private bool ProcessTransitionList()
{
if (!File.Exists(txtTransitionList.Text))
{
MessageDlg.Show(this, Resources.ChooseIrtStandardPeptides_OkDialog_Transition_list_field_must_contain_a_path_to_a_valid_file_);
txtTransitionList.Focus();
return(false);
}
try
{
var inputs = new MassListInputs(txtTransitionList.Text);
Document = Document.ImportMassList(inputs, new IdentityPath(Document.PeptideGroups.First().Id), out _, out _irtAdd, out _librarySpectra, out var errorList);
if (errorList.Any())
{
throw new InvalidDataException(errorList[0].ErrorMessage);
}
IrtFile = txtTransitionList.Text;
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Error_reading_iRT_standards_transition_list___0_, x.Message), x);
return(false);
}
return(true);
}
public void OkDialog()
{
if (radioProtein.Checked)
{
if (comboProteins.SelectedIndex == -1)
{
MessageDlg.Show(this, Resources.ChooseIrtStandardPeptidesDlg_OkDialog_Please_select_a_protein_containing_the_list_of_standard_peptides_for_the_iRT_calculator_);
comboProteins.Focus();
return;
}
var peptideGroupItem = comboProteins.SelectedItem as PeptideGroupItem;
if (peptideGroupItem != null)
{
var protein = peptideGroupItem.PeptideGroup;
_irtPeptideSequences = new HashSet <string>();
foreach (var peptide in protein.Peptides)
{
_irtPeptideSequences.Add(peptide.ModifiedSequence);
}
if (Document.PeptideGroupCount > 0)
{
var pathFrom = Document.GetPathTo(Document.FindNodeIndex(protein.Id));
var pathTo = Document.GetPathTo(Document.FindNodeIndex(Document.PeptideGroups.First().Id));
if (!Equals(pathFrom, pathTo))
{
IdentityPath newLocation;
Document = Document.MoveNode(pathFrom, pathTo, out newLocation);
}
}
}
}
else
{
if (!File.Exists(txtTransitionList.Text))
{
MessageDlg.Show(this, Resources.ChooseIrtStandardPeptides_OkDialog_Transition_list_field_must_contain_a_path_to_a_valid_file_);
txtTransitionList.Focus();
return;
}
try
{
IdentityPath selectPath;
List <TransitionImportErrorInfo> errorList;
var inputs = new MassListInputs(txtTransitionList.Text);
Document = Document.ImportMassList(inputs, new IdentityPath(Document.PeptideGroups.First().Id), out selectPath, out _irtPeptides, out _librarySpectra, out errorList);
if (errorList.Any())
{
throw new InvalidDataException(errorList[0].ErrorMessage);
}
IrtFile = txtTransitionList.Text;
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Error_reading_iRT_standards_transition_list___0_, x.Message), x);
return;
}
}
DialogResult = DialogResult.OK;
}
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 ImportTransitionListColumnSelectDlg(MassListImporter importer, SrmDocument docCurrent, MassListInputs inputs, IdentityPath insertPath)
{
Importer = importer;
_docCurrent = docCurrent;
_inputs = inputs;
_insertPath = insertPath;
InitializeComponent();
fileLabel.Text = Importer.Inputs.InputFilename;
InitializeComboBoxes();
DisplayData();
PopulateComboBoxes();
//dataGrid.Update();
ResizeComboBoxes();
}
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 OkDialog()
{
IrtType irtType = GetIrtType();
if (textCalculatorName.Text.Length == 0)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_Calculator_name_cannot_be_empty);
return;
}
if (_existing.Select(spec => spec.Name).Contains(textCalculatorName.Text))
{
var replaceResult = MultiButtonMsgDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_A_calculator_with_that_name_already_exists___Do_you_want_to_replace_it_,
MultiButtonMsgDlg.BUTTON_YES,
MultiButtonMsgDlg.BUTTON_NO,
false);
if (replaceResult == DialogResult.No)
{
return;
}
}
if (irtType == IrtType.existing)
{
try
{
if (!File.Exists(textOpenDatabase.Text))
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_iRT_database_field_must_contain_a_path_to_a_valid_file_);
textOpenDatabase.Focus();
return;
}
var db = IrtDb.GetIrtDb(textOpenDatabase.Text, null);
if (db == null)
{
throw new DatabaseOpeningException(string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Cannot_read_the_database_file__0_, textOpenDatabase.Text));
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Failed_to_open_the_database_file___0_, x.Message), x);
return;
}
}
else if (irtType == IrtType.separate_list)
{
if (textNewDatabase.Text.Length == 0)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_iRT_database_field_must_not_be_empty_);
textNewDatabase.Focus();
return;
}
if (!CreateIrtDatabase(textNewDatabase.Text))
{
return;
}
}
else
{
if (textNewDatabaseProteins.Text.Length == 0)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_iRT_database_field_must_not_be_empty_);
textNewDatabaseProteins.Focus();
return;
}
if (comboBoxProteins.SelectedIndex == -1)
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_Please_select_a_protein_containing_the_list_of_standard_peptides_for_the_iRT_calculator_);
comboBoxProteins.Focus();
return;
}
if (!CreateIrtDatabase(textNewDatabaseProteins.Text))
{
return;
}
}
// Make a version of the document with the new calculator in it
var databaseFileName = irtType == IrtType.existing ? textOpenDatabase.Text :
irtType == IrtType.separate_list ? textNewDatabase.Text :
textNewDatabaseProteins.Text;
var calculator = new RCalcIrt(textCalculatorName.Text, databaseFileName);
// CONSIDER: Probably can't use just a static default like 10 below
var retentionTimeRegression = new RetentionTimeRegression(calculator.Name, calculator, null, null, RetentionTimeRegression.DEFAULT_WINDOW, new List <MeasuredRetentionTime>());
var docNew = Document.ChangeSettings(Document.Settings.ChangePeptidePrediction(prediction =>
prediction.ChangeRetentionTime(retentionTimeRegression)));
// Import transition list of standards, if applicable
if (irtType == IrtType.separate_list)
{
try
{
if (!File.Exists(textImportText.Text))
{
MessageDlg.Show(this, Resources.CreateIrtCalculatorDlg_OkDialog_Transition_list_field_must_contain_a_path_to_a_valid_file_);
return;
}
IdentityPath selectPath;
List <MeasuredRetentionTime> irtPeptides;
List <TransitionImportErrorInfo> errorList;
var inputs = new MassListInputs(textImportText.Text);
docNew = docNew.ImportMassList(inputs, null, out selectPath, out irtPeptides, out _librarySpectra, out errorList);
if (errorList.Any())
{
throw new InvalidDataException(errorList[0].ErrorMessage);
}
_dbIrtPeptides = irtPeptides.Select(rt => new DbIrtPeptide(rt.PeptideSequence, rt.RetentionTime, true, TimeSource.scan)).ToList();
IrtFile = textImportText.Text;
}
catch (Exception x)
{
MessageDlg.ShowWithException(this, string.Format(Resources.CreateIrtCalculatorDlg_OkDialog_Error_reading_iRT_standards_transition_list___0_, x.Message), x);
return;
}
}
else if (irtType == IrtType.protein)
{
PeptideGroupDocNode selectedGroup = comboBoxProteins.SelectedItem as PeptideGroupDocNode;
// ReSharper disable PossibleNullReferenceException
_irtPeptideSequences = new HashSet <Target>(selectedGroup.Peptides.Select(pep => pep.ModifiedTarget));
// ReSharper restore PossibleNullReferenceException
}
Document = docNew;
DialogResult = DialogResult.OK;
}
