public bool Equals(IsolationScheme other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(base.Equals(other) &&
ArrayUtil.EqualsDeep(other._prespecifiedIsolationWindows, _prespecifiedIsolationWindows) &&
other.PrecursorFilter.Equals(PrecursorFilter) &&
other.PrecursorRightFilter.Equals(PrecursorRightFilter) &&
other.SpecialHandling.Equals(SpecialHandling) &&
other.WindowsPerScan.Equals(WindowsPerScan));
}
public FullScanSettingsControl(SkylineWindow skylineWindow)
{
SkylineWindow = skylineWindow;
InitializeComponent();
InitializeMs1FilterUI();
InitializeMsMsFilterUI();
InitializeRetentionTimeFilterUI();
// Update the precursor analyzer type in case the SelectedIndex is still -1
UpdatePrecursorAnalyzerType();
UpdateProductAnalyzerType();
PrecursorIsotopesCurrent = FullScan.PrecursorIsotopes;
PrecursorMassAnalyzer = FullScan.PrecursorMassAnalyzer;
_prevval_comboIsolationScheme = IsolationScheme; // initialize previous value to initial value
}
private void BrukerTOFMethodTest()
{
const string brukerOutputMethodFilename = "RetTimeMassListFile.Method";
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Bovine_std_curated_seq_small2-trigger.sky")));
string brukerActualMeth = TestFilesDir.GetTestPath("brukermethodexport.m");
string brukerExpectedMeth = TestFilesDir.GetTestPath("BrukerExpected.Method");
string brukerTemplateMeth = TestFilesDir.GetTestPath("Bruker Template Scheduled Precursor List.m");
WaitForDocumentLoaded();
// Export PRM method unscheduled
RunDlg<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method),
exportMethodDlg =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.BRUKER_TOF;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.SetTemplateFile(brukerTemplateMeth);
exportMethodDlg.MethodType = ExportMethodType.Standard;
Assert.IsTrue(exportMethodDlg.IsRunLengthVisible);
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
exportMethodDlg.RunLength = 20;
exportMethodDlg.OkDialog(brukerActualMeth);
});
Assert.IsTrue(Directory.Exists(brukerActualMeth));
AssertEx.NoDiff(File.ReadAllText(brukerExpectedMeth), File.ReadAllText(Path.Combine(brukerActualMeth, brukerOutputMethodFilename)));
DirectoryEx.SafeDelete(brukerActualMeth);
// Export PRM method scheduled
RunDlg<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method),
exportMethodDlg =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.BRUKER_TOF;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.SetTemplateFile(brukerTemplateMeth);
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
Assert.IsFalse(exportMethodDlg.IsRunLengthVisible);
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
exportMethodDlg.OkDialog(brukerActualMeth);
});
Assert.IsTrue(Directory.Exists(brukerActualMeth));
brukerExpectedMeth = TestFilesDir.GetTestPath("BrukerExpectedSched.Method");
AssertEx.NoDiff(File.ReadAllText(brukerExpectedMeth), File.ReadAllText(Path.Combine(brukerActualMeth, brukerOutputMethodFilename)));
DirectoryEx.SafeDelete(brukerActualMeth);
// Export PRM method scheduled error
{
RunUI(() => SkylineWindow.ModifyDocument("Remove RT prediction",
doc => doc.ChangeSettings(doc.Settings.ChangePeptidePrediction(predict => predict.ChangeRetentionTime(null)))));
var exportMethodDlgError = ShowDialog<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlgError.InstrumentType = ExportInstrumentType.BRUKER_TOF;
exportMethodDlgError.ExportStrategy = ExportStrategy.Single;
exportMethodDlgError.SetTemplateFile(brukerTemplateMeth);
});
RunDlg<MessageDlg>(() => exportMethodDlgError.MethodType = ExportMethodType.Scheduled,
dlg => dlg.CancelDialog());
OkDialog(exportMethodDlgError, exportMethodDlgError.CancelDialog);
}
// Export DIA Method
{
var isoWindows = new IsolationScheme("Prespecified", new[]
{
new IsolationWindow(500, 521, null, 0.5, 0.5),
new IsolationWindow(520, 541, null, 0.5, 0.5),
new IsolationWindow(540, 561, null, 0.5, 0.5),
});
RunUI(() => SkylineWindow.ModifyDocument("Add isolation window list",
doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(full => full.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA, isoWindows)))));
var exportMethodDlgDia = ShowDialog<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlgDia.InstrumentType = ExportInstrumentType.BRUKER_TOF;
exportMethodDlgDia.ExportStrategy = ExportStrategy.Single;
exportMethodDlgDia.SetTemplateFile(brukerTemplateMeth);
});
RunDlg<MessageDlg>(() => exportMethodDlgDia.MethodType = ExportMethodType.Scheduled, dlg =>
{
Assert.AreEqual(Resources.ExportMethodDlg_comboTargetType_SelectedIndexChanged_Scheduled_methods_are_not_yet_supported_for_DIA_acquisition, dlg.Message);
dlg.CancelDialog();
});
RunUI(() =>
{
Assert.IsTrue(exportMethodDlgDia.IsRunLengthVisible);
exportMethodDlgDia.RunLength = 20;
exportMethodDlgDia.OkDialog(brukerActualMeth);
});
Assert.IsTrue(Directory.Exists(brukerActualMeth));
brukerExpectedMeth = TestFilesDir.GetTestPath("BrukerExpectedDIA.Method");
AssertEx.NoDiff(File.ReadAllText(brukerExpectedMeth), File.ReadAllText(Path.Combine(brukerActualMeth, brukerOutputMethodFilename)));
}
// Export DIA method error not prespecified
{
var isoResults = new IsolationScheme("Results (20)", 20.0);
RunUI(() => SkylineWindow.ModifyDocument("Add results isolation scheme",
doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(full => full.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA, isoResults)))));
var exportMethodDlgDia = ShowDialog<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlgDia.InstrumentType = ExportInstrumentType.BRUKER_TOF;
exportMethodDlgDia.ExportStrategy = ExportStrategy.Single;
exportMethodDlgDia.SetTemplateFile(brukerTemplateMeth);
});
RunDlg<MessageDlg>(exportMethodDlgDia.OkDialog, dlg =>
{
Assert.AreEqual(Resources.ExportMethodDlg_OkDialog_The_DIA_isolation_list_must_have_prespecified_windows_, dlg.Message);
dlg.CancelDialog();
});
OkDialog(exportMethodDlgDia, exportMethodDlgDia.CancelDialog);
}
}
private void comboIsolationScheme_SelectedIndexChanged(object sender, EventArgs e)
{
_driverIsolationScheme.SelectedIndexChangedEvent(sender, e);
// If we have a callback function and the isolation scheme _did_ really change its value, we invoke the handler
if (IsolationSchemeChangedEvent != null && !Equals(_prevval_comboIsolationScheme, IsolationScheme))
{
IsolationSchemeChangedEvent.Invoke(sender, e);
}
_prevval_comboIsolationScheme = IsolationScheme; //update previous isolation scheme
}
public bool Equals(IsolationScheme other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return base.Equals(other) &&
ArrayUtil.EqualsDeep(other._prespecifiedIsolationWindows, _prespecifiedIsolationWindows) &&
other.PrecursorFilter.Equals(PrecursorFilter) &&
other.PrecursorRightFilter.Equals(PrecursorRightFilter) &&
other.SpecialHandling.Equals(SpecialHandling) &&
other.WindowsPerScan.Equals(WindowsPerScan);
}
protected AbstractDiaExporter(IsolationScheme isolationScheme, int? maxInstrumentWindows)
{
IsolationScheme = isolationScheme;
_maxInstrumentWindows = maxInstrumentWindows;
}
