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);
}
public void MultiParser_Run_With_TargetResolver()
{
var resolver = new TargetResolver();
resolver.RegisterTargetType(() => new Sample_02());
resolver.RegisterTargetType(() => new Sample_03());
var mock = new MethodInvokerMock();
var called = false;
mock.Action = (method, obj, parameters) =>
{
called = true;
Assert.IsTrue(method.Name == "Print");
Assert.IsTrue(obj.GetType().Name == "Sample_03");
};
MethodInvoker.Invoker = mock;
Parser.Run(new[]
{
"sample_03.print",
"-c=8",
"-prefix=xyz"
}, resolver);
Assert.IsTrue(called);
}
public PeptideGroupDocNode RemovePeptides(TargetResolver targetResolver, IEnumerable <string> pepLines)
{
var textTargets = TextTargets(targetResolver, pepLines);
return((PeptideGroupDocNode)Protein.ChangeChildren(Protein.Molecules
.Where(molecule => textTargets.ContainsKey(molecule.ModifiedTarget)).Cast <DocNode>().ToList()));
}
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();
}
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 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 ChangeIrtPeptidesDlg(IList <DbIrtPeptide> irtPeptides)
{
TargetResolver = new TargetResolver(irtPeptides.Select(p => p.Target));
_dictSequenceToPeptide = new Dictionary <Target, DbIrtPeptide>();
foreach (var peptide in irtPeptides)
{
if (!_dictSequenceToPeptide.ContainsKey(peptide.ModifiedTarget))
{
_dictSequenceToPeptide.Add(peptide.ModifiedTarget, peptide);
}
}
InitializeComponent();
Peptides = irtPeptides.Where(peptide => peptide.Standard).ToArray();
}
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 ChangeIrtPeptidesDlg(IList <DbIrtPeptide> irtPeptides, IEnumerable <PeptideGroupDocNode> proteins)
{
TargetResolver = new TargetResolver(irtPeptides.Select(p => p.Target));
_dictSequenceToPeptide = new TargetMap <DbIrtPeptide>(irtPeptides.Select(pep =>
new KeyValuePair <Target, DbIrtPeptide>(pep.ModifiedTarget, pep)));
InitializeComponent();
comboProteins.Items.Add(new ComboBoxProtein(null));
comboProteins.Items.AddRange(proteins.Select(protein => new ComboBoxProtein(protein))
.Where(protein => protein.PeptideStrings(TargetResolver).Any()).ToArray());
comboProteins.SelectedIndex = 0;
if (comboProteins.Items.Count == 1)
{
comboProteins.Enabled = false;
}
Peptides = irtPeptides.Where(peptide => peptide.Standard).ToArray();
}
public ChangeIrtPeptidesDlg(SrmDocument document, IList <DbIrtPeptide> irtPeptides)
{
TargetResolver = new TargetResolver(irtPeptides.Select(p => p.Target));
_dictSequenceToPeptide = new TargetMap <DbIrtPeptide>(irtPeptides.Select(pep =>
new KeyValuePair <Target, DbIrtPeptide>(pep.ModifiedTarget, pep)));
_document = document;
_picker = new IrtPeptidePicker();
InitializeComponent();
comboProteins.Items.Add(new ComboBoxProtein(null));
comboProteins.Items.AddRange(document.MoleculeGroups.Select(protein => new ComboBoxProtein(protein))
.Where(protein => protein.PeptideStrings(TargetResolver).Any()).ToArray());
comboProteins.SelectedIndex = 0;
if (comboProteins.Items.Count == 1)
{
comboProteins.Enabled = false;
}
Peptides = irtPeptides.Where(peptide => peptide.Standard).ToArray();
// Find and select matching protein
for (var i = 1; i < comboProteins.Items.Count; i++)
{
var item = (ComboBoxProtein)comboProteins.Items[i];
if (item.Protein.PeptideCount != PeptideLines.Length)
{
continue;
}
var targets = new TargetMap <bool>(((ComboBoxProtein)comboProteins.Items[i]).Protein.Peptides.Select(pep =>
new KeyValuePair <Target, bool>(pep.ModifiedTarget, true)));
if (PeptideLines.All(line => targets.ContainsKey(new Target(line))))
{
comboProteins.SelectedIndex = i;
break;
}
}
}
public IEnumerable <PeptideDocNode> RemovedPeptides(TargetResolver targetResolver, IEnumerable <string> pepLines)
{
var textTargets = TextTargets(targetResolver, pepLines);
return(Protein.Molecules.Where(nodePep => !textTargets.ContainsKey(nodePep.ModifiedTarget)));
}
public int RunTargets(string[] args, TargetResolver targetResolver)
{
ParserRunner parser;
try
{
if (args.None() || args.All(a => string.IsNullOrEmpty(a)))
{
HandleEmptyArguments(targetResolver);
return SuccessCode;
}
if (m_types.Length == 1)
{
parser = GetSingleTypeParser(args, Register);
}
else
{
Debug.Assert(m_types.Length > 1);
parser = GetMultiTypesParser(args, Register);
}
Debug.Assert(parser != null);
}
catch (Exception ex)
{
// handle error using the first available error handler
//
// (if returns true - should rethrow)
//
if (TryHandlePrematureError(ex, targetResolver))
{
throw;
}
else
{
return ErrorCode;
}
}
var target = (targetResolver == null || targetResolver.RegisteredTypes.None()) ? null : targetResolver.Resolve(parser.Type);
return parser.Run(args, target);
}
/// <summary>
/// Run a parser of instance verbs against instances of the verb classes
/// </summary>
/// <param name="args">The user arguments</param>
/// <param name="targets">The instances of the verb classes</param>
public int RunTargets(string[] args, params object[] targets)
{
var targetResolver = new TargetResolver(targets);
return RunTargets(args, targetResolver);
}
private bool TryHandlePrematureError(Exception ex, TargetResolver targetResolver)
{
var context = new ExceptionContext(ex);
if (Register.RegisteredErrorHandler != null)
{
Register.RegisteredErrorHandler(context);
return context.ReThrow;
}
else
{
for (int i = 0; i < m_types.Length; i++)
{
var type = m_types[i];
var errorHandler = ParserRunner.GetDefinedErrorHandlers(type).FirstOrDefault();
if (errorHandler != null)
{
var target = targetResolver == null ? null : targetResolver.Resolve(type);
errorHandler.Invoke(target, new[] { context });
return context.ReThrow;
}
}
}
return true;
}
private void HandleEmptyArguments(TargetResolver targetResolver)
{
if (Register.RegisteredEmptyHandler != null)
{
Register.RegisteredEmptyHandler();
}
else if (m_types.Length == 1)
{
var parser = new ParserRunner(m_types.First(), Register, HelpGenerator);
var target = targetResolver == null ? null : targetResolver.Resolve(m_types[0]);
parser.HandleEmptyArguments(target);
}
}
private static TargetMap <bool> TextTargets(TargetResolver targetResolver, IEnumerable <string> pepLines)
{
return(new TargetMap <bool>(pepLines.Select(line => line.Trim())
.Where(line => !string.IsNullOrEmpty(line))
.Select(line => new KeyValuePair <Target, bool>(targetResolver.ResolveTarget(line), true))));
}
public IEnumerable <string> PeptideStrings(TargetResolver targetResolver)
{
return(Protein?.Molecules.Select(pep => targetResolver.FormatTarget(pep.ModifiedTarget)) ?? new string[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;
}
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;
}
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);
}
public MeasuredDriftTimeTable(DataGridView gridMeasuredDriftTimePeptides, TargetResolver targetResolver)
{
_gridMeasuredDriftTimePeptides = gridMeasuredDriftTimePeptides;
_targetResolver = targetResolver;
}
public void MultiParser_Run_With_TargetResolver()
{
var resolver = new TargetResolver();
resolver.RegisterTargetType(() => new Sample_02());
resolver.RegisterTargetType(() => new Sample_03());
var mock = new MethodInvokerMock();
var called = false;
mock.Action = (method, obj, parameters) =>
{
called = true;
Assert.IsTrue(method.Name == "Print");
Assert.IsTrue(obj.GetType().Name == "Sample_03");
};
MethodInvoker.Invoker = mock;
Parser.Run(new[]
{
"sample_03.print",
"-c=8",
"-prefix=xyz"
}, resolver);
Assert.IsTrue(called);
}
