public EditIonMobilityLibraryDlg(IonMobilityLibrary library, IEnumerable <IonMobilityLibrarySpec> existingLibs)
{
_existingLibs = existingLibs;
InitializeComponent();
Icon = Resources.Skyline;
_gridViewLibraryDriver = new CollisionalCrossSectionGridViewDriver(gridViewMeasuredPeptides, bindingSourceLibrary,
new SortableBindingList <ValidatingIonMobilityPeptide>());
if (library != null)
{
textLibraryName.Text = _editingName = library.Name;
string databaseStartPath = library.DatabasePath;
OpenDatabase(databaseStartPath);
}
}
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);
}
}
