private void PopulateSettings()
{
settings = new FlashLfqSettings();
settings.Silent = false;
// basic
ppmToleranceTextBox.Text = settings.PpmTolerance.ToString("F1");
normalizeCheckbox.IsChecked = settings.Normalize;
mbrCheckbox.IsChecked = settings.MatchBetweenRuns;
sharedPeptideCheckbox.IsChecked = settings.UseSharedPeptidesForProteinQuant;
bayesianCheckbox.IsChecked = settings.BayesianProteinQuant;
FoldChangeCutoffManualTextBox.Text = "0.5";
// advanced
integrateCheckBox.IsChecked = settings.Integrate;
precursorIdOnlyCheckbox.IsChecked = settings.IdSpecificChargeState;
isotopePpmToleranceTextBox.Text = settings.IsotopePpmTolerance.ToString("F1");
numIsotopesRequiredTextBox.Text = settings.NumIsotopesRequired.ToString();
mbrRtWindowTextBox.Text = settings.MbrRtWindow.ToString("F1");
mcmcIterationsTextBox.Text = settings.McmcSteps.ToString();
mcmcRandomSeedTextBox.Text = settings.RandomSeed.ToString();
requireMsmsIdInConditionCheckbox.IsChecked = settings.RequireMsmsIdInCondition;
}
private static void Run(FlashLfqSettings settings)
{
try
{
settings.ValidateCommandLineSettings();
}
catch (Exception e)
{
if (!settings.Silent)
{
Console.WriteLine("Error: " + e.Message);
}
return;
}
// check to see if experimental design file exists
string assumedPathToExpDesign = Path.Combine(settings.SpectraFileRepository, "ExperimentalDesign.tsv");
if ((settings.Normalize || settings.BayesianProteinQuant) && !File.Exists(assumedPathToExpDesign))
{
if (!settings.Silent)
{
Console.WriteLine("Could not find experimental design file " +
"(required for normalization and Bayesian statistical analysis): " + assumedPathToExpDesign);
}
return;
}
// set up spectra file info
List <SpectraFileInfo> spectraFileInfos = new List <SpectraFileInfo>();
List <string> filePaths = Directory.GetFiles(settings.SpectraFileRepository)
.Where(f => acceptedSpectrumFileFormats.Contains(Path.GetExtension(f).ToLowerInvariant())).ToList();
// check for duplicate file names (agnostic of file extension)
foreach (var fileName in filePaths.GroupBy(p => Path.GetFileNameWithoutExtension(p)))
{
if (fileName.Count() > 1)
{
var types = fileName.Select(p => Path.GetFileNameWithoutExtension(p)).Distinct();
if (!settings.Silent)
{
Console.WriteLine("Multiple spectra files with the same name were detected (maybe " + string.Join(" and ", types) + "?). " +
"Please remove or rename duplicate files from the spectra file directory.");
}
return;
}
}
if (settings.PrintThermoLicenceViaCommandLine)
{
Console.WriteLine(ThermoRawFileReaderLicence.ThermoLicenceText);
return;
}
// check thermo licence agreement
if (filePaths.Select(v => Path.GetExtension(v).ToLowerInvariant()).Any(f => f == ".raw"))
{
var licenceAgreement = LicenceAgreementSettings.ReadLicenceSettings();
if (!licenceAgreement.HasAcceptedThermoLicence)
{
if (settings.AcceptThermoLicenceViaCommandLine)
{
if (!settings.ReadOnlyFileSystem)
{
licenceAgreement.AcceptLicenceAndWrite();
}
}
else
{
// decided to write this even if it's on silent mode...
Console.WriteLine(ThermoRawFileReaderLicence.ThermoLicenceText);
Console.WriteLine("\nIn order to search Thermo .raw files, you must agree to the above terms. Do you agree to the above terms? y/n\n");
string res = Console.ReadLine();
if (res.ToLowerInvariant() == "y")
{
try
{
if (!settings.ReadOnlyFileSystem)
{
licenceAgreement.AcceptLicenceAndWrite();
}
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
}
else
{
Console.WriteLine("Thermo licence has been declined. Exiting FlashLFQ. You can still search .mzML and .mgf files without agreeing to the Thermo licence.");
return;
}
}
}
}
if (File.Exists(assumedPathToExpDesign))
{
var experimentalDesign = File.ReadAllLines(assumedPathToExpDesign)
.ToDictionary(v => v.Split('\t')[0], v => v);
foreach (var file in filePaths)
{
string filename = Path.GetFileNameWithoutExtension(file);
var expDesignForThisFile = experimentalDesign[filename];
var split = expDesignForThisFile.Split('\t');
string condition = split[1];
int biorep = int.Parse(split[2]);
int fraction = int.Parse(split[3]);
int techrep = int.Parse(split[4]);
// experimental design info passed in here for each spectra file
spectraFileInfos.Add(new SpectraFileInfo(fullFilePathWithExtension: file,
condition: condition,
biorep: biorep - 1,
fraction: fraction - 1,
techrep: techrep - 1));
}
}
else
{
for (int i = 0; i < filePaths.Count; i++)
{
var file = filePaths[i];
spectraFileInfos.Add(new SpectraFileInfo(fullFilePathWithExtension: file,
condition: "Default",
biorep: i,
fraction: 0,
techrep: 0));
}
}
// check the validity of the settings and experimental design
try
{
settings.ValidateSettings(spectraFileInfos);
}
catch (Exception e)
{
if (!settings.Silent)
{
Console.WriteLine("Error: " + e.Message);
}
return;
}
// set up IDs
List <Identification> ids;
try
{
ids = PsmReader.ReadPsms(settings.PsmIdentificationPath, settings.Silent, spectraFileInfos);
}
catch (Exception e)
{
Console.WriteLine("Problem reading PSMs: " + e.Message);
return;
}
if (ids.Any())
{
if (!settings.Silent)
{
Console.WriteLine("Setup is OK; read in " + ids.Count + " identifications; starting FlashLFQ engine");
}
// write FlashLFQ settings to a file
if (!Directory.Exists(settings.OutputPath))
{
Directory.CreateDirectory(settings.OutputPath);
}
Nett.Toml.WriteFile(settings, Path.Combine(settings.OutputPath, "FlashLfqSettings.toml"));
// make engine with desired settings
FlashLfqEngine engine = null;
FlashLfqResults results = null;
try
{
engine = FlashLfqSettings.CreateEngineWithSettings(settings, ids);
// run
results = engine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(filePaths.First()).FullName;
if (settings.OutputPath != null)
{
errorReportPath = settings.OutputPath;
}
if (!settings.Silent)
{
Console.WriteLine("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath);
}
OutputWriter.WriteErrorReport(ex, Directory.GetParent(filePaths.First()).FullName, settings.OutputPath);
}
// output
if (results != null)
{
try
{
OutputWriter.WriteOutput(settings.PsmIdentificationPath, results, settings.Silent, settings.OutputPath);
}
catch (Exception ex)
{
if (!settings.Silent)
{
Console.WriteLine("Could not write FlashLFQ output: " + ex.Message);
}
}
}
}
else
{
if (!settings.Silent)
{
Console.WriteLine("No peptide IDs for the specified spectra files were found! " +
"Check to make sure the spectra file names match between the ID file and the spectra files");
}
}
}
///
/// The purpose of this unit test is to ensure that the settings passed by the user through the command-line or the GUI
/// are passed propertly into the FlashLFQ engine.
///
public static void TestSettingsPassing()
{
// make settings
FlashLfqSettings settings = new FlashLfqSettings();
// set the settings to non-default values
var properties = settings.GetType().GetProperties();
foreach (var property in properties)
{
Type type = property.PropertyType;
if (type == typeof(string))
{
property.SetValue(settings, "TEST_VALUE");
}
else if (type == typeof(bool) || type == typeof(bool?))
{
if (property.GetValue(settings) == null || (bool)property.GetValue(settings) == false)
{
property.SetValue(settings, true);
}
else
{
property.SetValue(settings, false);
}
}
else if (type == typeof(double) || type == typeof(double?))
{
property.SetValue(settings, double.MinValue);
}
else if (type == typeof(int) || type == typeof(int?))
{
property.SetValue(settings, int.MinValue);
}
else
{
Assert.IsTrue(false);
}
}
settings.MaxThreads = 1;
FlashLfqEngine e = FlashLfqSettings.CreateEngineWithSettings(settings, new List <Identification>());
var engineProperties = e.GetType().GetFields();
// check to make sure the settings got passed properly into the engine (the settings should have identical values)
foreach (var property in properties)
{
string name = property.Name;
// skip settings that don't exist in the FlashLFQ engine
// these are usually just command-line options for i/o stuff, etc.
if (name == "PsmIdentificationPath" ||
name == "SpectraFileRepository" ||
name == "OutputPath" ||
name == "ReadOnlyFileSystem" ||
name == "PrintThermoLicenceViaCommandLine" ||
name == "AcceptThermoLicenceViaCommandLine")
{
continue;
}
var engineProperty = engineProperties.First(p => p.Name == name);
var settingsValue = property.GetValue(settings);
var engineValue = engineProperty.GetValue(e);
Assert.AreEqual(settingsValue, engineValue);
}
}
/// <summary>
/// Runs the FlashLFQ engine with the user's defined spectra files, ID files, and FlashLFQ
/// settings.
/// </summary>
private void RunFlashLfq()
{
// read IDs
var ids = new List <Identification>();
try
{
foreach (var identFile in idFiles)
{
ids = ids.Concat(PsmReader.ReadPsms(identFile.FilePath, false, spectraFiles.Select(p => p.SpectraFileInfo).ToList())).ToList();
}
}
catch (Exception e)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(e, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + e.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ could not read the PSM file: " + e.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
if (!ids.Any())
{
MessageBox.Show("No peptide IDs for the specified spectra files were found! " +
"Check to make sure the spectra file names match between the ID file and the spectra files",
"Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// run FlashLFQ engine
try
{
flashLfqEngine = FlashLfqSettings.CreateEngineWithSettings(settings, ids);
results = flashLfqEngine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(ex, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// write output
if (results != null)
{
try
{
OutputWriter.WriteOutput(Directory.GetParent(spectraFiles.First().FilePath).FullName, results, flashLfqEngine.Silent,
outputFolderPath);
}
catch (Exception ex)
{
MessageBox.Show("Could not write FlashLFQ output: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
}
}
/// <summary>
/// Runs the FlashLFQ engine with the user's defined spectra files, ID files, and FlashLFQ
/// settings.
/// </summary>
private void RunFlashLfq()
{
// read IDs
var ids = new List <Identification>();
try
{
foreach (var identFile in idFiles)
{
ids = ids.Concat(PsmReader.ReadPsms(identFile.FilePath, false, spectraFiles.Select(p => p.SpectraFileInfo).ToList())).ToList();
}
}
catch (Exception e)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(e, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + e.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ could not read the PSM file: " + e.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
if (!ids.Any())
{
MessageBox.Show("No peptide IDs for the specified spectra files were found! " +
"Check to make sure the spectra file names match between the ID file and the spectra files",
"Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
if (ids.Any(p => p.Ms2RetentionTimeInMinutes > 500))
{
var res = MessageBox.Show("It seems that some of the retention times in the PSM file(s) are in seconds and not minutes; FlashLFQ requires the RT to be in minutes. " +
"Continue with the FlashLFQ run? (only click yes if the RTs are actually in minutes)",
"Error", MessageBoxButton.YesNo, MessageBoxImage.Hand);
if (res == MessageBoxResult.No)
{
return;
}
}
// run FlashLFQ engine
try
{
flashLfqEngine = FlashLfqSettings.CreateEngineWithSettings(settings, ids);
results = flashLfqEngine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(ex, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// write output
if (results != null)
{
try
{
OutputWriter.WriteOutput(Directory.GetParent(spectraFiles.First().FilePath).FullName, results, flashLfqEngine.Silent,
outputFolderPath);
MessageBox.Show("Run complete");
}
catch (Exception ex)
{
MessageBox.Show("Could not write FlashLFQ output: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
}
}
