public static void CalibrationTestLowRes()
{
CalibrationTask calibrationTask = new CalibrationTask();
EngineLayer.CommonParameters CommonParameters = new EngineLayer.CommonParameters
(dissociationType: MassSpectrometry.DissociationType.LowCID,
scoreCutoff: 1);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestCalibrationLow");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\sliced_b6.mzML");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\LowResSnip_B6_mouse_11700_117500.xml.gz");
Directory.CreateDirectory(outputFolder);
calibrationTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
myFile
}, "test");
Assert.That(File.Exists(Path.Combine(outputFolder, @"sliced_b6-calib.mzML")));
Assert.That(File.Exists(Path.Combine(outputFolder, @"sliced_b6-calib.toml")));
var lines = File.ReadAllLines(Path.Combine(outputFolder, @"sliced_b6-calib.toml"));
var tolerance = Regex.Match(lines[0], @"\d+\.\d*").Value;
var tolerance1 = Regex.Match(lines[1], @"\d+\.\d*").Value;
Assert.That(double.TryParse(tolerance, out double tol) == true);
Assert.That(double.TryParse(tolerance1, out double tol1) == true);
Assert.That(lines[0].Contains("PrecursorMassTolerance"));
Assert.That(lines[1].Contains("ProductMassTolerance"));
Directory.Delete(outputFolder, true);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
public static void GenerateDefaultTaskTomls(string folderLocation)
{
try
{
if (!Directory.Exists(folderLocation))
{
Directory.CreateDirectory(folderLocation);
}
CalibrationTask c = new CalibrationTask();
Toml.WriteFile(c, Path.Combine(folderLocation, @"CalibrationTask.toml"), MetaMorpheusTask.tomlConfig);
GptmdTask g = new GptmdTask();
Toml.WriteFile(g, Path.Combine(folderLocation, @"GptmdTask.toml"), MetaMorpheusTask.tomlConfig);
SearchTask s = new SearchTask();
Toml.WriteFile(s, Path.Combine(folderLocation, @"SearchTask.toml"), MetaMorpheusTask.tomlConfig);
XLSearchTask xl = new XLSearchTask();
Toml.WriteFile(xl, Path.Combine(folderLocation, @"XLSearchTask.toml"), MetaMorpheusTask.tomlConfig);
GlycoSearchTask glyco = new GlycoSearchTask();
Toml.WriteFile(glyco, Path.Combine(folderLocation, @"GlycoSearchTask.toml"), MetaMorpheusTask.tomlConfig);
}
catch (Exception e)
{
throw new MetaMorpheusException("Default tomls could not be written: " + e.Message);
}
}
public static void ExperimentalDesignCalibrationAndSearch(string nonCalibratedFile)
{
// set up output directories
string unitTestFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"ExperimentalDesignCalibrationAndSearch");
string outputFolder = Path.Combine(unitTestFolder, @"TaskOutput");
Directory.CreateDirectory(unitTestFolder);
Directory.CreateDirectory(outputFolder);
// set up original spectra file (input to calibration)
string nonCalibratedFilePath = Path.Combine(unitTestFolder, nonCalibratedFile);
File.Copy(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"), nonCalibratedFilePath, true);
// set up original experimental design (input to calibration)
SpectraFileInfo fileInfo = new SpectraFileInfo(nonCalibratedFilePath, "condition", 0, 0, 0);
var experimentalDesignFilePath = ExperimentalDesign.WriteExperimentalDesignToFile(new List <SpectraFileInfo> {
fileInfo
});
// set up tasks (calibration + search)
CalibrationTask calibrationTask = new CalibrationTask();
SearchTask searchTask = new SearchTask();
// protein db
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
// run the tasks
EverythingRunnerEngine a = new EverythingRunnerEngine(
new List <(string, MetaMorpheusTask)> {
("", calibrationTask), ("", searchTask)
},
public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
{
InitializeComponent();
PopulateChoices();
TheTask = myCalibrateTask;
UpdateFieldsFromTask(TheTask);
}
public CalibrateTaskWindow()
{
InitializeComponent();
PopulateChoices();
TheTask = new CalibrationTask();
UpdateFieldsFromTask(TheTask);
this.saveButton.Content = "Add the Calibration Task";
}
protected void ProcessScanData(ScanData data)
{
if (data != null)
{
IqrFilter task1 = new IqrFilter();
task1.Factor = 0.1f;
ScanData step1 = task1.Run(data);
CalibrationTask task = new CalibrationTask();
task.NumClass = NumClass;
ScanInfo = task.Run(step1);
}
this.PreviewPanel.Invalidate();
}
public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
{
InitializeComponent();
PopulateChoices();
TheTask = myCalibrateTask ?? new CalibrationTask();
UpdateFieldsFromTask(TheTask);
if (myCalibrateTask == null)
{
this.saveButton.Content = "Add the Calibration Task";
}
SearchModifications.Timer.Tick += new EventHandler(TextChangeTimerHandler);
base.Closing += this.OnClosing;
}
public static void ExperimentalDesignCalibrationTest(string originalFileName)
{
CalibrationTask calibrationTask = new CalibrationTask();
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestCalibration");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\" + originalFileName);
File.Copy(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"), myFile, true);
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
string experimentalDesignFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\ExperimentalDesign.tsv");
Directory.CreateDirectory(outputFolder);
using (StreamWriter output = new StreamWriter(experimentalDesignFilePath))
{
output.WriteLine("FileName\tCondition\tBiorep\tFraction\tTechrep");
output.WriteLine(Path.GetFileNameWithoutExtension(myFile) + "\t" + "condition" + "\t" + "1" + "\t" + "1" + "\t" + "1");
}
calibrationTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
myFile
}, "test");
var expDesignPath = Path.Combine(outputFolder, @"ExperimentalDesign.tsv");
var expDesign = File.ReadAllLines(expDesignPath);
string expectedCalibratedFileName = Path.GetFileNameWithoutExtension(myFile) + "-calib.mzML";
string expectedTomlName = Path.GetFileNameWithoutExtension(myFile) + "-calib.toml";
Assert.That(expDesign[1].Contains(Path.GetFileNameWithoutExtension(expectedCalibratedFileName)));
Assert.That(File.Exists(Path.Combine(outputFolder, myFile)));
Assert.That(File.Exists(Path.Combine(outputFolder, expectedTomlName)));
var lines = File.ReadAllLines(Path.Combine(outputFolder, expectedTomlName));
var tolerance = Regex.Match(lines[0], @"\d+\.\d*").Value;
var tolerance1 = Regex.Match(lines[1], @"\d+\.\d*").Value;
Assert.That(double.TryParse(tolerance, out double tol) == true);
Assert.That(double.TryParse(tolerance1, out double tol1) == true);
Assert.That(lines[0].Contains("PrecursorMassTolerance"));
Assert.That(lines[1].Contains("ProductMassTolerance"));
File.Delete(experimentalDesignFilePath);
File.Delete(myFile);
Directory.Delete(outputFolder, true);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
{
InitializeComponent();
TheTask = myCalibrateTask ?? new CalibrationTask();
AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
PopulateChoices();
UpdateFieldsFromTask(TheTask);
AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
if (myCalibrateTask == null)
{
SaveButton.Content = "Add the Calibration Task";
}
SearchModifications.Timer.Tick += new EventHandler(TextChangeTimerHandler);
base.Closing += this.OnClosing;
}
public static void TestEverythingRunner()
{
foreach (var modFile in Directory.GetFiles(@"Mods"))
{
GlobalVariables.AddMods(PtmListLoader.ReadModsFromFile(modFile));
}
CalibrationTask task1 = new CalibrationTask
{
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)),
CalibrationParameters = new CalibrationParameters
{
WriteIntermediateFiles = true,
NumFragmentsNeededForEveryIdentification = 6,
}
};
GptmdTask task2 = new GptmdTask
{
CommonParameters = new CommonParameters()
};
SearchTask task3 = new SearchTask
{
CommonParameters = new CommonParameters(),
SearchParameters = new SearchParameters
{
DoParsimony = true,
SearchTarget = true,
SearchType = SearchType.Modern
}
};
SearchTask task4 = new SearchTask
{
CommonParameters = new CommonParameters(),
SearchParameters = new SearchParameters
{
SearchType = SearchType.Modern,
}
};
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("task1", task1),
("task2", task2),
("task3", task3),
("task4", task4),
};
List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => task1.CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => task1.CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
// Generate data for files
Protein ParentProtein = new Protein("MPEPTIDEKANTHE", "accession1");
var digestedList = ParentProtein.Digest(task1.CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
Assert.AreEqual(3, digestedList.Count);
PeptideWithSetModifications pepWithSetMods1 = digestedList[0];
PeptideWithSetModifications pepWithSetMods2 = digestedList[2];
var dictHere = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
dictHere.Add(3, new List <Modification> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
});
Protein ParentProteinToNotInclude = new Protein("MPEPTIDEK", "accession2", "organism", new List <Tuple <string, string> >(), dictHere);
digestedList = ParentProteinToNotInclude.Digest(task1.CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetMods1, pepWithSetMods2, digestedList[1]
});
Protein proteinWithChain = new Protein("MAACNNNCAA", "accession3", "organism", new List <Tuple <string, string> >(), new Dictionary <int, List <Modification> >(), new List <ProteolysisProduct> {
new ProteolysisProduct(4, 8, "chain")
}, "name2", "fullname2");
string mzmlName = @"ok.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
string xmlName = "okk.xml";
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
ParentProtein, proteinWithChain
}, xmlName);
// RUN!
var engine = new EverythingRunnerEngine(taskList, new List <string> {
mzmlName
}, new List <DbForTask> {
new DbForTask(xmlName, false)
}, Environment.CurrentDirectory);
engine.Run();
}
private void UpdateFieldsFromTask(CalibrationTask task)
{
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
txtMinPeptideLength.Text = task.CommonParameters.DigestionParams.MinPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MinPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
txtMaxPeptideLength.Text = task.CommonParameters.DigestionParams.MaxPeptideLength.HasValue ? task.CommonParameters.DigestionParams.MaxPeptideLength.Value.ToString(CultureInfo.InvariantCulture) : "";
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
bCheckBox.IsChecked = task.CommonParameters.BIons;
yCheckBox.IsChecked = task.CommonParameters.YIons;
//maxDegreesOfParallelism.Text = task.CommonParameters.MaxParallelFilesToAnalyze.ToString();
zdotCheckBox.IsChecked = task.CommonParameters.ZdotIons;
cCheckBox.IsChecked = task.CommonParameters.CIons;
//conserveMemoryCheckBox.IsChecked = task.CommonParameters.ConserveMemory;
//writeIntermediateFilesCheckBox.IsChecked = task.CalibrationParameters.WriteIntermediateFiles;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.DisplayName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
//localizeAllCheckBox.IsChecked = task.CommonParameters.LocalizeAll;
if (task.CommonParameters.LocalizeAll)
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
}
else
{
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
if (task.CommonParameters.ListOfModTypesLocalize.Contains(heh.DisplayName))
{
heh.Use = true;
}
else
{
heh.Use = false;
}
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(CalibrationTask task)
{
ProteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease; //protease needs to come first or recommended settings can overwrite the actual settings
MissedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxModsPerPeptideTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
MaxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
InitiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
MaxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
PrecursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
writeIndexMzmlCheckbox.IsChecked = task.CalibrationParameters.WriteIndexedMzml;
//writeIntermediateFilesCheckBox.IsChecked = task.CalibrationParameters.WriteIntermediateFiles;
MinScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in LocalizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
public static void ExperimentalDesignCalibrationTest(string nonCalibratedFile)
{
// set up directories
string unitTestFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"ExperimentalDesignCalibrationTest");
string outputFolder = Path.Combine(unitTestFolder, @"TaskOutput");
Directory.CreateDirectory(unitTestFolder);
Directory.CreateDirectory(outputFolder);
// set up original spectra file (input to calibration)
string nonCalibratedFilePath = Path.Combine(unitTestFolder, nonCalibratedFile);
File.Copy(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"), nonCalibratedFilePath, true);
// protein db
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
// set up original experimental design (input to calibration)
SpectraFileInfo fileInfo = new SpectraFileInfo(nonCalibratedFilePath, "condition", 0, 0, 0);
var experimentalDesignFilePath = ExperimentalDesign.WriteExperimentalDesignToFile(new List <SpectraFileInfo> {
fileInfo
});
// run calibration
CalibrationTask calibrationTask = new CalibrationTask();
calibrationTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
nonCalibratedFilePath
}, "test");
// test new experimental design written by calibration
var newExpDesignPath = Path.Combine(outputFolder, @"ExperimentalDesign.tsv");
string expectedCalibratedFileName = Path.GetFileNameWithoutExtension(nonCalibratedFilePath) + "-calib.mzML";
var expectedCalibratedFilePath = Path.Combine(outputFolder, expectedCalibratedFileName);
var newExperDesign = ExperimentalDesign.ReadExperimentalDesign(newExpDesignPath, new List <string> {
expectedCalibratedFilePath
}, out var errors);
Assert.That(!errors.Any());
Assert.That(newExperDesign.Count == 1);
// test file-specific toml written by calibration w/ suggested ppm tolerances
string expectedTomlName = Path.GetFileNameWithoutExtension(nonCalibratedFilePath) + "-calib.toml";
Assert.That(File.Exists(Path.Combine(outputFolder, expectedTomlName)));
var lines = File.ReadAllLines(Path.Combine(outputFolder, expectedTomlName));
var tolerance = Regex.Match(lines[0], @"\d+\.\d*").Value;
var tolerance1 = Regex.Match(lines[1], @"\d+\.\d*").Value;
Assert.That(double.TryParse(tolerance, out double tol) == true);
Assert.That(double.TryParse(tolerance1, out double tol1) == true);
Assert.That(lines[0].Contains("PrecursorMassTolerance"));
Assert.That(lines[1].Contains("ProductMassTolerance"));
// check that calibrated .mzML exists
Assert.That(File.Exists(Path.Combine(outputFolder, expectedCalibratedFilePath)));
// clean up
Directory.Delete(unitTestFolder, true);
}
