/*
* public override List<double> ScoreSequences(List<string> seqs)
* {
* List<DbIrtPeptide> dbPeps;
* try
* {
* dbPeps = Database.GetPeptides(seqs);
* }
* catch (NullReferenceException)
* {
* throw new DatabaseNotConnectedException(this);
* }
* var scores = new List<double>();
*
* foreach(var pep in dbPeps)
* scores.Add(pep == null? 0 : pep.Irt);
* return scores;
* }
*/
public RCalcIrt ChangeDatabasePath(string path)
{
return(ChangeProp(ImClone(this), im =>
{
im.DatabasePath = path;
im.Database = IrtDb.GetIrtDb(path);
}));
}
public static void CreateIrtDb(string path, ProcessedIrtAverages processed, DbIrtPeptide[] standardPeptides, bool recalibrate, IrtRegressionType regressionType, IProgressMonitor monitor)
{
DbIrtPeptide[] newStandards = null;
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], regressionType);
}
var irtDb = IrtDb.CreateIrtDb(path);
irtDb.AddPeptides(monitor, (newStandards ?? standardPeptides).Concat(processed.DbIrtPeptides).ToList());
}
private bool CheckConnection()
{
if (!File.Exists(DatabasePath) || Database == null)
{
return(false);
}
try
{
IrtDb.GetIrtDb(DatabasePath);
return(true);
}
catch (DatabaseOpeningException)
{
return(false);
}
}
public static void CreateIrtDatabase(string path)
{
FileEx.SafeDelete(path);
//Create file, initialize db
try
{
IrtDb.CreateIrtDb(path);
}
catch (DatabaseOpeningException)
{
throw;
}
catch (Exception x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.EditIrtCalcDlg_CreateDatabase_The_file__0__could_not_be_created, path),
x.Message);
throw new IOException(message, x);
}
}
public void ExportSpectralLibrary(string path, IProgressMonitor progressMonitor)
{
const string name = "exported";
var spectra = new Dictionary <LibKey, SpectrumMzInfo>();
foreach (var nodePepGroup in Document.MoleculeGroups)
{
foreach (var nodePep in nodePepGroup.Molecules)
{
foreach (var nodeTranGroup in nodePep.TransitionGroups)
{
for (var i = 0; i < Document.Settings.MeasuredResults.Chromatograms.Count; i++)
{
ProcessTransitionGroup(spectra, nodePepGroup, nodePep, nodeTranGroup, i);
}
}
}
}
var rCalcIrt = Document.Settings.HasRTPrediction
? Document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator as RCalcIrt
: null;
IProgressStatus status = new ProgressStatus();
if (rCalcIrt != null && progressMonitor != null)
{
progressMonitor.UpdateProgress(status = status.ChangeSegments(0, 2));
}
using (var blibDb = BlibDb.CreateBlibDb(path))
{
var libSpec = new BiblioSpecLiteSpec(name, path);
blibDb.CreateLibraryFromSpectra(libSpec, spectra.Values.ToList(), name, progressMonitor, ref status);
}
if (rCalcIrt != null)
{
IrtDb.CreateIrtDb(path).AddPeptides(progressMonitor, rCalcIrt.GetDbIrtPeptides().ToList(), ref status);
}
}
protected override void DoTest()
{
const int numStandardPeps = 11;
const int numLibraryPeps = 18;
const string irtCalc = "iRT-C18";
const string ssrCalc = "SSRCalc 3.0 (300A)";
var testFilesDir = new TestFilesDir(TestContext, TestFilesZip);
string databasePath = testFilesDir.GetTestPath("irt-c18.irtdb");
string documentPath = testFilesDir.GetTestPath("iRT Test.sky");
RunUI(() => SkylineWindow.OpenFile(documentPath));
var peptideSettingsDlg1 = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
var editRT1 = ShowDialog <EditRTDlg>(peptideSettingsDlg1.AddRTRegression);
var irtDlg1 = ShowDialog <EditIrtCalcDlg>(editRT1.AddCalculator);
RunUI(() =>
{
irtDlg1.CalcName = irtCalc;
irtDlg1.CreateDatabase(databasePath);
});
var calibratePeptides = new List <MeasuredPeptide>();
/*
* Check several error handling cases
* Check the peptide choosing algorithm for sanity (correct # peptides)
* Check that the info dialog comes up when too many are requested
* Check the peptide linear transformation for sanity
* Check that the peptides get passed back to EditIrtCalcDlg
*/
var calibrateDlg = ShowDialog <CalibrateIrtDlg>(irtDlg1.Calibrate);
//Check the peptide choosing algorithm
int peptideCount = SkylineWindow.Document.PeptideCount; //29 peptides in the document
//Use the dialog box UI
var countDlg = ShowDialog <AddIrtStandardsDlg>(calibrateDlg.UseResults);
RunUI(() => countDlg.StandardCount = CalibrateIrtDlg.MIN_STANDARD_PEPTIDES - 1);
RunDlg <MessageDlg>(countDlg.OkDialog, messageDlg => messageDlg.OkDialog());
RunUI(() =>
{
countDlg.StandardCount = peptideCount;
countDlg.OkDialog();
});
WaitForClosedForm(countDlg);
Assert.AreEqual(peptideCount, calibrateDlg.StandardPeptideCount);
//Bypass the UI
foreach (int i in new[]
{
peptideCount,
peptideCount / 2,
CalibrateIrtDlg.MIN_STANDARD_PEPTIDES *2,
CalibrateIrtDlg.MIN_STANDARD_PEPTIDES
})
{
int j = i;
RunUI(() =>
{
calibratePeptides = calibrateDlg.Recalculate(SkylineWindow.Document, j);
Assert.AreEqual(calibratePeptides.Count, j);
Assert.IsNull(FindOpenForm <MessageDlg>());
});
}
RunUI(() =>
{
calibrateDlg.Recalculate(SkylineWindow.Document, 11);
//After closing this dialog, there should be 3 iRT values below 0
//and 3 above 100
calibrateDlg.SetFixedPoints(3, 7);
calibrateDlg.OkDialog();
});
WaitForClosedForm(calibrateDlg);
//Now check that the peptides were passed to the EditIrtCalcDlg
RunUI(() =>
{
Assert.AreEqual(numStandardPeps, irtDlg1.StandardPeptideCount);
//And that there are 3 below 0 and 3 above 100
Assert.AreEqual(3, irtDlg1.StandardPeptides.Count(pep => pep.Irt < 0));
Assert.AreEqual(3, irtDlg1.StandardPeptides.Count(pep => pep.Irt > 100));
irtDlg1.ClearStandardPeptides();
});
/*
* Test pasting into EditIrtCalcDlg
* Test that the dialog requires the whole standard to be in the document
* Test that add results gets everything in the document besides the standard
* Test that there were no errors along the way
*/
//Now paste in iRT with each peptide truncated by one amino acid
var standard = new[]
{
BuildMeasuredPeptide("LGGNEQVTR", -24.92),
BuildMeasuredPeptide("GAGSSEPVTGLDAK", 0.00),
BuildMeasuredPeptide("VEATFGVDESNAK", 12.39),
BuildMeasuredPeptide("YILAGVENSK", 19.79),
BuildMeasuredPeptide("TPVISGGPYEYR", 28.71),
BuildMeasuredPeptide("TPVITGAPYEYR", 33.38),
BuildMeasuredPeptide("DGLDAASYYAPVR", 42.26),
BuildMeasuredPeptide("ADVTPADFSEWSK", 54.62),
BuildMeasuredPeptide("GTFIIDPGGVIR", 70.52),
BuildMeasuredPeptide("GTFIIDPAAVIR", 87.23),
BuildMeasuredPeptide("LFLQFGAQGSPFLK", 100.00),
};
RunUI(() =>
{
string standardText = BuildStandardText(standard, seq => seq.Substring(0, seq.Length - 1));
SetClipboardText(standardText);
irtDlg1.DoPasteStandard();
});
// Cannot add results because standard peptides are not in the document
RunDlg <AddIrtPeptidesDlg>(irtDlg1.AddResults, messageDlg => messageDlg.OkDialog());
// Paste Biognosys-provided values
RunUI(() =>
{
string standardText = BuildStandardText(standard, seq => seq);
SetClipboardText(standardText);
irtDlg1.ClearStandardPeptides();
irtDlg1.DoPasteStandard();
//Check count
Assert.AreEqual(numStandardPeps, irtDlg1.StandardPeptideCount);
});
//Add results
var addPeptidesDlg1 = ShowDialog <AddIrtPeptidesDlg>(irtDlg1.AddResults);
var recalibrateDlg1 = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg1.OkDialog);
OkDialog(recalibrateDlg1, recalibrateDlg1.Btn1Click);
RunUI(() => Assert.AreEqual(numLibraryPeps, irtDlg1.LibraryPeptideCount));
// Recalibrate
const int shift = 100;
const int skew = 10;
RunDlg <RecalibrateIrtDlg>(irtDlg1.Calibrate, recalDlg =>
{
recalDlg.MinIrt = standard[1].RetentionTime + shift;
recalDlg.MaxIrt = standard[standard.Length - 1].RetentionTime * skew + shift;
recalDlg.FixedPoint1 = standard[1].Sequence;
recalDlg.FixedPoint2 = standard[standard.Length - 1].Sequence;
recalDlg.OkDialog();
});
RunUI(() =>
{
for (int i = 0; i < irtDlg1.StandardPeptideCount; i++)
{
Assert.AreEqual(standard[i].RetentionTime * skew + shift,
irtDlg1.StandardPeptides.Skip(i).First().Irt);
}
});
RunDlg <RecalibrateIrtDlg>(irtDlg1.Calibrate, recalDlg =>
{
recalDlg.FixedPoint1 = standard[2].Sequence;
recalDlg.FixedPoint2 = standard[standard.Length - 2].Sequence;
recalDlg.MinIrt = standard[2].RetentionTime;
recalDlg.MaxIrt = standard[standard.Length - 2].RetentionTime;
recalDlg.OkDialog();
});
// Change peptides
var changePeptides = irtDlg1.LibraryPeptides.Where((p, i) => i % 2 == 0).ToArray();
var resetPeptides = irtDlg1.StandardPeptides.ToArray();
RunDlg <ChangeIrtPeptidesDlg>(irtDlg1.ChangeStandardPeptides, changeDlg =>
{
changeDlg.Peptides = changePeptides;
changeDlg.OkDialog();
});
Assert.IsTrue(ArrayUtil.EqualsDeep(changePeptides.Select(p => p.Target).ToArray(),
irtDlg1.StandardPeptides.Select(p => p.Target).ToArray()));
Assert.IsTrue(ArrayUtil.EqualsDeep(changePeptides.Select(p => p.Irt).ToArray(),
irtDlg1.StandardPeptides.Select(p => p.Irt).ToArray()));
RunDlg <ChangeIrtPeptidesDlg>(irtDlg1.ChangeStandardPeptides, changeDlg =>
{
changeDlg.Peptides = resetPeptides;
changeDlg.OkDialog();
});
OkDialog(irtDlg1, irtDlg1.OkDialog);
Assert.IsNull(FindOpenForm <MessageDlg>());
/*
* Check that the database was created successfully
* Check that it has the correct numbers of standard and library peptides
*/
IrtDb db = IrtDb.GetIrtDb(databasePath, null);
Assert.AreEqual(numStandardPeps, db.StandardPeptideCount);
Assert.AreEqual(numLibraryPeps, db.LibraryPeptideCount);
/*
* Make sure that loading the database brings back up the right numbers of peptides
*/
//Rather than rigging SettingsListComboDriver, just create a new one and load
var irtDlg1A = ShowDialog <EditIrtCalcDlg>(editRT1.AddCalculator);
RunDlg <MessageDlg>(() => irtDlg1A.OpenDatabase(testFilesDir.GetTestPath("bogus.irtdb")),
messageDlg => messageDlg.OkDialog());
//There was a _bug_ where opening a path and then clicking OK would save all the peptides
//twice, doubling the size of the database. So check that that is fixed.
EditIrtCalcDlgPepCountTest(irtDlg1A, numStandardPeps, numLibraryPeps, databasePath, false);
EditIrtCalcDlgPepCountTest(ShowDialog <EditIrtCalcDlg>(editRT1.AddCalculator),
numStandardPeps, numLibraryPeps, databasePath, false);
EditIrtCalcDlgPepCountTest(ShowDialog <EditIrtCalcDlg>(editRT1.AddCalculator),
numStandardPeps, numLibraryPeps, databasePath, true);
EditIrtCalcDlgPepCountTest(ShowDialog <EditIrtCalcDlg>(editRT1.AddCalculator),
numStandardPeps, numLibraryPeps, databasePath, false);
/*
* Create a regression based on the new calculator
* Create a regression based on SSRCalc
* Open the graph
* Switch to new calculator, verify r = 1.00 and graph is labeled iRT-C18
* Switch to SSRCalc, verify graph label changes
*/
RunUI(() =>
{
editRT1.SetRegressionName("iRT Regression");
editRT1.AddResults();
editRT1.ChooseCalculator(irtCalc);
editRT1.OkDialog();
});
WaitForClosedForm(editRT1);
var editRT1A = ShowDialog <EditRTDlg>(peptideSettingsDlg1.AddRTRegression);
RunUI(() =>
{
editRT1A.SetRegressionName("SSRCalc Regression");
editRT1A.AddResults();
editRT1A.ChooseCalculator(ssrCalc);
});
RunDlg <RTDetails>(editRT1A.ShowDetails, detailsDlg => detailsDlg.Close());
OkDialog(editRT1A, editRT1A.OkDialog);
RunUI(peptideSettingsDlg1.CancelButton.PerformClick);
WaitForClosedForm(peptideSettingsDlg1);
var docPeptides = new List <MeasuredRetentionTime>();
RunUI(() =>
{
var document = Program.ActiveDocumentUI;
foreach (var docPepNode in document.Peptides)
{
docPeptides.Add(new MeasuredRetentionTime(document.Settings.GetModifiedSequence(docPepNode),
docPepNode.AverageMeasuredRetentionTime ?? 0));
}
});
RetentionTimeStatistics stats = null;
RegressionLineElement line = null;
RunUI(() => SkylineWindow.ShowRTRegressionGraphScoreToRun());
WaitForRegression();
RunUI(() =>
{
SkylineWindow.SetupCalculatorChooser();
SkylineWindow.ChooseCalculator(irtCalc);
});
WaitForRegression();
RunUI(() =>
{
stats = SkylineWindow.RTGraphController.RegressionRefined.CalcStatistics(docPeptides, null);
line = SkylineWindow.RTGraphController.RegressionRefined.Conversion as RegressionLineElement;
});
Assert.IsNotNull(stats);
Assert.IsTrue(stats.R > 0.999);
Assert.IsNotNull(line);
//These values were taken from the graph, which shows values to 2 decimal places, so the real values must
//be +/- 0.01 from these values
Assert.IsTrue(Math.Abs(line.Intercept - 14.17) < 0.01);
Assert.IsTrue(Math.Abs(line.Slope - 0.15) < 0.01);
RunUI(() => SkylineWindow.ChooseCalculator(ssrCalc));
WaitForRegression();
RunUI(() => stats = SkylineWindow.RTGraphController.RegressionRefined.CalcStatistics(docPeptides, null));
Assert.IsNotNull(stats);
Assert.IsTrue(Math.Abs(stats.R - 0.97) < 0.01);
/*
* Delete all peptides except the standard
* Create a new calculator with the document standard (instead of pasting)
* Create a regression with that calculator
* Export a transition list using measured retention times
* Export a method using predicted retention times
* Test that they are identical
*/
//Delete from the document all but the last protein, which has all the standard peptides
RunUI(() =>
{
SkylineWindow.CollapseProteins();
var seqTree = SkylineWindow.SequenceTree;
seqTree.SelectedNode = seqTree.Nodes[0];
seqTree.KeysOverride = Keys.Shift;
seqTree.SelectedNode = seqTree.Nodes[17];
SkylineWindow.EditDelete();
});
//Peptide settings dialog -> Add a regression
var peptideSettingsDlg2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editRT2 = ShowDialog <EditRTDlg>(peptideSettingsDlg2.AddRTRegression);
//Set regression name
RunUI(() => editRT2.SetRegressionName("iRT Document Regression"));
//Regression dialog -> add a calculator
var irtDlg2 = ShowDialog <EditIrtCalcDlg>(editRT2.AddCalculator);
//Set calc name, database
RunUI(() =>
{
irtDlg2.CalcName = "iRT Document Calculator";
irtDlg2.CreateDatabase(testFilesDir.GetTestPath("irt-doc.irtdb"));
});
//Calc dialog -> calibrate standard
RunDlg <CalibrateIrtDlg>(irtDlg2.Calibrate, calibrateDlg2 =>
{
//Get 11 peptides from the document (all of them) and go back to calculator dialog
calibrateDlg2.Recalculate(SkylineWindow.Document, 11);
calibrateDlg2.OkDialog();
});
Assert.AreEqual(11, irtDlg2.StandardPeptideCount);
Assert.AreEqual(0, irtDlg2.LibraryPeptideCount);
// Close dialog to save calculator
OkDialog(irtDlg2, irtDlg2.OkDialog);
// Test adding irt calculator
{
var irtDlgAdd = ShowDialog <EditIrtCalcDlg>(editRT2.EditCurrentCalculator);
var addDlg = ShowDialog <AddIrtCalculatorDlg>(irtDlgAdd.AddIrtDatabase);
// Check error messages
RunUI(() => addDlg.Source = IrtCalculatorSource.file);
RunDlg <MessageDlg>(addDlg.OkDialog, messageDlg =>
{
Assert.AreEqual(Resources.AddIrtCalculatorDlg_OkDialog_Please_specify_a_path_to_an_existing_iRT_database, messageDlg.Message);
messageDlg.OkDialog();
});
RunUI(() => addDlg.FilePath = "not_irtdb.docx");
RunDlg <MessageDlg>(addDlg.OkDialog, messageDlg =>
{
AssertEx.AreComparableStrings(Resources.AddIrtCalculatorDlg_OkDialog_The_file__0__is_not_an_iRT_database, messageDlg.Message);
messageDlg.OkDialog();
});
RunUI(() => addDlg.FilePath = "not_exist.irtdb");
RunDlg <MessageDlg>(addDlg.OkDialog, messageDlg =>
{
AssertEx.AreComparableStrings(TextUtil.LineSeparate(
Resources.AddIrtCalculatorDlgOkDialogThe_file__0__does_not_exist,
Resources.AddIrtCalculatorDlg_OkDialog_Please_specify_a_path_to_an_existing_iRT_database), messageDlg.Message);
messageDlg.OkDialog();
});
RunUI(() => addDlg.CalculatorName = "noexist");
PauseForScreenShot();
RunDlg <MessageDlg>(addDlg.OkDialog, messageDlg =>
{
Assert.AreEqual(Resources.AddIrtCalculatorDlg_OkDialog_Please_choose_the_iRT_calculator_you_would_like_to_add, messageDlg.Message);
messageDlg.OkDialog();
});
RunUI(() => addDlg.FilePath = databasePath);
var addPepDlg = ShowDialog <AddIrtPeptidesDlg>(addDlg.OkDialog);
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPepDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
Assert.AreEqual(18, irtDlgAdd.LibraryPeptideCount);
OkDialog(irtDlgAdd, irtDlgAdd.CancelButton.PerformClick);
}
// Add from existing calculator
{
var irtDlgAdd = ShowDialog <EditIrtCalcDlg>(editRT2.EditCurrentCalculator);
var addDlg = ShowDialog <AddIrtCalculatorDlg>(irtDlgAdd.AddIrtDatabase);
RunUI(() => addDlg.CalculatorName = irtCalc);
var addPepDlg = ShowDialog <AddIrtPeptidesDlg>(addDlg.OkDialog);
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPepDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
Assert.AreEqual(18, irtDlgAdd.LibraryPeptideCount);
OkDialog(irtDlgAdd, irtDlgAdd.CancelButton.PerformClick);
}
var docIrtBefore = SkylineWindow.Document;
OkDialog(editRT2, editRT2.OkDialog);
OkDialog(peptideSettingsDlg2, peptideSettingsDlg2.OkDialog);
WaitForClosedForm(peptideSettingsDlg2);
var docIrt = VerifyIrtStandards(docIrtBefore, true);
RunUI(() =>
{
// Select 3 of the standards and delete them
SkylineWindow.SequenceTree.KeysOverride = Keys.None;
SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.SequenceTree.KeysOverride = Keys.Shift;
SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 2);
SkylineWindow.SequenceTree.KeysOverride = Keys.None;
SkylineWindow.EditDelete();
});
// Should still have iRT peptides
docIrt = VerifyIrtStandards(docIrt, true);
// Remove one more and standards should be cleared
RunUI(SkylineWindow.Cut);
docIrt = VerifyIrtStandards(docIrt, false);
RunUI(SkylineWindow.Paste);
docIrt = VerifyIrtStandards(docIrt, true);
// Repeat without results
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
dlg.RemoveAllReplicates();
dlg.OkDialog();
});
docIrt = VerifyIrtStandards(docIrt, true);
RunUI(SkylineWindow.EditDelete);
docIrt = VerifyIrtStandards(docIrt, false);
RunUI(SkylineWindow.Paste);
VerifyIrtStandards(docIrt, true);
//Restore the document to contain all 29 peptides
RunUI(() => SkylineWindow.UndoRestore(7));
//Open peptide settings
var peptideSettingsDlg3 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunDlg <EditListDlg <SettingsListBase <RetentionTimeRegression>, RetentionTimeRegression> >(peptideSettingsDlg3.EditRegressionList,
dlg =>
{
dlg.SelectLastItem();
dlg.RemoveItem();
dlg.OkDialog();
});
//Add a new regression
var editRT3 = ShowDialog <EditRTDlg>(peptideSettingsDlg3.AddRTRegression);
RunUI(() => editRT3.SetRegressionName("iRT Document Regression"));
//Edit the calculator list
var editCalculator =
ShowDialog <EditListDlg <SettingsListBase <RetentionScoreCalculatorSpec>, RetentionScoreCalculatorSpec> >(
editRT3.EditCalculatorList);
RunUI(() => editCalculator.SelectItem("iRT Document Calculator"));
//Edit the document-based calculator
var irtDlg3 = ShowDialog <EditIrtCalcDlg>(editCalculator.EditItem);
//Add the 18 non-standard peptides to the calculator, then OkDialog back to Skyline
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(irtDlg3.AddResults);
var recalibrateDlg2 = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg.OkDialog);
OkDialog(recalibrateDlg2, recalibrateDlg2.Btn1Click);
RunUI(() =>
{
Assert.AreEqual(18, irtDlg3.LibraryPeptideCount);
irtDlg3.OkDialog();
});
WaitForClosedForm(irtDlg3);
RunUI(editCalculator.OkDialog);
WaitForClosedForm(editCalculator);
RunUI(() =>
{
editRT3.AddResults();
editRT3.ChooseCalculator("iRT Document Calculator");
editRT3.SetTimeWindow(2.0);
editRT3.OkDialog();
});
WaitForClosedForm(editRT3);
//Then choose the new, document-based regression and turn off prediction
RunUI(() =>
{
peptideSettingsDlg3.ChooseRegression("iRT Document Regression");
peptideSettingsDlg3.IsUseMeasuredRT = true;
peptideSettingsDlg3.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg3);
Assert.IsNull(FindOpenForm <MessageDlg>());
//Export the measurement-based transition list
ExportMethod(testFilesDir.GetTestPath("EmpiricalTL.csv"));
//Turn on prediction for scheduling
var peptideSettingsDlg4 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsDlg4.IsUseMeasuredRT = false;
peptideSettingsDlg4.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg4);
//Export the prediction-based transition list
ExportMethod(testFilesDir.GetTestPath("PredictionTL.csv"));
//Now open both files and compare
AssertEx.NoDiff(File.ReadAllText(testFilesDir.GetTestPath("EmpiricalTL.csv")),
File.ReadAllText(testFilesDir.GetTestPath("PredictionTL.csv")));
// Close and re-open, and try again
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.SaveDocument());
SkylineWindow.NewDocument();
Assert.IsTrue(SkylineWindow.OpenFile(documentPath));
});
WaitForDocumentLoaded();
ExportMethod(testFilesDir.GetTestPath("PredictionTL_reopen.csv"));
AssertEx.NoDiff(File.ReadAllText(testFilesDir.GetTestPath("EmpiricalTL.csv")),
File.ReadAllText(testFilesDir.GetTestPath("PredictionTL_reopen.csv")));
/*
* Rename the database
* Switch to the calculator in EditRTDlg and check for an error
* Go to edit the calculator and check for an error
* Try to export a transition list and check for an error
* Switch to the calculator in the graph and check for an error
*/
var stream = File.Create(testFilesDir.GetTestPath("irt-c18-copy.irtdb"));
stream.Close();
File.Replace(databasePath, testFilesDir.GetTestPath("irt-c18-copy.irtdb"),
testFilesDir.GetTestPath("backup.irtdb"));
// The database renaming doesn't break usage anymore, since
// the iRT databases are loaded into memory during initialization.
// So, create a new calculator with a bogus path.
const string irtCalcMissing = "iRT-C18-missing";
Settings.Default.RTScoreCalculatorList.SetValue(new RCalcIrt(irtCalcMissing, testFilesDir.GetTestPath("irt-c18-missing.irtdb")));
var peptideSettingsDlg5 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editRT5 = ShowDialog <EditRTDlg>(peptideSettingsDlg5.AddRTRegression);
//Add results and switch to a calculator whose database is not connected: error
RunDlg <MessageDlg>(() =>
{
editRT5.AddResults();
editRT5.ChooseCalculator(irtCalcMissing);
},
errorMessage => errorMessage.OkDialog());
//Go to add a new calculator
var irtDlg5 = ShowDialog <EditIrtCalcDlg>(editRT5.AddCalculator);
//Try to open a file that does not exist: error
RunDlg <MessageDlg>(() => irtDlg5.OpenDatabase(databasePath), messageDlg => messageDlg.OkDialog());
RunUI(() => irtDlg5.CancelButton.PerformClick());
WaitForClosedForm(irtDlg5);
//In order to export a transition list, we have to set the RT regression to have the iRT Calc.
//This means that the iRT calc must have its database connected - else the dialog will not let
//the user choose it. So here we will restore the file so we can choose the calculator.
//Then once that dialog is closed and the regression is saved, switch the file back again.
stream = File.Create(databasePath);
stream.Close();
File.Replace(testFilesDir.GetTestPath("irt-c18-copy.irtdb"), databasePath,
testFilesDir.GetTestPath("backup.irtdb"));
RunUI(() =>
{
editRT5.SetRegressionName("iRT Test Regression");
editRT5.AddResults();
editRT5.ChooseCalculator(irtCalc);
editRT5.OkDialog();
});
WaitForClosedForm(editRT5);
RunUI(() =>
{
peptideSettingsDlg5.ChooseRegression("iRT Test Regression");
peptideSettingsDlg5.IsUseMeasuredRT = false; //Use prediction
peptideSettingsDlg5.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg5);
RunUI(() => SkylineWindow.SaveDocument());
//Switch the file back to the copy, destroying the original
stream = File.Create(testFilesDir.GetTestPath("irt-c18-copy.irtdb"));
stream.Close();
File.Replace(databasePath, testFilesDir.GetTestPath("irt-c18-copy.irtdb"),
testFilesDir.GetTestPath("backup.irtdb"));
var exportTransList = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg);
// Used to cause a message box, but should work now, because iRT databases get loaded once
RunUI(() => exportTransList.SetMethodType(ExportMethodType.Scheduled));
RunUI(() => exportTransList.CancelButton.PerformClick());
WaitForClosedForm(exportTransList);
// Used to cause a message box, but should work now, because iRT databases get loaded once
RunUI(() => SkylineWindow.ChooseCalculator(irtCalc));
/*
* Now clean up by deleting all these calculators. If we don't, then the next functional test
* will fail because it will try to use a calculator from settings which will not have its
* database.
*/
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, peptideSettingsDlg6 =>
{
peptideSettingsDlg6.ChooseRegression(Resources.SettingsList_ELEMENT_NONE_None);
peptideSettingsDlg6.OkDialog();
});
// Finally, close and re-open the document to see MissingFileDlg
int pepCount = SkylineWindow.Document.PeptideCount;
RunUI(() => SkylineWindow.NewDocument(true));
Assert.AreEqual(0, SkylineWindow.Document.PeptideCount);
RunDlg <MissingFileDlg>(() => SkylineWindow.OpenFile(documentPath),
dlg => dlg.OkDialog());
Assert.AreEqual(pepCount, SkylineWindow.Document.PeptideCount);
RunUI(() => SkylineWindow.NewDocument(true));
RunDlg <MissingFileDlg>(() => SkylineWindow.OpenFile(documentPath),
dlg => dlg.CancelDialog());
Assert.AreEqual(0, SkylineWindow.Document.PeptideCount);
// Make sure no message boxes are left open
Assert.IsNull(FindOpenForm <MessageDlg>());
}
private bool AddIrts(LibraryManager.BuildState buildState)
{
try
{
Library lib;
ProcessedIrtAverages processed = null;
var initialMessage = Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_Adding_iRTs_to_library;
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_Adding_iRTs_to_library
})
{
var status = longWait.PerformWork(TopMostApplicationForm, 800, monitor =>
{
var initStatus = new ProgressStatus(initialMessage).ChangeSegments(0, 2);
monitor.UpdateProgress(initStatus);
lib = NotificationContainer.LibraryManager.TryGetLibrary(buildState.LibrarySpec) ??
NotificationContainer.LibraryManager.LoadLibrary(buildState.LibrarySpec, () => new DefaultFileLoadMonitor(monitor));
foreach (var stream in lib.ReadStreams)
{
stream.CloseStream();
}
if (longWait.IsCanceled)
{
return;
}
var irtProviders = lib.RetentionTimeProvidersIrt.ToArray();
if (!irtProviders.Any())
{
irtProviders = lib.RetentionTimeProviders.ToArray();
}
processed = RCalcIrt.ProcessRetentionTimes(monitor, irtProviders, irtProviders.Length,
buildState.IrtStandard.Peptides.ToArray(), new DbIrtPeptide[0]);
});
if (status.IsCanceled)
{
return(false);
}
if (status.IsError)
{
throw status.ErrorException;
}
}
using (var resultsDlg = new AddIrtPeptidesDlg(AddIrtPeptidesLocation.spectral_library, processed))
{
if (resultsDlg.ShowDialog(TopMostApplicationForm) != DialogResult.OK)
{
return(false);
}
}
var recalibrate = false;
if (processed.CanRecalibrateStandards(buildState.IrtStandard.Peptides))
{
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))
{
if (dlg.ShowDialog(TopMostApplicationForm) == DialogResult.Yes)
{
recalibrate = true;
}
}
}
var processedDbIrtPeptides = processed.DbIrtPeptides.ToArray();
if (!processedDbIrtPeptides.Any())
{
return(false);
}
using (var longWait = new LongWaitDlg {
Text = Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_Adding_iRTs_to_library
})
{
ImmutableList <DbIrtPeptide> newStandards = null;
var status = longWait.PerformWork(TopMostApplicationForm, 800, monitor =>
{
if (recalibrate)
{
monitor.UpdateProgress(new ProgressStatus().ChangeSegments(0, 2));
newStandards = ImmutableList.ValueOf(processed.RecalibrateStandards(buildState.IrtStandard.Peptides));
processed = RCalcIrt.ProcessRetentionTimes(
monitor, processed.ProviderData.Select(data => data.Value.RetentionTimeProvider),
processed.ProviderData.Count, newStandards.ToArray(), new DbIrtPeptide[0]);
}
var irtDb = IrtDb.CreateIrtDb(buildState.LibrarySpec.FilePath);
irtDb.AddPeptides(monitor, (newStandards ?? buildState.IrtStandard.Peptides).Concat(processedDbIrtPeptides).ToList());
});
if (status.IsError)
{
throw status.ErrorException;
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(TopMostApplicationForm,
TextUtil.LineSeparate(Resources.LibraryBuildNotificationHandler_LibraryBuildCompleteCallback_An_error_occurred_trying_to_add_iRTs_to_the_library_, x.Message), x);
return(false);
}
return(true);
}
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;
}
private bool AddIrtLibraryTable(string path, IrtStandard standard)
{
if (!ImportPeptideSearch.HasDocLib || !ImportPeptideSearch.DocLib.IsLoaded)
{
return(false);
}
var lib = ImportPeptideSearch.DocLib;
ProcessedIrtAverages processed = null;
using (var longWait = new LongWaitDlg
{
Text = Resources.BuildPeptideSearchLibraryControl_AddIrtLibraryTable_Processing_Retention_Times
})
{
try
{
var status = longWait.PerformWork(WizardForm, 800, monitor =>
{
var irtProviders = lib.RetentionTimeProvidersIrt.ToArray();
if (!irtProviders.Any())
{
irtProviders = lib.RetentionTimeProviders.ToArray();
}
processed = RCalcIrt.ProcessRetentionTimes(monitor, irtProviders, irtProviders.Length, standard.Peptides.ToArray(), new DbIrtPeptide[0]);
});
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm,
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(this) != DialogResult.OK)
{
return(false);
}
}
var recalibrate = false;
if (processed.CanRecalibrateStandards(standard.Peptides))
{
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))
{
if (dlg.ShowDialog(WizardForm) == DialogResult.Yes)
{
recalibrate = true;
}
}
}
using (var longWait = new LongWaitDlg
{
Text = Resources.BuildPeptideSearchLibraryControl_AddIrtLibraryTable_Adding_iRTs_to_Library
})
{
try
{
ImmutableList <DbIrtPeptide> newStandards = null;
var status = longWait.PerformWork(WizardForm, 800, monitor =>
{
if (recalibrate)
{
monitor.UpdateProgress(new ProgressStatus().ChangeSegments(0, 2));
newStandards = ImmutableList.ValueOf(processed.RecalibrateStandards(standard.Peptides));
processed = RCalcIrt.ProcessRetentionTimes(
monitor, processed.ProviderData.Select(data => data.Value.RetentionTimeProvider),
processed.ProviderData.Count, newStandards.ToArray(), new DbIrtPeptide[0]);
}
var irtDb = IrtDb.CreateIrtDb(path);
irtDb.AddPeptides(monitor, (newStandards ?? standard.Peptides).Concat(processed.DbIrtPeptides).ToList());
});
if (status.IsError)
{
throw status.ErrorException;
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm,
TextUtil.LineSeparate(Resources.BuildPeptideSearchLibraryControl_AddIrtLibraryTable_An_error_occurred_trying_to_add_iRTs_to_the_library_, x.Message), x);
return(false);
}
}
return(true);
}
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);
}
public void ConsoleImportPeptideSearchTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
var docPath = testFilesDir.GetTestPath("blank.sky");
var outPath = testFilesDir.GetTestPath("import-search.sky");
var searchFilePath = testFilesDir.GetTestPath("CAexample.pep.xml");
var fastaPath = testFilesDir.GetTestPath("bov-5-prot.fasta");
// with mods and invalid cutoff score
const double badCutoff = 1.1;
var args = new[]
{
"--in=" + docPath,
"--out=" + outPath,
"--import-search-file=" + searchFilePath,
"--import-search-cutoff-score=" + badCutoff,
"--import-search-add-mods",
"--import-fasta=" + fastaPath
};
var output = RunCommand(args);
AssertEx.Contains(output, new CommandArgs.ValueOutOfRangeDoubleException(CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_CUTOFF, badCutoff, 0, 1).Message);
args[3] = "--import-search-cutoff-score=" + Settings.Default.LibraryResultCutOff;
output = RunCommand(args);
AssertEx.Contains(output, TextUtil.LineSeparate(Resources.CommandLine_ImportSearch_Creating_spectral_library_from_files_,
Path.GetFileName(searchFilePath)));
AssertEx.Contains(output, string.Format(Resources.CommandLine_ImportSearch_Adding__0__modifications_, 2));
AssertEx.Contains(output, string.Format(Resources.CommandLine_ImportFasta_Importing_FASTA_file__0____,
Path.GetFileName(fastaPath)));
var doc = ResultsUtil.DeserializeDocument(outPath);
Assert.IsTrue(doc.Settings.HasResults);
Assert.AreEqual(1, doc.Settings.MeasuredResults.Chromatograms.Count);
Assert.IsTrue(doc.Settings.MeasuredResults.ContainsChromatogram("CAexample"));
Assert.AreEqual(5, doc.PeptideGroupCount);
Assert.AreEqual(26, doc.PeptideCount);
Assert.AreEqual(26, doc.PeptideTransitionGroupCount);
Assert.AreEqual(78, doc.PeptideTransitionCount);
// without mods
var outPath2 = testFilesDir.GetTestPath("import-search2.sky");
output = RunCommand("--in=" + docPath,
"--out=" + outPath2,
"--import-search-file=" + searchFilePath,
"--import-fasta=" + fastaPath);
AssertEx.Contains(output, TextUtil.LineSeparate(Resources.CommandLine_ImportSearch_Creating_spectral_library_from_files_,
Path.GetFileName(searchFilePath)));
AssertEx.Contains(output, string.Format(Resources.CommandLine_ImportFasta_Importing_FASTA_file__0____,
Path.GetFileName(fastaPath)));
doc = ResultsUtil.DeserializeDocument(outPath2);
Assert.IsTrue(doc.Settings.HasResults);
Assert.AreEqual(1, doc.Settings.MeasuredResults.Chromatograms.Count);
Assert.IsTrue(doc.Settings.MeasuredResults.ContainsChromatogram("CAexample"));
Assert.AreEqual(5, doc.PeptideGroupCount);
Assert.AreEqual(23, doc.PeptideCount);
Assert.AreEqual(23, doc.PeptideTransitionGroupCount);
Assert.AreEqual(69, doc.PeptideTransitionCount);
// test setting cutoff and accepting mods when not importing a search
output = RunCommand(
"--import-search-cutoff-score=" + 0.99,
"--import-search-add-mods");
AssertEx.Contains(output, CommandArgs.WarnArgRequirementText(CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_CUTOFF, CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_FILE));
AssertEx.Contains(output, CommandArgs.WarnArgRequirementText(CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_MODS, CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_FILE));
// MaxQuant embedding error
searchFilePath = testFilesDir.GetTestPath("yeast-wiff-msms.txt");
output = RunCommand("--in=" + docPath,
"--out=" + outPath2,
"--import-search-file=" + searchFilePath,
"--import-fasta=" + fastaPath);
AssertEx.Contains(output, TextUtil.LineSeparate(Resources.CommandLine_ImportSearch_Creating_spectral_library_from_files_,
Path.GetFileName(searchFilePath)));
AssertEx.Contains(output, string.Format(Resources.VendorIssueHelper_ShowLibraryMissingExternalSpectraError_Could_not_find_an_external_spectrum_file_matching__0__in_the_same_directory_as_the_MaxQuant_input_file__1__,
"wine yeast sampleA_2", searchFilePath));
AssertEx.Contains(output, string.Format(Resources.CommandLine_ShowLibraryMissingExternalSpectraError_DescriptionWithSupportedExtensions__0__, BiblioSpecLiteBuilder.BiblioSpecSupportedFileExtensions));
output = RunCommand("--in=" + docPath,
"--out=" + outPath2,
"--import-search-file=" + searchFilePath,
"--import-fasta=" + fastaPath,
"--import-search-prefer-embedded-spectra");
AssertEx.Contains(output, TextUtil.LineSeparate(Resources.CommandLine_ImportSearch_Creating_spectral_library_from_files_,
Path.GetFileName(searchFilePath)));
Assert.IsTrue(!output.Contains(string.Format(Resources.VendorIssueHelper_ShowLibraryMissingExternalSpectraError_Could_not_find_an_external_spectrum_file_matching__0__in_the_same_directory_as_the_MaxQuant_input_file__1__,
"wine yeast sampleA_2", searchFilePath)));
Assert.IsTrue(!output.Contains(string.Format(Resources.CommandLine_ShowLibraryMissingExternalSpectraError_DescriptionWithSupportedExtensions__0__, BiblioSpecLiteBuilder.BiblioSpecSupportedFileExtensions)));
// iRTs
File.Copy(testFilesDir.GetTestPath("cirts.mqpar.xml"), testFilesDir.GetTestPath("mqpar.xml"), true);
searchFilePath = testFilesDir.GetTestPath("cirts.msms.txt");
// test setting num cirts and recalibrate when no irts
output = RunCommand("--in=" + docPath,
"--import-search-file=" + searchFilePath,
"--import-search-num-cirts=10",
"--import-search-recalibrate-irts");
AssertEx.Contains(output,
CommandArgs.WarnArgRequirementText(CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_NUM_CIRTS, CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_IRTS),
CommandArgs.WarnArgRequirementText(CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_RECALIBRATE_IRTS, CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_IRTS));
// test cirt without num cirts set
output = RunCommand("--in=" + docPath,
"--import-search-file=" + searchFilePath,
"--import-search-irts=CiRT (iRT-C18)");
AssertEx.Contains(output, string.Format(Resources.CommandLine_ImportSearchInternal__0__must_be_set_when_using_CiRT_peptides_, CommandArgs.ARG_IMPORT_PEPTIDE_SEARCH_NUM_CIRTS.Name));
// test with irts
output = RunCommand("--in=" + docPath,
"--import-search-file=" + searchFilePath,
"--import-search-irts=CiRT (iRT-C18)",
"--import-search-num-cirts=10");
var libIrts = IrtDb.GetIrtDb(testFilesDir.GetTestPath("blank.blib"), null).StandardPeptides.ToArray();
AssertEx.AreEqual(10, libIrts.Length);
foreach (var libIrt in libIrts)
{
AssertEx.IsTrue(IrtStandard.CIRT.Contains(libIrt));
}
}
