/// <summary>
/// Parse the mass list text, then show a status dialog if:
/// errors are found, or
/// errors are not found and "silentSuccess" arg is false
/// Shows a special error message and forces the user to alter their entry if the list is missing Precursor m/z, Product m/z or Peptide Sequence.
/// Return false if no errors found.
/// </summary>
/// <param name="silentSuccess">If true, don't show the confirmation dialog when there are no errors</param>
/// <returns>True if list contains any errors and user does not elect to ignore them</returns>
private bool CheckForErrors(bool silentSuccess)
{
IdentityPath testSelectPath = null;
List <MeasuredRetentionTime> testIrtPeptides = null;
List <SpectrumMzInfo> testLibrarySpectra = null;
List <TransitionImportErrorInfo> testErrorList = null;
List <PeptideGroupDocNode> testPeptideGroups = null;
var columns = Importer.RowReader.Indices;
MissingEssentialColumns = new List <string>();
CheckEssentialColumn(new Tuple <int, string>(columns.PeptideColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Peptide_Modified_Sequence));
CheckEssentialColumn(new Tuple <int, string>(columns.PrecursorColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Precursor_m_z));
CheckEssentialColumn(new Tuple <int, string>(columns.ProductColumn, Resources.ImportTransitionListColumnSelectDlg_PopulateComboBoxes_Product_m_z));
var docNew = _docCurrent.ImportMassList(_inputs, Importer, null,
_insertPath, out testSelectPath, out testIrtPeptides, out testLibrarySpectra,
out testErrorList, out testPeptideGroups);
if (testErrorList.Any())
{
// There are errors, show them to user
var isErrorAll = ReferenceEquals(docNew, _docCurrent);
DialogResult response;
if (MissingEssentialColumns.Count != 0)
{
// If the transition list is missing essential columns, tell the user in a
// readable way
string errorMessage = Resources.ImportTransitionListErrorDlg_ImportTransitionListErrorDlg_This_transition_list_cannot_be_imported_as_it_does_not_provide_values_for_;
for (var i = 0; i < MissingEssentialColumns.Count; i++)
{
errorMessage = errorMessage + @" " + MissingEssentialColumns[i];
}
MessageDlg.Show(this, errorMessage);
return(true);
}
else
{
using (var dlg = new ImportTransitionListErrorDlg(testErrorList, isErrorAll, silentSuccess))
{
response = dlg.ShowDialog(this);
}
return(response == DialogResult.Cancel); // There are errors, and user does not want to ignore them
}
}
else if (!silentSuccess)
{
// No errors, confirm this to user
MessageDlg.Show(this, Resources.PasteDlg_ShowNoErrors_No_errors);
}
return(false); // No errors
}
private static SrmDocument InitWiffDocument(TestFilesDir testFilesDir)
{
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
List <StaticMod> heavyMods = new List <StaticMod>
{
new StaticMod("Heavy K", "K", ModTerminus.C, null, labelAtoms, null, null),
new StaticMod("Heavy R", "R", ModTerminus.C, null, labelAtoms, null, null),
};
SrmSettings settings = SrmSettingsList.GetDefault();
settings = settings.ChangePeptideModifications(mods => mods.ChangeHeavyModifications(heavyMods));
SrmDocument doc = new SrmDocument(settings);
IdentityPath selectPath;
string path = testFilesDir.GetTestPath("051309_transition list.csv");
// Product m/z out of range
var docError = doc;
List <MeasuredRetentionTime> irtPeptides;
List <SpectrumMzInfo> librarySpectra;
List <TransitionImportErrorInfo> errorList;
var inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
docError.ImportMassList(inputs, null, out selectPath, out irtPeptides, out librarySpectra, out errorList);
Assert.AreEqual(errorList.Count, 1);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
errorList[0].ErrorMessage,
2);
Assert.AreEqual(errorList[0].Column, 1);
Assert.AreEqual(errorList[0].Row, 19);
doc = doc.ChangeSettings(settings.ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
doc = doc.ImportMassList(inputs, null, out selectPath);
AssertEx.IsDocumentState(doc, 2, 9, 9, 18, 54);
return(doc);
}
public static SrmDocument RoundTripTransitionList(AbstractMassListExporter exporter)
{
exporter.Export(null);
// Reverse the output lines and import into a new document
var docExport = exporter.Document;
var docImport = new SrmDocument(docExport.Settings);
string transitionList = exporter.MemoryOutput.Values.ToArray()[0].ToString();
IdentityPath pathAdded;
var inputs = new MassListInputs(DuplicateAndReverseLines(transitionList, exporter.HasHeaders),
CultureInfo.InvariantCulture, TextUtil.SEPARATOR_CSV);
docImport = docImport.ImportMassList(inputs, IdentityPath.ROOT, out pathAdded);
IsDocumentState(docImport, 1,
docExport.MoleculeGroupCount,
docExport.MoleculeCount,
docExport.MoleculeTransitionGroupCount,
docExport.MoleculeTransitionCount);
return(docImport);
}
public void VariableModImportListTest()
{
// TODO: Deal with multiple variable modifications that produce the same
// precursor mass but different product ion masses
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
var staticMods = new List<StaticMod>(document.Settings.PeptideSettings.Modifications.StaticModifications);
staticMods.AddRange(new[]
{
new StaticMod("Met Sulfoxide", "M", null, true, "O", LabelAtoms.None,
RelativeRT.Matching, null, null, new[] { new FragmentLoss("SOCH4") }),
new StaticMod("Met Sulfone", "M", null, true, "O2", LabelAtoms.None,
RelativeRT.Matching, null, null, null),
new StaticMod("Phospho", "S,T,Y", null, true, "PO3H", LabelAtoms.None,
RelativeRT.Matching, null, null, new[] {new FragmentLoss("PO4H3")}),
new StaticMod("K(GlyGly)", "K", null, true, "N2H6C4O2", LabelAtoms.None,
RelativeRT.Matching, null, null, null),
});
document = document.ChangeSettings(document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(staticMods)));
IdentityPath pathTo;
List<MeasuredRetentionTime> irtPeptides;
List<SpectrumMzInfo> librarySpectra;
List<TransitionImportErrorInfo> errorList;
var inputsPhospho = new MassListInputs(TEXT_PHOSPHO_TRANSITION_LIST, CultureInfo.InvariantCulture, TextUtil.SEPARATOR_CSV);
document.ImportMassList(inputsPhospho, null, out pathTo, out irtPeptides, out librarySpectra, out errorList);
Assert.AreEqual(27, errorList.Count);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
errorList[0].ErrorMessage,
2);
Assert.AreEqual(1, errorList[0].Column);
Assert.AreEqual(40, errorList[0].Row);
var docHighMax = document.ChangeSettings(document.Settings.ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
var docList = docHighMax.ImportMassList(inputsPhospho, null, out pathTo);
AssertEx.Serializable(docList);
AssertEx.IsDocumentState(docList, 3, 68, 134, 157, 481);
foreach (var nodeTran in docList.PeptideTransitions)
{
var it = nodeTran.Transition.IonType;
Assert.IsTrue(it == IonType.y || it == IonType.b || it == IonType.precursor, "Found unexpected non b, y or precursor ion type.");
}
var inputsMultiLoss = new MassListInputs(TEXT_PHOSPHO_MULTI_LOSS, CultureInfo.InvariantCulture, TextUtil.SEPARATOR_CSV);
docHighMax.ImportMassList(inputsMultiLoss, null, out pathTo, out irtPeptides, out librarySpectra, out errorList);
Assert.AreEqual(5, errorList.Count);
AssertEx.AreComparableStrings(Resources.MassListRowReader_CalcTransitionExplanations_Product_m_z_value__0__in_peptide__1__has_no_matching_product_ion,
errorList[0].ErrorMessage,
2);
Assert.AreEqual(1, errorList[0].Column);
Assert.AreEqual(2, errorList[0].Row);
var docMultiLos = docHighMax.ChangeSettings(docHighMax.Settings.ChangePeptideModifications(mods =>
mods.ChangeMaxNeutralLosses(2)));
docList = docMultiLos.ImportMassList(inputsMultiLoss, null, out pathTo);
AssertEx.IsDocumentState(docList, 4, 4, 4, 12);
}
private static SrmDocument InitWiffDocument(TestFilesDir testFilesDir)
{
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
List<StaticMod> heavyMods = new List<StaticMod>
{
new StaticMod("Heavy K", "K", ModTerminus.C, null, labelAtoms, null, null),
new StaticMod("Heavy R", "R", ModTerminus.C, null, labelAtoms, null, null),
};
SrmSettings settings = SrmSettingsList.GetDefault();
settings = settings.ChangePeptideModifications(mods => mods.ChangeHeavyModifications(heavyMods));
SrmDocument doc = new SrmDocument(settings);
IdentityPath selectPath;
string path = testFilesDir.GetTestPath("051309_transition list.csv");
// Product m/z out of range
var docError = doc;
List<MeasuredRetentionTime> irtPeptides;
List<SpectrumMzInfo> librarySpectra;
List<TransitionImportErrorInfo> errorList;
var inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
docError.ImportMassList(inputs, null, out selectPath, out irtPeptides, out librarySpectra, out errorList);
Assert.AreEqual(errorList.Count, 1);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
errorList[0].ErrorMessage,
2);
Assert.AreEqual(errorList[0].Column, 1);
Assert.AreEqual(errorList[0].Row, 19);
doc = doc.ChangeSettings(settings.ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
doc = doc.ImportMassList(inputs, null, out selectPath);
AssertEx.IsDocumentState(doc, 2, 9, 9, 18, 54);
return doc;
}
