public static void TestFileSpecificParametersClone()
{
var fileSpecificToml = Toml.ReadFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "testFileSpecfic.toml"), MetaMorpheusTask.tomlConfig);
FileSpecificParameters fsp = new FileSpecificParameters(fileSpecificToml);
FileSpecificParameters fspClone = fsp.Clone();
Assert.AreEqual(fsp.DissociationType, fspClone.DissociationType);
Assert.AreEqual(fsp.MaxMissedCleavages, fspClone.MaxMissedCleavages);
Assert.AreEqual(fsp.MaxModsForPeptide, fspClone.MaxModsForPeptide);
Assert.AreEqual(fsp.MaxPeptideLength, fspClone.MaxPeptideLength);
Assert.AreEqual(fsp.MinPeptideLength, fspClone.MinPeptideLength);
Assert.AreEqual(fsp.PrecursorMassTolerance, fspClone.PrecursorMassTolerance);
Assert.AreEqual(fsp.ProductMassTolerance, fspClone.ProductMassTolerance);
Assert.AreEqual(fsp.Protease, fspClone.Protease);
Assert.AreEqual(fsp.SeparationType, fspClone.SeparationType);
}
private void PopulateChoices()
{
// use default settings to populate
var defaultParams = new CommonParameters();
Protease tempProtease = defaultParams.DigestionParams.Protease;
int tempMinPeptideLength = defaultParams.DigestionParams.MinPeptideLength;
int tempMaxPeptideLength = defaultParams.DigestionParams.MaxPeptideLength;
int tempMaxMissedCleavages = defaultParams.DigestionParams.MaxMissedCleavages;
int tempMaxModsForPeptide = defaultParams.DigestionParams.MaxModsForPeptide;
var tempPrecursorMassTolerance = defaultParams.PrecursorMassTolerance;
var tempProductMassTolerance = defaultParams.ProductMassTolerance;
// do any of the selected files already have file-specific parameters specified?
var spectraFiles = SelectedSpectra.Select(p => p.FilePath);
foreach (string file in spectraFiles)
{
string tomlPath = Path.Combine(Directory.GetParent(file).ToString(), Path.GetFileNameWithoutExtension(file)) + ".toml";
if (File.Exists(tomlPath))
{
TomlTable tomlTable = Toml.ReadFile(tomlPath, MetaMorpheusTask.tomlConfig);
FileSpecificParameters fileSpecificParams = new FileSpecificParameters(tomlTable);
if (fileSpecificParams.PrecursorMassTolerance != null)
{
tempPrecursorMassTolerance = fileSpecificParams.PrecursorMassTolerance;
fileSpecificPrecursorMassTolEnabled.IsChecked = true;
}
if (fileSpecificParams.ProductMassTolerance != null)
{
tempProductMassTolerance = fileSpecificParams.ProductMassTolerance;
fileSpecificProductMassTolEnabled.IsChecked = true;
}
if (fileSpecificParams.Protease != null)
{
tempProtease = (fileSpecificParams.Protease);
fileSpecificProteaseEnabled.IsChecked = true;
}
if (fileSpecificParams.MinPeptideLength != null)
{
tempMinPeptideLength = (fileSpecificParams.MinPeptideLength.Value);
fileSpecificMinPeptideLengthEnabled.IsChecked = true;
}
if (fileSpecificParams.MaxPeptideLength != null)
{
tempMaxPeptideLength = (fileSpecificParams.MaxPeptideLength.Value);
fileSpecificMaxPeptideLengthEnabled.IsChecked = true;
}
if (fileSpecificParams.MaxMissedCleavages != null)
{
tempMaxMissedCleavages = (fileSpecificParams.MaxMissedCleavages.Value);
fileSpecificMissedCleavagesEnabled.IsChecked = true;
}
if (fileSpecificParams.MaxModsForPeptide != null)
{
tempMaxModsForPeptide = (fileSpecificParams.MaxMissedCleavages.Value);
fileSpecificMaxModNumEnabled.IsChecked = true;
}
}
}
DigestionParams digestParams = new DigestionParams(
protease: tempProtease.Name,
maxMissedCleavages: tempMaxMissedCleavages,
minPeptideLength: tempMinPeptideLength,
maxPeptideLength: tempMaxPeptideLength,
maxModsForPeptides: tempMaxModsForPeptide);
// populate the GUI
foreach (Protease protease in ProteaseDictionary.Dictionary.Values)
{
fileSpecificProtease.Items.Add(protease);
}
fileSpecificProtease.SelectedItem = digestParams.Protease;
productMassToleranceComboBox.Items.Add("Da");
productMassToleranceComboBox.Items.Add("ppm");
productMassToleranceComboBox.SelectedIndex = 1;
precursorMassToleranceComboBox.Items.Add("Da");
precursorMassToleranceComboBox.Items.Add("ppm");
precursorMassToleranceComboBox.SelectedIndex = 1;
precursorMassToleranceTextBox.Text = tempPrecursorMassTolerance.Value.ToString();
productMassToleranceTextBox.Text = tempProductMassTolerance.Value.ToString();
MinPeptideLengthTextBox.Text = digestParams.MinPeptideLength.ToString();
if (int.MaxValue != digestParams.MaxPeptideLength)
{
MaxPeptideLengthTextBox.Text = digestParams.MaxPeptideLength.ToString();
}
MaxModNumTextBox.Text = digestParams.MaxModsForPeptide.ToString();
if (int.MaxValue != digestParams.MaxMissedCleavages)
{
missedCleavagesTextBox.Text = digestParams.MaxMissedCleavages.ToString();
}
//yCheckBox.IsChecked = tempCommonParams.YIons;
//bCheckBox.IsChecked = tempCommonParams.BIons;
//cCheckBox.IsChecked = tempCommonParams.CIons;
//zdotCheckBox.IsChecked = tempCommonParams.ZdotIons;
}
// write the toml settings file on clicking "save"
private void Save_Click(object sender, RoutedEventArgs e)
{
var parametersToWrite = new FileSpecificParameters();
// parse the file-specific parameters to text
int paramsToSaveCount = 0;
if (fileSpecificPrecursorMassTolEnabled.IsChecked.Value)
{
paramsToSaveCount++;
if (GlobalGuiSettings.CheckPrecursorMassTolerance(precursorMassToleranceTextBox.Text))
{
double value = double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture);
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
parametersToWrite.PrecursorMassTolerance = new AbsoluteTolerance(value);
}
else
{
parametersToWrite.PrecursorMassTolerance = new PpmTolerance(value);
}
}
else
{
return;
}
}
if (fileSpecificProductMassTolEnabled.IsChecked.Value)
{
paramsToSaveCount++;
if (GlobalGuiSettings.CheckProductMassTolerance(productMassToleranceTextBox.Text))
{
double value = double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture);
if (productMassToleranceComboBox.SelectedIndex == 0)
{
parametersToWrite.ProductMassTolerance = new AbsoluteTolerance(value);
}
else
{
parametersToWrite.ProductMassTolerance = new PpmTolerance(value);
}
}
else
{
return;
}
}
if (fileSpecificProteaseEnabled.IsChecked.Value)
{
paramsToSaveCount++;
parametersToWrite.Protease = (Protease)fileSpecificProtease.SelectedItem;
}
if (fileSpecificMinPeptideLengthEnabled.IsChecked.Value)
{
paramsToSaveCount++;
if (int.TryParse(MinPeptideLengthTextBox.Text, out int i) && i > 0)
{
parametersToWrite.MinPeptideLength = i;
}
else
{
MessageBox.Show("The minimum peptide length must be a positive integer");
return;
}
}
if (fileSpecificMaxPeptideLengthEnabled.IsChecked.Value)
{
paramsToSaveCount++;
string lengthMaxPeptide = GlobalGuiSettings.MaxValueConversion(MaxPeptideLengthTextBox.Text);
if (GlobalGuiSettings.CheckPeptideLength(MinPeptideLengthTextBox.Text, lengthMaxPeptide))
{
parametersToWrite.MaxPeptideLength = int.Parse(lengthMaxPeptide);
}
else
{
return;
}
}
if (fileSpecificMissedCleavagesEnabled.IsChecked.Value)
{
paramsToSaveCount++;
string lengthCleavage = GlobalGuiSettings.MaxValueConversion(missedCleavagesTextBox.Text);
if (GlobalGuiSettings.CheckMaxMissedCleavages(lengthCleavage))
{
parametersToWrite.MaxMissedCleavages = int.Parse(lengthCleavage);
}
else
{
return;
}
}
if (fileSpecificMaxModNumEnabled.IsChecked.Value)
{
paramsToSaveCount++;
if (GlobalGuiSettings.CheckMaxModsPerPeptide(MaxModNumTextBox.Text))
{
parametersToWrite.MaxModsForPeptide = int.Parse(MaxModNumTextBox.Text);
}
else
{
return;
}
}
//if (fileSpecificIonTypesEnabled.IsChecked.Value)
//{
// paramsToSaveCount++;
// // don't think there's any way to mess up checkboxes... no error message needed
// parametersToWrite.BIons = bCheckBox.IsChecked;
// parametersToWrite.YIons = yCheckBox.IsChecked;
// parametersToWrite.CIons = cCheckBox.IsChecked;
// parametersToWrite.ZdotIons = zdotCheckBox.IsChecked;
//}
// write parameters to toml files for the selected spectra files
var tomlPathsForSelectedFiles = SelectedSpectra.Select(p => Path.Combine(Directory.GetParent(p.FilePath).ToString(), Path.GetFileNameWithoutExtension(p.FileName)) + ".toml");
foreach (var tomlToWrite in tomlPathsForSelectedFiles)
{
if (paramsToSaveCount > 0)
{
Toml.WriteFile(parametersToWrite, tomlToWrite, MetaMorpheusTask.tomlConfig);
// make sure the settings are able to be parsed...
var tempTomlTable = Toml.ReadFile(tomlToWrite, MetaMorpheusTask.tomlConfig);
FileSpecificParameters tempParams = new FileSpecificParameters(tempTomlTable);
}
else
{
// user has specified that no file-specific settings should be used; delete the file-specific toml if it exists
File.Delete(tomlToWrite);
}
}
// done
DialogResult = true;
}
// write the toml settings file on clicking "save"
private void Save_Click(object sender, RoutedEventArgs e)
{
var parametersToWrite = new FileSpecificParameters();
bool fileSpecificParameterExists = false;
// parse the file-specific parameters to text
if (fileSpecificPrecursorMassTolEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
if (GlobalGuiSettings.CheckPrecursorMassTolerance(precursorMassToleranceTextBox.Text))
{
double value = double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture);
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
parametersToWrite.PrecursorMassTolerance = new AbsoluteTolerance(value);
}
else
{
parametersToWrite.PrecursorMassTolerance = new PpmTolerance(value);
}
}
else
{
return;
}
}
if (fileSpecificProductMassTolEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
if (GlobalGuiSettings.CheckProductMassTolerance(productMassToleranceTextBox.Text))
{
double value = double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture);
if (productMassToleranceComboBox.SelectedIndex == 0)
{
parametersToWrite.ProductMassTolerance = new AbsoluteTolerance(value);
}
else
{
parametersToWrite.ProductMassTolerance = new PpmTolerance(value);
}
}
else
{
return;
}
}
if (fileSpecificProteaseEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
parametersToWrite.Protease = (Protease)fileSpecificProtease.SelectedItem;
}
if (fileSpecificSeparationTypesEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
parametersToWrite.SeparationType = (string)fileSpecificSeparationType.SelectedItem;
}
if (fileSpecificMinPeptideLengthEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
if (int.TryParse(MinPeptideLengthTextBox.Text, out int i) && i > 0)
{
parametersToWrite.MinPeptideLength = i;
}
else
{
MessageBox.Show("The minimum peptide length must be a positive integer");
return;
}
}
if (fileSpecificMaxPeptideLengthEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
string lengthMaxPeptide = GlobalGuiSettings.MaxValueConversion(MaxPeptideLengthTextBox.Text);
if (GlobalGuiSettings.CheckPeptideLength(MinPeptideLengthTextBox.Text, lengthMaxPeptide))
{
parametersToWrite.MaxPeptideLength = int.Parse(lengthMaxPeptide);
}
else
{
return;
}
}
if (fileSpecificMissedCleavagesEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
string lengthCleavage = GlobalGuiSettings.MaxValueConversion(missedCleavagesTextBox.Text);
if (GlobalGuiSettings.CheckMaxMissedCleavages(lengthCleavage))
{
parametersToWrite.MaxMissedCleavages = int.Parse(lengthCleavage);
}
else
{
return;
}
}
if (fileSpecificMaxModNumEnabled.IsChecked.Value)
{
fileSpecificParameterExists = true;
if (GlobalGuiSettings.CheckMaxModsPerPeptide(MaxModNumTextBox.Text))
{
parametersToWrite.MaxModsForPeptide = int.Parse(MaxModNumTextBox.Text);
}
else
{
return;
}
}
//if (fileSpecificIonTypesEnabled.IsChecked.Value)
//{
// paramsToSaveCount++;
// // don't think there's any way to mess up checkboxes... no error message needed
// parametersToWrite.BIons = bCheckBox.IsChecked;
// parametersToWrite.YIons = yCheckBox.IsChecked;
// parametersToWrite.CIons = cCheckBox.IsChecked;
// parametersToWrite.ZdotIons = zdotCheckBox.IsChecked;
//}
// write parameters to toml files for the selected spectra files
foreach (var spectra in SelectedSpectra)
{
string directoryForThisMsFile = Directory.GetParent(spectra.FilePath).ToString();
string filename = Path.GetFileNameWithoutExtension(spectra.FileName) + ".toml";
string tomlToWrite = Path.Combine(directoryForThisMsFile, filename);
//check if a toml file already exists
if (File.Exists(tomlToWrite))
{
//store the previous file-specific tomls (if any) in a folder for reproducibility
AccomodateNewFileSpecificToml(directoryForThisMsFile, filename);
//check that an old toml doesn't already exist. If it does, move it to another nested folder.
}
if (fileSpecificParameterExists)
{
Toml.WriteFile(parametersToWrite, tomlToWrite, MetaMorpheusTask.tomlConfig);
// make sure the settings are able to be parsed...
var tempTomlTable = Toml.ReadFile(tomlToWrite, MetaMorpheusTask.tomlConfig);
FileSpecificParameters tempParams = new FileSpecificParameters(tempTomlTable);
}
else
{
// user has specified that no file-specific settings should be used; delete the file-specific toml if it exists
File.Delete(tomlToWrite);
}
}
// done
DialogResult = true;
}
