public static void GetLibIrtProviders(Library lib, IrtStandard standard, IProgressMonitor monitor,
out IRetentionTimeProvider[] irtProviders, out List <IrtStandard> autoStandards, out DbIrtPeptide[] cirtPeptides)
{
monitor?.UpdateProgress(new ProgressStatus().ChangePercentComplete(-1));
irtProviders = lib.RetentionTimeProvidersIrt.ToArray();
if (!irtProviders.Any())
{
irtProviders = lib.RetentionTimeProviders.ToArray();
}
var isAuto = ReferenceEquals(standard, IrtStandard.AUTO);
autoStandards = isAuto
? IrtStandard.BestMatch(irtProviders.SelectMany(provider => provider.PeptideRetentionTimes).Select(rt => rt.PeptideSequence))
: null;
if (ReferenceEquals(standard, IrtStandard.CIRT_SHORT) || isAuto && autoStandards.Count == 0)
{
var libPeptides = new TargetMap <bool>(irtProviders
.SelectMany(provider => provider.PeptideRetentionTimes)
.Select(rt => new KeyValuePair <Target, bool>(rt.PeptideSequence, true)));
cirtPeptides = IrtStandard.CIRT.Peptides.Where(pep => libPeptides.ContainsKey(pep.ModifiedTarget)).ToArray();
}
else
{
cirtPeptides = new DbIrtPeptide[0];
}
}
public void OkDialog()
{
var reader = new StringReader(textPeptides.Text);
var standardPeptides = new List <DbIrtPeptide>();
var invalidLines = new List <string>();
string line;
while ((line = reader.ReadLine()) != null)
{
line = line.Trim();
// Skip blank lines
if (string.IsNullOrEmpty(line))
{
continue;
}
DbIrtPeptide peptide = null;
var target = TargetResolver.ResolveTarget(line);
if (target == null || !_dictSequenceToPeptide.TryGetValue(target, out peptide)) // CONSIDER(bspratt) - small molecule equivalent?
{
invalidLines.Add(line);
}
standardPeptides.Add(peptide);
}
if (invalidLines.Count > 0)
{
string message;
if (invalidLines.Count == 1)
{
message = ModeUIAwareStringFormat(Resources.ChangeIrtPeptidesDlg_OkDialog_The_sequence__0__is_not_currently_in_the_database,
invalidLines[0]);
MessageBox.Show(this, message, Program.Name);
}
else
{
message = TextUtil.LineSeparate(GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_The_following_sequences_are_not_currently_in_the_database),
string.Empty,
TextUtil.LineSeparate(invalidLines),
string.Empty,
GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_Standard_peptides_must_exist_in_the_database));
MessageBox.Show(this, message, Program.Name);
}
return;
}
_standardPeptides = standardPeptides.ToArray();
DialogResult = DialogResult.OK;
}
public IrtDb UpdatePeptides(IList<DbIrtPeptide> newPeptides, IList<DbIrtPeptide> oldPeptides)
{
var setNew = new HashSet<long>(newPeptides.Select(pep => pep.Id.HasValue ? pep.Id.Value : 0));
var dictOld = oldPeptides.ToDictionary(pep => pep.PeptideModSeq);
using (var session = OpenWriteSession())
using (var transaction = session.BeginTransaction())
{
// Remove peptides that are no longer in the list
foreach (var peptideOld in oldPeptides)
{
if (!peptideOld.Id.HasValue)
continue;
if (!setNew.Contains(peptideOld.Id.Value))
session.Delete(peptideOld);
}
// Add or update peptides that have changed from the old list
foreach (var peptideNew in newPeptides)
{
DbIrtPeptide peptideOld;
if (dictOld.TryGetValue(peptideNew.PeptideModSeq, out peptideOld) &&
Equals(peptideNew, peptideOld))
continue;
// Create a new instance, because not doing this causes a BindingSource leak
var peptideNewDisconnected = new DbIrtPeptide(peptideNew);
session.SaveOrUpdate(peptideNewDisconnected);
}
transaction.Commit();
}
return ChangeProp(ImClone(this), im => im.LoadPeptides(newPeptides));
}
public static bool AddIrts(Library lib, LibrarySpec libSpec, IrtStandard standard, Control parent, bool useTopMostForm = false)
{
if (lib == null || !lib.IsLoaded || standard == null || standard.Name.Equals(IrtStandard.EMPTY.Name))
{
return(false);
}
Control GetParent()
{
return(useTopMostForm ? FormUtil.FindTopLevelOpenForm(f => f is BuildLibraryNotification) ?? parent : parent);
}
IRetentionTimeProvider[] irtProviders = null;
var cirtPeptides = new DbIrtPeptide[0];
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Loading_retention_time_providers
})
{
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
monitor.UpdateProgress(new ProgressStatus().ChangePercentComplete(-1));
irtProviders = lib.RetentionTimeProvidersIrt.ToArray();
if (!irtProviders.Any())
{
irtProviders = lib.RetentionTimeProviders.ToArray();
}
if (ReferenceEquals(standard, IrtStandard.CIRT_SHORT))
{
var libPeptides = irtProviders.SelectMany(provider => provider.PeptideRetentionTimes).Select(rt => rt.PeptideSequence).ToHashSet();
cirtPeptides = IrtStandard.CIRT.Peptides.Where(pep => libPeptides.Contains(pep.ModifiedTarget)).ToArray();
}
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
int?numCirt = null;
if (cirtPeptides.Length >= RCalcIrt.MIN_PEPTIDES_COUNT)
{
using (var dlg = new AddIrtStandardsDlg(cirtPeptides.Length,
string.Format(
Resources.LibraryBuildNotificationHandler_AddIrts__0__distinct_CiRT_peptides_were_found__How_many_would_you_like_to_use_as_iRT_standards_,
cirtPeptides.Length)))
{
if (dlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
numCirt = dlg.StandardCount;
}
}
var standardPeptides = standard.Peptides.ToArray();
ProcessedIrtAverages processed = null;
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Processing_retention_times
})
{
try
{
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
processed = !numCirt.HasValue
? RCalcIrt.ProcessRetentionTimes(monitor, irtProviders, standardPeptides, new DbIrtPeptide[0])
: RCalcIrt.ProcessRetentionTimesCirt(monitor, irtProviders, cirtPeptides, numCirt.Value, out standardPeptides);
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(GetParent(),
TextUtil.LineSeparate(
Resources.BuildPeptideSearchLibraryControl_AddIrtLibraryTable_An_error_occurred_while_processing_retention_times_,
x.Message), x);
return(false);
}
}
using (var resultsDlg = new AddIrtPeptidesDlg(AddIrtPeptidesLocation.spectral_library, processed))
{
if (resultsDlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
}
var recalibrate = false;
if (processed.CanRecalibrateStandards(standardPeptides))
{
using (var dlg = new MultiButtonMsgDlg(
TextUtil.LineSeparate(Resources.LibraryGridViewDriver_AddToLibrary_Do_you_want_to_recalibrate_the_iRT_standard_values_relative_to_the_peptides_being_added_,
Resources.LibraryGridViewDriver_AddToLibrary_This_can_improve_retention_time_alignment_under_stable_chromatographic_conditions_),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false))
{
recalibrate = dlg.ShowDialog(GetParent()) == DialogResult.Yes;
}
}
var processedDbIrtPeptides = processed.DbIrtPeptides.ToArray();
if (!processedDbIrtPeptides.Any())
{
return(false);
}
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Adding_iRTs_to_library
})
{
try
{
DbIrtPeptide[] newStandards = null;
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
if (recalibrate)
{
monitor.UpdateProgress(new ProgressStatus().ChangeSegments(0, 2));
newStandards = processed.RecalibrateStandards(standardPeptides).ToArray();
processed = RCalcIrt.ProcessRetentionTimes(monitor,
processed.ProviderData.Select(data => data.RetentionTimeProvider).ToArray(),
newStandards.ToArray(), new DbIrtPeptide[0]);
}
var irtDb = IrtDb.CreateIrtDb(libSpec.FilePath);
irtDb.AddPeptides(monitor, (newStandards ?? standardPeptides).Concat(processed.DbIrtPeptides).ToList());
});
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(GetParent(),
TextUtil.LineSeparate(
Resources.LibraryBuildNotificationHandler_AddIrts_An_error_occurred_trying_to_add_iRTs_to_the_library_,
x.Message), x);
return(false);
}
}
return(true);
}
private DbIrtPeptide NewPeptide(DbIrtPeptide dbPeptide)
{
return new DbIrtPeptide(dbPeptide.PeptideModSeq,
dbPeptide.Irt,
dbPeptide.Standard,
dbPeptide.TimeSource);
}
private static void CheckIrtStandardPeptides(DbIrtPeptide[] standardPeptidesArray, string irtDefText, double threshold)
{
int iRow = 0;
var irtDefReader = new StringReader(irtDefText);
string line;
while ((line = irtDefReader.ReadLine()) != null)
{
Assert.AreEqual(standardPeptidesArray[iRow].Irt, double.Parse(line.Split(TextUtil.SEPARATOR_TSV)[1]), threshold);
iRow++;
}
}
public void OkDialog()
{
var reader = new StringReader(textPeptides.Text);
var standardPeptides = new List <DbIrtPeptide>();
var invalidLines = new List <string>();
string line;
while ((line = reader.ReadLine()) != null)
{
line = line.Trim();
// Skip blank lines
if (string.IsNullOrEmpty(line))
{
continue;
}
DbIrtPeptide peptide = null;
var target = TargetResolver.ResolveTarget(line);
if (target == null || !_dictSequenceToPeptide.TryGetValue(target, out peptide)) // CONSIDER(bspratt) - small molecule equivalent?
{
invalidLines.Add(line);
}
standardPeptides.Add(peptide);
}
if (invalidLines.Count > 0)
{
string message;
if (invalidLines.Count == 1)
{
message = ModeUIAwareStringFormat(Resources.ChangeIrtPeptidesDlg_OkDialog_The_sequence__0__is_not_currently_in_the_database,
invalidLines[0]);
MessageBox.Show(this, message, Program.Name);
}
else
{
message = TextUtil.LineSeparate(GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_The_following_sequences_are_not_currently_in_the_database),
string.Empty,
TextUtil.LineSeparate(invalidLines),
string.Empty,
GetModeUIHelper().Translate(Resources.ChangeIrtPeptidesDlg_OkDialog_Standard_peptides_must_exist_in_the_database));
MessageBox.Show(this, message, Program.Name);
}
return;
}
ReplacementProtein = null;
var selected = (ComboBoxProtein)comboProteins.SelectedItem;
if (selected.IsNotNull)
{
var removedPeptides = selected.RemovedPeptides(TargetResolver, textPeptides.Lines).ToArray();
if (removedPeptides.Any())
{
switch (MultiButtonMsgDlg.Show(this, TextUtil.LineSeparate(
Resources.ChangeIrtPeptidesDlg_OkDialog_The_following_peptides_were_removed_,
TextUtil.LineSeparate(removedPeptides.Select(nodePep => nodePep.ModifiedSequenceDisplay)),
Resources.ChangeIrtPeptidesDlg_OkDialog_Would_you_like_to_remove_them_from_the_document_),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true))
{
case DialogResult.Yes:
ReplacementProtein = selected.RemovePeptides(TargetResolver, textPeptides.Lines);
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return;
}
}
}
_standardPeptides = standardPeptides.ToArray();
DialogResult = DialogResult.OK;
}
/// <summary>
/// Determines whether a peptide is contained in this set of standard peptides.
/// </summary>
/// <param name="peptide">The peptide to check for.</param>
/// <param name="irtTolerance">Tolerance used to compare iRTs; if null, iRTs are not required to match.</param>
/// <returns>True if the peptide is contained in this set of standard peptides; false otherwise.</returns>
public bool Contains(DbIrtPeptide peptide, double? irtTolerance)
{
return ContainsMatch(Peptides, peptide, irtTolerance);
}
private DbIrtPeptide MatchingStandard(DbIrtPeptide peptide, double? irtTolerance)
{
return Peptides.FirstOrDefault(p => Match(peptide, p, irtTolerance));
}
public static bool Match(DbIrtPeptide x, DbIrtPeptide y, double? irtTolerance)
{
return Equals(x.PeptideModSeq, y.PeptideModSeq) && (!irtTolerance.HasValue || Math.Abs(x.Irt - y.Irt) < irtTolerance.Value);
}
public static bool ContainsMatch(IEnumerable<DbIrtPeptide> peptides, DbIrtPeptide peptide, double? irtTolerance)
{
return peptides.Any(p => Match(p, peptide, irtTolerance));
}
/// <summary>
/// Determines whether any of the iRT standards contain the peptide.
/// </summary>
/// <param name="peptide">The peptide to check for.</param>
/// <param name="irtTolerance">Tolerance used to compare iRTs; if null, iRTs are not required to match.</param>
/// <returns>True if the peptide is in any of the iRT standards; false otherwise.</returns>
public static bool AnyContains(DbIrtPeptide peptide, double? irtTolerance)
{
return ALL.Any(standard => standard.Contains(peptide, irtTolerance));
}
/// <summary>
/// This function requires that Database not be null, that is, either OpenDatabase has been
/// successfully called (nothing thrown), or a valid IrtDb was passed to the constructor
/// </summary>
public override double ScoreSequence(string seq)
{
DbIrtPeptide pep = Database.GetPeptide(seq);
return(pep == null ? 0 : pep.Irt);
}
public static bool AddIrts(IrtRegressionType regressionType, Library lib, LibrarySpec libSpec, IrtStandard standard, Control parent, bool useTopMostForm)
{
if (lib == null || !lib.IsLoaded || standard == null || standard.Name.Equals(IrtStandard.EMPTY.Name))
{
return(false);
}
Control GetParent()
{
return(useTopMostForm ? FormUtil.FindTopLevelOpenForm(f => f is BuildLibraryNotification) ?? parent : parent);
}
IRetentionTimeProvider[] irtProviders = null;
var isAuto = ReferenceEquals(standard, IrtStandard.AUTO);
List <IrtStandard> autoStandards = null;
var cirtPeptides = new DbIrtPeptide[0];
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Loading_retention_time_providers
})
{
var standard1 = standard;
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
ImportPeptideSearch.GetLibIrtProviders(lib, standard1, monitor, out irtProviders, out autoStandards, out cirtPeptides);
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
int?numCirt = null;
if (cirtPeptides.Length >= RCalcIrt.MIN_PEPTIDES_COUNT)
{
using (var dlg = new AddIrtStandardsDlg(cirtPeptides.Length,
string.Format(
Resources.LibraryBuildNotificationHandler_AddIrts__0__distinct_CiRT_peptides_were_found__How_many_would_you_like_to_use_as_iRT_standards_,
cirtPeptides.Length)))
{
if (dlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
numCirt = dlg.StandardCount;
}
}
else if (isAuto)
{
switch (autoStandards.Count)
{
case 0:
standard = new IrtStandard(XmlNamedElement.NAME_INTERNAL, null, null, IrtPeptidePicker.Pick(irtProviders, 10));
break;
case 1:
standard = autoStandards[0];
break;
default:
using (var selectIrtStandardDlg = new SelectIrtStandardDlg(autoStandards))
{
if (selectIrtStandardDlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
standard = selectIrtStandardDlg.Selected;
}
break;
}
}
var standardPeptides = standard.Peptides.ToArray();
ProcessedIrtAverages processed = null;
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Processing_retention_times
})
{
try
{
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
processed = ImportPeptideSearch.ProcessRetentionTimes(numCirt, irtProviders, standardPeptides, cirtPeptides, regressionType, monitor, out var newStandardPeptides);
if (newStandardPeptides != null)
{
standardPeptides = newStandardPeptides;
}
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(GetParent(),
TextUtil.LineSeparate(
Resources.BuildPeptideSearchLibraryControl_AddIrtLibraryTable_An_error_occurred_while_processing_retention_times_,
x.Message), x);
return(false);
}
}
using (var resultsDlg = new AddIrtPeptidesDlg(AddIrtPeptidesLocation.spectral_library, processed))
{
if (resultsDlg.ShowDialog(GetParent()) != DialogResult.OK)
{
return(false);
}
}
var recalibrate = false;
if (processed.CanRecalibrateStandards(standardPeptides))
{
using (var dlg = new MultiButtonMsgDlg(
TextUtil.LineSeparate(Resources.LibraryGridViewDriver_AddToLibrary_Do_you_want_to_recalibrate_the_iRT_standard_values_relative_to_the_peptides_being_added_,
Resources.LibraryGridViewDriver_AddToLibrary_This_can_improve_retention_time_alignment_under_stable_chromatographic_conditions_),
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, false))
{
recalibrate = dlg.ShowDialog(GetParent()) == DialogResult.Yes;
}
}
if (!processed.DbIrtPeptides.Any())
{
return(false);
}
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_AddIrts_Adding_iRTs_to_library
})
{
try
{
var status = longWait.PerformWork(GetParent(), 800, monitor =>
{
ImportPeptideSearch.CreateIrtDb(libSpec.FilePath, processed, standardPeptides, recalibrate, regressionType, monitor);
});
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(GetParent(),
TextUtil.LineSeparate(
Resources.LibraryBuildNotificationHandler_AddIrts_An_error_occurred_trying_to_add_iRTs_to_the_library_,
x.Message), x);
return(false);
}
}
return(true);
}
