),
string.Format(
Resources.EditDriftTimePredictorDlg_ValidateRegressionCellValues_the_value__0__is_not_a_valid_charge__Charges_must_be_integer_values_between_1_and__1__,
values[0], TransitionGroup.MAX_PRECURSOR_CHARGE));
values[0] = "1";
AssertEx.Contains(ChargeRegressionTable.ValidateRegressionCellValues(values),
string.Format(Resources.EditDriftTimePredictorDlg_ValidateRegressionCellValues_the_value__0__is_not_a_valid_slope_, values[1]));
values[1] = "1";
AssertEx.Contains(ChargeRegressionTable.ValidateRegressionCellValues(values),
string.Format(Resources.EditDriftTimePredictorDlg_ValidateRegressionCellValues_the_value__0__is_not_a_valid_intercept_, values[2]));
values[2] = "1";
Assert.IsNull(ChargeRegressionTable.ValidateRegressionCellValues(values));
object[] column = { "1" };
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(column, 1),
Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_The_pasted_text_must_have_at_least_two_columns_);
object[] columns = { "", "", "" };
const int lineNumber = 1;
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Missing_peptide_sequence_on_line__0__, lineNumber));
columns[0] = "@#%!";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_The_text__0__is_not_a_valid_peptide_sequence_on_line__1__, columns[0], lineNumber));
columns[0] = "JKLM";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Missing_collisional_cross_section_value_on_line__0__, lineNumber));
columns[1] = "fish";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Invalid_number_format__0__for_collisional_cross_section_on_line__1__,
columns[1], lineNumber));
columns[1] = "0";
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_The_collisional_cross_section__0__must_be_greater_than_zero_on_line__1__,
columns[1], lineNumber));
columns[1] = "1";
Assert.IsNull(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber));
columns[2] = "zeke"; // HighEnergyDriftTimeOffsetMsec
AssertEx.Contains(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber),
string.Format(Resources.CollisionalCrossSectionGridViewDriverBase_ValidateRow_Invalid_number_format__0__for_high_energy_drift_time_offset_on_line__1__,
columns[2], lineNumber));
columns[2] = ""; // HighEnergyDriftTimeOffsetMsec
Assert.IsNull(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber));
columns[2] = "1"; // HighEnergyDriftTimeOffsetMsec (usually negative, but we don't demand it)
Assert.IsNull(CollisionalCrossSectionGridViewDriverBase <ValidatingIonMobilityPeptide> .ValidateRow(columns, lineNumber));
var pep = new ValidatingIonMobilityPeptide(null, 0, 0);
AssertEx.Contains(pep.Validate(), Resources.ValidatingIonMobilityPeptide_ValidateSequence_A_modified_peptide_sequence_is_required_for_each_entry_);
const string seq = "@#%!";
pep = new ValidatingIonMobilityPeptide(seq, 0, 0);
AssertEx.Contains(pep.Validate(), string.Format(
Resources.ValidatingIonMobilityPeptide_ValidateSequence_The_sequence__0__is_not_a_valid_modified_peptide_sequence_, seq));
pep = new ValidatingIonMobilityPeptide("JLKM", 0, 0);
AssertEx.Contains(pep.Validate(),
Resources.ValidatingIonMobilityPeptide_ValidateCollisionalCrossSection_Measured_collisional_cross_section_values_must_be_valid_decimal_numbers_greater_than_zero_);
pep = new ValidatingIonMobilityPeptide("JLKM", 1, 0);
Assert.IsNull(pep.Validate());
}
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();
}
