public EditDriftTimePredictorDlg(IEnumerable <IonMobilityPredictor> existing)
{
_existing = existing;
_showRegressions = true;
InitializeComponent();
foreach (eIonMobilityUnits units in Enum.GetValues(typeof(eIonMobilityUnits)))
{
if (units != eIonMobilityUnits.none) // Don't present "none" as an option
{
comboBoxIonMobilityUnits.Items.Add(IonMobilityFilter.IonMobilityUnitsL10NString(units));
}
}
_smallMoleculeUI = Program.MainWindow.Document.HasSmallMolecules || Program.MainWindow.ModeUI != SrmDocument.DOCUMENT_TYPE.proteomic;
if (_smallMoleculeUI)
{
gridMeasuredDriftTimes.Columns[COLUMN_SEQUENCE].HeaderText = Resources.EditDriftTimePredictorDlg_EditDriftTimePredictorDlg_Molecule;
gridMeasuredDriftTimes.Columns[COLUMN_CHARGE].HeaderText = Resources.EditDriftTimePredictorDlg_EditDriftTimePredictorDlg_Adduct;
}
var targetResolver = TargetResolver.MakeTargetResolver(Program.ActiveDocumentUI);
MeasuredDriftTimeSequence.TargetResolver = targetResolver;
// TODO: ion mobility libraries are more complex than initially thought - leave these conversions to the mass spec vendors for now
labelIonMobilityLibrary.Visible = comboLibrary.Visible = false;
Icon = Resources.Skyline;
_driverIonMobilityLibraryListComboDriver = new SettingsListComboDriver <IonMobilityLibrarySpec>(comboLibrary, Settings.Default.IonMobilityLibraryList);
_driverIonMobilityLibraryListComboDriver.LoadList(null);
UpdateControls();
}
public void UseResults()
{
CheckDisposed();
var document = Program.ActiveDocumentUI;
if (!document.Settings.HasResults)
{
MessageDlg.Show(this, Resources.CalibrateIrtDlg_UseResults_The_document_must_contain_results_to_calibrate_a_standard);
return;
}
var targetResolver = TargetResolver.MakeTargetResolver(document);
calibratePeptides.TargetResolver = targetResolver;
int count = document.Molecules.Count(nodePep => nodePep.SchedulingTime.HasValue);
if (count > 20)
{
using (var dlg = new AddIrtStandardsDlg(count))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return;
}
count = dlg.StandardCount;
}
}
_gridViewDriver.Recalculate(document, count);
}
private bool SetCalibrationPeptides(ICollection <PeptideDocNode> exclude)
{
CheckDisposed();
var document = Program.ActiveDocumentUI;
if (!document.Settings.HasResults)
{
MessageDlg.Show(this, Resources.CalibrateIrtDlg_UseResults_The_document_must_contain_results_to_calibrate_a_standard);
return(false);
}
var targetResolver = TargetResolver.MakeTargetResolver(document);
_gridViewDriver.TargetResolver = targetResolver;
var peptides = document.Molecules.Where(nodePep => nodePep.SchedulingTime.HasValue).ToArray();
var count = peptides.Length;
if (exclude != null && exclude.Count > 0)
{
peptides = peptides.Where(nodePep => !exclude.Contains(nodePep)).ToArray();
count = peptides.Length;
if (count < MIN_STANDARD_PEPTIDES)
{
MessageDlg.Show(this,
ModeUIAwareStringFormat(
Resources.CalibrateIrtDlg_SetCalibrationPeptides_The_document_contains_results_for__0__peptide_s__not_in_this_standard__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_,
count, MIN_STANDARD_PEPTIDES));
return(false);
}
else if (count < MIN_SUGGESTED_STANDARD_PEPTIDES)
{
if (MultiButtonMsgDlg.Show(this,
ModeUIAwareStringFormat(
Resources.CalibrateIrtDlg_SetCalibrationPeptides_The_document_only_contains_results_for__0__peptide_s__not_in_this_standard__It_is_recommended_to_use_at_least__1__peptides_to_calibrate_a_standard__Are_you_sure_you_wish_to_continue_,
count, MIN_SUGGESTED_STANDARD_PEPTIDES),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false) != DialogResult.Yes)
{
return(false);
}
}
}
if (count > 20)
{
using (var dlg = new AddIrtStandardsDlg(count, exclude != null && exclude.Count > 0))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return(false);
}
count = dlg.StandardCount;
}
}
_gridViewDriver.Recalculate(document, count, exclude);
return(true);
}
protected override void DoTest()
{
var documentPath = TestFilesDir.GetTestPath("TargetResolverTest.sky");
TargetResolver resolver;
RunUI(() =>
{
SkylineWindow.OpenFile(documentPath);
resolver = TargetResolver.MakeTargetResolver(SkylineWindow.DocumentUI);
var target = resolver.ResolveTarget("Glc(04)"); // Find by name
Assert.AreEqual("Glc(04)", target.DisplayName);
target = resolver.ResolveTarget("ZXPLRDFHBYIQOX-BTBVOZEKSA-N"); // Find by InChiKey
Assert.AreEqual("Glc(04)", target.DisplayName);
target = resolver.ResolveTarget("PEPTIDER"); // Find by sequence
Assert.AreEqual("PEPTIDER", target.DisplayName);
});
}
public bool SetCalibrationPeptides()
{
CheckDisposed();
var document = Program.ActiveDocumentUI;
if (!document.Settings.HasResults)
{
MessageDlg.Show(this, Resources.CalibrateIrtDlg_UseResults_The_document_must_contain_results_to_calibrate_a_standard);
return(false);
}
var targetResolver = TargetResolver.MakeTargetResolver(document);
_gridViewDriver.TargetResolver = targetResolver;
var docTargets = document.Molecules.Where(nodePep => nodePep.SchedulingTime.HasValue).Select(nodePep => nodePep.ModifiedTarget).Distinct().ToArray();
var count = docTargets.Length;
// If calibrating against another standard, exclude peptides in that standard
var excludePeps = SelectedRegressionOption?.MatchedRegressionPeptides?.Select(match => match.Item2.ModifiedTarget).ToHashSet();
var exclude = excludePeps != null && excludePeps.Count > 0;
if (exclude)
{
docTargets = docTargets.Where(target => !excludePeps.Contains(target)).ToArray();
count = docTargets.Length;
}
if (count < MIN_STANDARD_PEPTIDES)
{
MessageDlg.Show(this,
ModeUIAwareStringFormat(!exclude
? Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_
: Resources.CalibrateIrtDlg_SetCalibrationPeptides_The_document_contains_results_for__0__peptide_s__not_in_this_standard__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_,
count, MIN_STANDARD_PEPTIDES));
return(false);
}
else if (count < MIN_SUGGESTED_STANDARD_PEPTIDES)
{
if (MultiButtonMsgDlg.Show(this,
ModeUIAwareStringFormat(!exclude
? Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides__but_using_fewer_than__1__standard_peptides_is_not_recommended__Are_you_sure_you_want_to_continue_
: Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides_not_in_this_standard__but_using_fewer_than__1__standard_peptides_is_not_recommended__Are_you_sure_you_want_to_continue_,
count, MIN_SUGGESTED_STANDARD_PEPTIDES),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false) != DialogResult.Yes)
{
return(false);
}
}
else if (count > 20)
{
using (var dlg = new AddIrtStandardsDlg(count, excludePeps != null && excludePeps.Count > 0))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return(false);
}
count = dlg.StandardCount;
}
}
_gridViewDriver.Recalculate(document, count, SelectedRegressionOption, excludePeps);
return(true);
}
