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);
}
public void UseResults()
{
if (!_document.Settings.HasResults)
{
MessageDlg.Show(this, Resources.CalibrateIrtDlg_UseResults_The_document_must_contain_results_to_calibrate_a_standard);
return;
}
var count = _document.Molecules.Where(nodePep => nodePep.SchedulingTime.HasValue).Select(nodePep => nodePep.ModifiedTarget).Distinct().Count();
if (count < CalibrateIrtDlg.MIN_STANDARD_PEPTIDES)
{
MessageDlg.Show(this,
string.Format(
Resources.CalibrateIrtDlg_UseResults_The_document_contains_results_for__0__peptides__which_is_less_than_the_minimum_requirement_of__1__to_calibrate_a_standard_,
count, CalibrateIrtDlg.MIN_STANDARD_PEPTIDES));
return;
}
else if (count < CalibrateIrtDlg.MIN_SUGGESTED_STANDARD_PEPTIDES)
{
if (MultiButtonMsgDlg.Show(this,
string.Format(
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_,
count, CalibrateIrtDlg.MIN_SUGGESTED_STANDARD_PEPTIDES),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false) != DialogResult.Yes)
{
return;
}
}
else if (count > 20)
{
using (var dlg = new AddIrtStandardsDlg(count, false))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return;
}
count = dlg.StandardCount;
}
}
if (!_picker.HasScoredPeptides)
{
using (var longWaitDlg = new LongWaitDlg {
Text = Resources.CalibrationGridViewDriver_FindEvenlySpacedPeptides_Calculating_scores
})
{
longWaitDlg.PerformWork(this, 1000, pm => _picker.ScorePeptides(_document, pm));
if (longWaitDlg.IsCanceled)
{
return;
}
}
}
var useCirt = false;
if (_picker.TryGetCirtRegression(count, out _, out _))
{
switch (MultiButtonMsgDlg.Show(this, 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:
useCirt = true;
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return;
}
}
comboProteins.SelectedIndex = 0;
PeptideLines = _picker.Pick(count, null, useCirt).Select(pep => pep.Target.ToString()).ToArray();
}
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);
}
