public void OpenDatabase(string path)
{
if (!File.Exists(path))
{
MessageDlg.Show(this, String.Format(Resources.EditIonMobilityLibraryDlg_OpenDatabase_The_file__0__does_not_exist__Click_the_Create_button_to_create_a_new_ion_mobility_library_or_click_the_Open_button_to_find_the_missing_file_,
path));
return;
}
try
{
IonMobilityDb db = IonMobilityDb.GetIonMobilityDb(path, null); // TODO: (copied from iRT code) LongWaitDlg
var dbPeptides = db.GetPeptides().ToArray();
LoadLibrary(dbPeptides);
// Clone all of the peptides to use for comparison in OkDialog
_originalPeptides = dbPeptides.Select(p => new ValidatingIonMobilityPeptide(p.Sequence, p.CollisionalCrossSection, p.HighEnergyDriftTimeOffsetMsec)).ToArray();
textDatabase.Text = path;
}
catch (DatabaseOpeningException e)
{
MessageDlg.ShowException(this, e);
}
}
public void CreateDatabase(string path)
{
//The file that was just created does not have a schema, so SQLite won't touch it.
//The file must have a schema or not exist for use with SQLite, so we'll delete
//it and install a schema
try
{
FileEx.SafeDelete(path);
}
catch (IOException x)
{
MessageDlg.ShowException(this, x);
return;
}
//Create file, initialize db
try
{
IonMobilityDb.CreateIonMobilityDb(path);
textDatabase.Text = path;
}
catch (DatabaseOpeningException x)
{
MessageDlg.ShowException(this, x);
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.EditIonMobilityLibraryDlg_CreateDatabase_The_ion_mobility_library_file__0__could_not_be_created, path),
x.Message);
MessageDlg.ShowWithException(this, message, x);
}
}
/// <summary>
/// Test various error conditions in IonMobilityDb.cs
/// </summary>
public void TestGetIonMobilityDBErrorHandling(TestFilesDir testFilesDir)
{
AssertEx.ThrowsException <DatabaseOpeningException>(() => IonMobilityDb.GetIonMobilityDb(null, null),
Resources.IonMobilityDb_GetIonMobilityDb_Please_provide_a_path_to_an_existing_ion_mobility_library_);
const string badfilename = "nonexistent_file.imdb";
AssertEx.ThrowsException <DatabaseOpeningException>(
() => IonMobilityDb.GetIonMobilityDb(badfilename, null),
String.Format(
Resources.IonMobilityDb_GetIonMobilityDb_The_ion_mobility_library_file__0__could_not_be_found__Perhaps_you_did_not_have_sufficient_privileges_to_create_it_,
badfilename));
string bogusfile = testFilesDir.GetTestPath("bogus.imdb");
using (FileStream fs = File.Create(bogusfile))
{
Byte[] info = new UTF8Encoding(true).GetBytes("This is a bogus file.");
fs.Write(info, 0, info.Length);
}
AssertEx.ThrowsException <DatabaseOpeningException>(
() => IonMobilityDb.GetIonMobilityDb(bogusfile, null),
String.Format(
Resources.IonMobilityDb_GetIonMobilityDb_The_file__0__is_not_a_valid_ion_mobility_library_file_,
bogusfile));
}
public void OkDialog()
{
if (string.IsNullOrEmpty(textLibraryName.Text))
{
MessageDlg.Show(this, Resources.EditIonMobilityLibraryDlg_OkDialog_Please_enter_a_name_for_the_ion_mobility_library_);
textLibraryName.Focus();
return;
}
if (_existingLibs != null)
{
foreach (var existingLib in _existingLibs)
{
if (Equals(existingLib.Name, textLibraryName.Text) && !Equals(existingLib.Name, _editingName))
{
if (MessageBox.Show(this, string.Format(Resources.EditIonMobilityLibraryDlg_OkDialog_An_ion_mobility_library_with_the_name__0__already_exists__Do_you_want_to_overwrite_it_,
textLibraryName.Text),
Program.Name, MessageBoxButtons.YesNo) != DialogResult.Yes)
{
textLibraryName.Focus();
return;
}
}
}
}
string message;
if (string.IsNullOrEmpty(textDatabase.Text))
{
message = TextUtil.LineSeparate(Resources.EditIonMobilityLibraryDlg_OkDialog_Please_choose_a_file_for_the_ion_mobility_library,
Resources.EditIonMobilityLibraryDlg_OkDialog_Click_the_Create_button_to_create_a_new_library_or_the_Open_button_to_open_an_existing_library_file_);
MessageDlg.Show(this, message);
textDatabase.Focus();
return;
}
string path = Path.GetFullPath(textDatabase.Text);
if (!Equals(path, textDatabase.Text))
{
message = TextUtil.LineSeparate(Resources.EditIonMobilityLibraryDlg_OkDialog_Please_use_a_full_path_to_a_file_for_the_ion_mobility_library_,
Resources.EditIonMobilityLibraryDlg_OkDialog_Click_the_Create_button_to_create_a_new_library_or_the_Open_button_to_open_an_existing_library_file_);
MessageDlg.Show(this, message);
textDatabase.Focus();
return;
}
if (!string.Equals(Path.GetExtension(path), IonMobilityDb.EXT))
{
path += IonMobilityDb.EXT;
}
// This function MessageBox.Show's error messages
if (!ValidatePeptideList(LibraryPeptideList, textLibraryName.Text ?? string.Empty))
{
gridViewMeasuredPeptides.Focus();
return;
}
try
{
var calculator = new IonMobilityLibrary(textLibraryName.Text, path);
IonMobilityDb db = File.Exists(path)
? IonMobilityDb.GetIonMobilityDb(path, null)
: IonMobilityDb.CreateIonMobilityDb(path);
db = db.UpdatePeptides(LibraryPeptides.ToArray(), _originalPeptides ?? new ValidatingIonMobilityPeptide[0]);
IonMobilityLibrary = calculator.ChangeDatabase(db);
}
catch (DatabaseOpeningException x)
{
MessageDlg.Show(this, x.Message);
textDatabase.Focus();
return;
}
catch (StaleStateException staleStateException)
{
// CONSIDER: (copied from iRT code) Not sure if this is the right thing to do. It would
// be nice to solve whatever is causing this, but this is
// better than showing an unexpected error form with stack trace.
MessageDlg.ShowWithException(this, Resources.EditIonMobilityLibraryDlg_OkDialog_Failure_updating_peptides_in_the_ion_mobility_library__The_library_may_be_out_of_synch_, staleStateException);
return;
}
DialogResult = DialogResult.OK;
}
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);
}
}
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();
}
