public CalibrateIrtDlg(IrtStandard standard, IEnumerable <IrtStandard> existing, DbIrtPeptide[] updatePeptides)
{
InitializeComponent();
Icon = Resources.Skyline;
_standard = standard;
_standardPeptidesSorted = standard != null?standard.Peptides.OrderBy(pep => pep.Irt).ToArray() : new DbIrtPeptide[0];
_existing = existing;
_updatePeptides = updatePeptides;
_gridViewDriver = new CalibrationGridViewDriver(this, gridViewCalibrate, bindingSourceStandard,
new SortableBindingList <StandardPeptide>());
FireStandardsChanged = true;
comboRegression.Items.AddRange(RegressionOption.All(Program.ActiveDocumentUI).ToArray());
comboRegression.SelectedIndex = 0;
if (IsRecalibration)
{
textName.Text = standard?.Name;
FormBorderStyle = FormBorderStyle.Fixed3D;
panelPeptides.Hide();
btnUseCurrent.Hide();
Height -= panelPeptides.Height;
var standardPeptides = _standardPeptidesSorted.Select(pep => pep.PeptideModSeq).ToArray();
comboMinPeptide.Items.AddRange(standardPeptides);
comboMaxPeptide.Items.AddRange(standardPeptides);
if (standardPeptides.Length > 0)
{
// Look for standard peptides with whole number values as the suggested fixed points
var iFixed1 = _standardPeptidesSorted.IndexOf(pep => Math.Round(pep.Irt, 8) == Math.Round(pep.Irt));
var iFixed2 = _standardPeptidesSorted.LastIndexOf(pep => Math.Round(pep.Irt, 8) == Math.Round(pep.Irt));
if (iFixed1 == -1 || iFixed2 == -1)
{
iFixed1 = 0;
iFixed2 = _standardPeptidesSorted.Length - 1;
}
else if (iFixed1 == iFixed2)
{
if (iFixed1 < _standardPeptidesSorted.Length / 2)
{
iFixed2 = _standardPeptidesSorted.Length - 1;
}
else
{
iFixed1 = 0;
}
}
comboMinPeptide.SelectedIndex = iFixed1;
comboMaxPeptide.SelectedIndex = iFixed2;
SetIrtRange(_standardPeptidesSorted[iFixed1].Irt, _standardPeptidesSorted[iFixed2].Irt);
}
}
}
private List <MeasuredPeptide> PickPeptides(SrmDocument doc, int count, ICollection <Target> exclude, RegressionOption currentRegression, out RegressionOption cirt)
{
cirt = null;
if (!_picker.HasScoredPeptides)
{
using (var longWaitDlg = new LongWaitDlg {
Text = Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Calculating_scores
})
{
longWaitDlg.PerformWork(_parent, 1000, pm => _picker.ScorePeptides(doc, pm));
if (longWaitDlg.IsCanceled)
{
return(null);
}
}
}
RegressionLine cirtRegression = null;
var useCirt = false;
var cirtUsePredefined = false;
if (_picker.TryGetCirtRegression(count, out var tryCirtRegression, out var matchedPeptides))
{
var currentIsCirt = currentRegression != null && currentRegression.IsCirtDiscovered;
switch (MultiButtonMsgDlg.Show(_parent, string.Format(
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_This_document_contains__0__CiRT_peptides__Would_you_like_to_use__1__of_them_as_your_iRT_standards_,
_picker.CirtPeptideCount, count), MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true))
{
case DialogResult.Yes:
cirtRegression = tryCirtRegression;
useCirt = true;
if (currentRegression?.RegressionLine == null || currentIsCirt)
{
switch (MultiButtonMsgDlg.Show(_parent,
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Would_you_like_to_use_the_predefined_iRT_values_,
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Predefined_values,
Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Calculate_from_regression,
true))
{
case DialogResult.Yes:
cirtUsePredefined = true;
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return(null);
}
}
break;
case DialogResult.No:
if (currentIsCirt)
{
cirtRegression = tryCirtRegression;
}
break;
case DialogResult.Cancel:
return(null);
}
}
var bestPeptides = _picker.Pick(count, exclude, useCirt);
if (cirtRegression != null)
{
var standardPeptides = bestPeptides.Select(pep => new StandardPeptide
{
Irt = cirtUsePredefined ? _picker.CirtIrt(pep.Target).Value : double.NaN,
RetentionTime = pep.RetentionTime,
Target = pep.Target
}).ToList();
cirt = new RegressionOption(Resources.CalibrationGridViewDriver_CiRT_option_name, cirtRegression,
matchedPeptides.ToList(), standardPeptides, false, false);
}
return(bestPeptides);
}
public List <StandardPeptide> Recalculate(SrmDocument document, int peptideCount, RegressionOption currentRegression, ICollection <Target> exclude)
{
var bestPeptides = PickPeptides(document, peptideCount, exclude, currentRegression, out var cirt);
if (bestPeptides == null)
{
return(null);
}
if ((currentRegression?.RegressionLine != null && !currentRegression.IsCirtDiscovered) || cirt == null)
{
SetPeptides(bestPeptides);
}
else
{
var existingCirt = _parent.RegressionOptions.IndexOf(opt => opt.Name.Equals(Resources.CalibrationGridViewDriver_CiRT_option_name));
if (existingCirt < 0)
{
_parent.comboRegression.Items.Add(cirt);
}
else
{
_parent.comboRegression.Items[existingCirt] = cirt;
}
_parent.SelectedRegressionOption = cirt;
}
return(Items.ToList());
}
