private void ExportIsolationList(
string csvFilename, string instrumentType, FullScanAcquisitionMethod acquisitionMethod,
ExportMethodType methodType, params string[] checkStrings)
{
// Set acquisition method, mass analyzer type, resolution, etc.
if (Equals(instrumentType, ExportInstrumentType.AGILENT_TOF))
{
RunUI(() => SkylineWindow.ModifyDocument("Set TOF full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeProductResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
else
{
RunUI(() => SkylineWindow.ModifyDocument("Set Orbitrap full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeProductResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
// Open Export Method dialog, and set method to scheduled or standard.
string csvPath = TestContext.GetTestPath(csvFilename);
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
RunUI(() =>
{
exportMethodDlg.InstrumentType = instrumentType;
exportMethodDlg.MethodType = methodType;
exportMethodDlg.UseSlens = WithSLens;
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
Assert.IsTrue(exportMethodDlg.IsTargetTypeEnabled);
Assert.IsFalse(exportMethodDlg.IsDwellTimeVisible);
Assert.IsFalse(exportMethodDlg.IsMaxTransitionsEnabled);
});
if (methodType == ExportMethodType.Standard)
{
// Simply close the dialog.
OkDialog(exportMethodDlg, () => exportMethodDlg.OkDialog(csvPath));
}
else
{
// Close the SchedulingOptionsDlg, then wait for export dialog to close.
RunDlg <SchedulingOptionsDlg>(() => exportMethodDlg.OkDialog(csvPath), schedulingOptionsDlg => schedulingOptionsDlg.OkDialog());
WaitForClosedForm(exportMethodDlg);
}
// Check for expected output.
string csvOut = File.ReadAllText(csvPath);
AssertEx.Contains(csvOut, checkStrings);
}
private void ExportIsolationList(
string csvFilename, string instrumentType, FullScanAcquisitionMethod acquisitionMethod,
ExportMethodType methodType, params string[] checkStrings)
{
// Set acquisition method, mass analyzer type, resolution, etc.
if (Equals(instrumentType, ExportInstrumentType.AGILENT_TOF))
{
RunUI(() => SkylineWindow.ModifyDocument("Set TOF full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeProductResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
else
{
RunUI(() => SkylineWindow.ModifyDocument("Set Orbitrap full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeProductResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
// Open Export Method dialog, and set method to scheduled or standard.
string csvPath = TestFilesDirs[0].GetTestPath(csvFilename);
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
var exportPolarityFilter =
AsSmallMoleculesNegativeMode != RefinementSettings.ConvertToSmallMoleculesChargesMode.none &&
SkylineWindow.Document.IsMixedPolarity() ?
ExportPolarity.separate :
ExportPolarity.all;
RunUI(() =>
{
exportMethodDlg.InstrumentType = instrumentType;
exportMethodDlg.MethodType = methodType;
exportMethodDlg.UseSlens = WithSLens;
exportMethodDlg.PolarityFilter = exportPolarityFilter;
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
Assert.IsTrue(exportMethodDlg.IsTargetTypeEnabled);
Assert.IsFalse(exportMethodDlg.IsDwellTimeVisible);
Assert.IsFalse(exportMethodDlg.IsMaxTransitionsEnabled);
});
if (methodType == ExportMethodType.Standard)
{
// Simply close the dialog.
OkDialog(exportMethodDlg, () => exportMethodDlg.OkDialog(csvPath));
}
else
{
// Close the SchedulingOptionsDlg, then wait for export dialog to close.
RunDlg <SchedulingOptionsDlg>(() => exportMethodDlg.OkDialog(csvPath), schedulingOptionsDlg => schedulingOptionsDlg.OkDialog());
WaitForClosedForm(exportMethodDlg);
}
// Check for expected output.
var csvResult = csvPath;
if (exportPolarityFilter == ExportPolarity.separate)
{
// We will have emitted two docs, one for pos and one for neg
var ext = csvPath.Substring(csvPath.LastIndexOf('.'));
csvResult = csvPath.Replace(ext, string.Format("_{0}_0001{1}", ExportPolarity.negative, ext));
var csvPos = File.ReadAllText(csvPath.Replace(ext, string.Format("_{0}_0001{1}", ExportPolarity.positive, ext)));
var csvNeg = File.ReadAllText(csvResult);
Assert.IsFalse(csvNeg.Equals(csvPos));
}
string csvOut = File.ReadAllText(csvResult);
AssertEx.Contains(csvOut, checkStrings);
}
private void UpdateTriggerControls(ExportMethodType targetType)
{
panelTriggered.Visible = (targetType == ExportMethodType.Triggered);
}
private void UpdateThermoSLensControl(ExportMethodType targetType)
{
cbSlens.Visible = cbSlens.Enabled =
InstrumentType == ExportInstrumentType.THERMO_QUANTIVA ||
InstrumentType == ExportInstrumentType.THERMO; // TODO bspratt is this specific enough?
}
private void UpdateThermoRtControls(ExportMethodType targetType)
{
panelThermoRt.Visible =
InstrumentType == ExportInstrumentType.THERMO_QUANTIVA ||
(targetType != ExportMethodType.Standard && InstrumentType == ExportInstrumentType.THERMO);
if (panelThermoColumns.Visible)
{
panelThermoRt.Top = panelThermoColumns.Top - (int)(panelThermoRt.Height * 0.8);
}
else
{
panelThermoRt.Top = labelDwellTime.Visible
? labelDwellTime.Top - panelThermoRt.Height
: labelDwellTime.Top + (panelThermoRt.Height / 2);
}
}
private void UpdateThermoColumns(ExportMethodType targetType)
{
panelThermoColumns.Visible = targetType == ExportMethodType.Scheduled &&
InstrumentType == ExportInstrumentType.THERMO;
}
private void UpdateInstrumentControls(ExportMethodType targetType)
{
bool standard = (targetType == ExportMethodType.Standard);
bool triggered = (targetType == ExportMethodType.Triggered);
if (triggered && !(InstrumentType == ExportInstrumentType.ABI || InstrumentType == ExportInstrumentType.ABI_QTRAP))
{
comboOptimizing.Enabled = false;
}
else
{
comboOptimizing.Enabled = !IsFullScanInstrument;
}
if (!comboOptimizing.Enabled)
{
OptimizeType = ExportOptimize.NONE;
}
UpdateTriggerControls(targetType);
UpdateDwellControls(standard);
UpdateThermoColumns(targetType);
UpdateAbSciexControls();
UpdateWatersControls();
UpdateThermoRtControls(targetType);
UpdateThermoSLensControl(targetType);
UpdateMaxLabel(standard);
}
public void SetMethodType(ExportMethodType type)
{
comboTargetType.SelectedItem = type == ExportMethodType.Standard
? Resources.ExportMethodDlg_SetMethodType_Standard
: Resources.ExportMethodDlg_SetMethodType_Scheduled;
}
private void ExportIsolationList(
string csvFilename, string instrumentType, FullScanAcquisitionMethod acquisitionMethod,
ExportMethodType methodType, params string[] checkStrings)
{
// Set acquisition method, mass analyzer type, resolution, etc.
if (Equals(instrumentType, ExportInstrumentType.AGILENT_TOF))
{
RunUI(() => SkylineWindow.ModifyDocument("Set TOF full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeProductResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
else
{
RunUI(() => SkylineWindow.ModifyDocument("Set Orbitrap full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeProductResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
// Open Export Method dialog, and set method to scheduled or standard.
string csvPath = TestContext.GetTestPath(csvFilename);
var exportMethodDlg = ShowDialog<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
RunUI(() =>
{
exportMethodDlg.InstrumentType = instrumentType;
exportMethodDlg.MethodType = methodType;
exportMethodDlg.UseSlens = WithSLens;
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
Assert.IsTrue(exportMethodDlg.IsTargetTypeEnabled);
Assert.IsFalse(exportMethodDlg.IsDwellTimeVisible);
Assert.IsFalse(exportMethodDlg.IsMaxTransitionsEnabled);
});
if (methodType == ExportMethodType.Standard)
{
// Simply close the dialog.
OkDialog(exportMethodDlg, ()=> exportMethodDlg.OkDialog(csvPath));
}
else
{
// Close the SchedulingOptionsDlg, then wait for export dialog to close.
RunDlg<SchedulingOptionsDlg>(() => exportMethodDlg.OkDialog(csvPath), schedulingOptionsDlg => schedulingOptionsDlg.OkDialog());
WaitForClosedForm(exportMethodDlg);
}
// Check for expected output.
string csvOut = File.ReadAllText(csvPath);
AssertEx.Contains(csvOut, checkStrings);
}
