private void SaveButton_Click(object sender, RoutedEventArgs e)
{
#region Check Task Validity
if (!int.TryParse(maxCandidatesPerSpectrumTextBox.Text, out int mcps) || mcps <= 0)
{
MessageBox.Show("The number of maximum candidates per spectra contains unrecognized characters. \n You entered " + '"' + maxCandidatesPerSpectrumTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if (!int.TryParse(maxMissedConsecutiveTextBox.Text, out int mmc) || mmc < 0)
{
MessageBox.Show("The number of maximum missed consecutive cleavages contains unrecognized characters. \n You entered " + '"' + maxMissedConsecutiveTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if (!int.TryParse(maxMissedTextBox.Text, out int mm) || mm <= 0)
{
MessageBox.Show("The number of maximum missed cleavages contains unrecognized characters. \n You entered " + '"' + maxMissedTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if (missedCleavagesTextBox.Text.Length == 0)
{
MessageBox.Show("The number of missed cleavages was left empty. For no missed cleavages, please enter zero.");
return;
}
if ((!double.TryParse(productMassToleranceTextBox.Text, out double pmt) || pmt <= 0) && productMassToleranceTextBox.Text.Length != 0)
{
MessageBox.Show("The product mass tolerance contains unrecognized characters. \n You entered " + '"' + productMassToleranceTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if ((!double.TryParse(precursorMassToleranceTextBox.Text, out double premt) || premt <= 0) && precursorMassToleranceTextBox.Text.Length != 0)
{
MessageBox.Show("The precursor mass tolerance contains unrecognized characters. \n You entered " + '"' + precursorMassToleranceTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
#endregion Check Task Validity
#region Save Parameters
CommonParameters CommonParamsToSave = new CommonParameters();
if (OutputFileNameTextBox.Text != "")
{
CommonParamsToSave.TaskDescriptor = OutputFileNameTextBox.Text;
}
else
{
CommonParamsToSave.TaskDescriptor = "NeoSearchTask";
}
//Code for determining SemiSpecific
NeoParameters neoParameters = new NeoParameters();
neoParameters.Calibrate = calibrate.IsChecked.Value;
neoParameters.GPTMD = gptmd.IsChecked.Value;
neoParameters.TargetSearch = searchTarget.IsChecked.Value;
neoParameters.DecoySearch = searchDecoy.IsChecked.Value;
neoParameters.SearchNTerminus = searchN.IsChecked.Value;
neoParameters.SearchCTerminus = searchC.IsChecked.Value;
neoParameters.MaxMissedConsecutiveCleavages = int.Parse(maxMissedConsecutiveTextBox.Text);
neoParameters.MaxMissedCleavages = int.Parse(maxMissedConsecutiveTextBox.Text);
neoParameters.MaxCandidatesPerSpectrum = int.Parse(maxMissedConsecutiveTextBox.Text);
neoParameters.MinDistanceAllowed = int.Parse(minCisLengthTextBox.Text);
neoParameters.MaxDistanceAllowed = int.Parse(maxCisLengthTextBox.Text);
neoParameters.NormalCis = searchNormalCis.IsChecked.Value;
neoParameters.ReverseCis = searchReverseCis.IsChecked.Value;
if (!searchTarget.IsChecked.Value)
{
neoParameters.TargetFilePath = targetPath.Text;
}
if (!searchDecoy.IsChecked.Value)
{
neoParameters.DecoyFilePath = decoyPath.Text;
}
if (!searchN.IsChecked.Value)
{
neoParameters.NFilePath = NPath.Text;
}
if (!searchC.IsChecked.Value)
{
neoParameters.CFilePath = CPath.Text;
}
DigestionParams digestionParamsToSave = new DigestionParams();
digestionParamsToSave.MaxMissedCleavages = int.Parse(missedCleavagesTextBox.Text, CultureInfo.InvariantCulture);
digestionParamsToSave.MinPeptideLength = int.TryParse(txtMinPeptideLength.Text, NumberStyles.Any, CultureInfo.InvariantCulture, out int temp) ? (int?)temp : null;
digestionParamsToSave.MaxPeptideLength = int.TryParse(txtMaxPeptideLength.Text, NumberStyles.Any, CultureInfo.InvariantCulture, out temp) ? (int?)temp : null;
digestionParamsToSave.Protease = (Protease)proteaseComboBox.SelectedItem;
digestionParamsToSave.MaxModificationIsoforms = int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture);
digestionParamsToSave.MaxModsForPeptide = int.Parse(txtMaxModNum.Text, CultureInfo.InvariantCulture);
digestionParamsToSave.InitiatorMethionineBehavior = (InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex;
CommonParamsToSave.DigestionParams = digestionParamsToSave;
CommonParamsToSave.BIons = bCheckBox.IsChecked.Value;
CommonParamsToSave.YIons = yCheckBox.IsChecked.Value;
CommonParamsToSave.CIons = cCheckBox.IsChecked.Value;
CommonParamsToSave.ZdotIons = zdotCheckBox.IsChecked.Value;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
CommonParamsToSave.ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else if (productMassToleranceTextBox.Text.Length == 0 || precursorMassToleranceTextBox.Text.Length == 0)
{
CommonParamsToSave.ProductMassTolerance = new PpmTolerance(25);
}
else
{
CommonParamsToSave.ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
CommonParamsToSave.PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else if (productMassToleranceTextBox.Text.Length == 0 || precursorMassToleranceTextBox.Text.Length == 0)
{
CommonParamsToSave.PrecursorMassTolerance = new PpmTolerance(15);
}
else
{
CommonParamsToSave.PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in variableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.DisplayName)));
}
CommonParamsToSave.ListOfModsVariable = listOfModsVariable;
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in fixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.DisplayName)));
}
CommonParamsToSave.ListOfModsFixed = listOfModsFixed;
if (localizeAllCheckBox.IsChecked.Value)
{
CommonParamsToSave.ListOfModTypesLocalize = null;
CommonParamsToSave.LocalizeAll = true;
}
else
{
CommonParamsToSave.LocalizeAll = false;
CommonParamsToSave.ListOfModTypesLocalize = localizeModTypeForTreeViewObservableCollection.Where(b => b.Use.HasValue && b.Use.Value).Select(b => b.DisplayName).ToList();
}
TheTask.NeoParameters = neoParameters;
TheTask.CommonParameters = CommonParamsToSave;
#endregion Save Parameters
DialogResult = true;
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
if (!int.TryParse(maxCandidatesPerSpectrumTextBox.Text, out int mcps) || mcps <= 0)
{
MessageBox.Show("The number of maximum candidates per spectra contains unrecognized characters. \n You entered " + '"' + maxCandidatesPerSpectrumTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if (!int.TryParse(maxMissedConsecutiveTextBox.Text, out int mmc) || mmc < 0)
{
MessageBox.Show("The number of maximum missed consecutive cleavages contains unrecognized characters. \n You entered " + '"' + maxMissedConsecutiveTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if (!int.TryParse(maxMissedTextBox.Text, out int mm) || mm <= 0)
{
MessageBox.Show("The number of maximum missed cleavages contains unrecognized characters. \n You entered " + '"' + maxMissedTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if (missedCleavagesTextBox.Text.Length == 0)
{
MessageBox.Show("The number of missed cleavages was left empty. For no missed cleavages, please enter zero.");
return;
}
if ((!double.TryParse(productMassToleranceTextBox.Text, out double pmt) || pmt <= 0) && productMassToleranceTextBox.Text.Length != 0)
{
MessageBox.Show("The product mass tolerance contains unrecognized characters. \n You entered " + '"' + productMassToleranceTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
if ((!double.TryParse(precursorMassToleranceTextBox.Text, out double premt) || premt <= 0) && precursorMassToleranceTextBox.Text.Length != 0)
{
MessageBox.Show("The precursor mass tolerance contains unrecognized characters. \n You entered " + '"' + precursorMassToleranceTextBox.Text + '"' + "\n Please enter a positive number.");
return;
}
//Code for determining SemiSpecific
NeoParameters neoParameters = new NeoParameters
{
Calibrate = calibrate.IsChecked.Value,
GPTMD = gptmd.IsChecked.Value,
TargetSearch = searchTarget.IsChecked.Value,
DecoySearch = searchDecoy.IsChecked.Value,
SearchNTerminus = searchN.IsChecked.Value,
SearchCTerminus = searchC.IsChecked.Value,
MaxMissedConsecutiveCleavages = int.Parse(maxMissedConsecutiveTextBox.Text),
MaxMissedCleavages = int.Parse(maxMissedConsecutiveTextBox.Text),
MaxCandidatesPerSpectrum = int.Parse(maxMissedConsecutiveTextBox.Text),
MinDistanceAllowed = int.Parse(minCisLengthTextBox.Text),
MaxDistanceAllowed = int.Parse(maxCisLengthTextBox.Text),
NormalCis = searchNormalCis.IsChecked.Value,
ReverseCis = searchReverseCis.IsChecked.Value
};
if (!searchTarget.IsChecked.Value)
{
neoParameters.TargetFilePath = targetPath.Text;
}
if (!searchDecoy.IsChecked.Value)
{
neoParameters.DecoyFilePath = decoyPath.Text;
}
if (!searchN.IsChecked.Value)
{
neoParameters.NFilePath = NPath.Text;
}
if (!searchC.IsChecked.Value)
{
neoParameters.CFilePath = CPath.Text;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
int maxMissedCleavages = (int.Parse(missedCleavagesTextBox.Text, CultureInfo.InvariantCulture));
int minPeptideLength = (int.Parse(txtMinPeptideLength.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int maxPeptideLength = (int.Parse(txtMaxPeptideLength.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int maxModificationIsoforms = (int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture));
int maxModsForPeptide = (int.Parse(txtMaxModNum.Text, CultureInfo.InvariantCulture));
InitiatorMethionineBehavior initiatorMethionineBehavior = (InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex;
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: maxMissedCleavages,
minPeptideLength: minPeptideLength,
maxPeptideLength: maxPeptideLength,
maxModificationIsoforms: maxModificationIsoforms,
initiatorMethionineBehavior: initiatorMethionineBehavior,
maxModsForPeptides: maxModsForPeptide);
Tolerance ProductMassTolerance;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else if (productMassToleranceTextBox.Text.Length == 0 || precursorMassToleranceTextBox.Text.Length == 0)
{
ProductMassTolerance = new PpmTolerance(25);
}
else
{
ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance PrecursorMassTolerance;
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else if (productMassToleranceTextBox.Text.Length == 0 || precursorMassToleranceTextBox.Text.Length == 0)
{
PrecursorMassTolerance = new PpmTolerance(15);
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in VariableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.DisplayName)));
}
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in FixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.DisplayName)));
}
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "NeoSearchTask",
digestionParams: digestionParamsToSave,
bIons: bCheckBox.IsChecked.Value,
yIons: yCheckBox.IsChecked.Value,
cIons: cCheckBox.IsChecked.Value,
zDotIons: zdotCheckBox.IsChecked.Value,
productMassTolerance: ProductMassTolerance,
precursorMassTolerance: PrecursorMassTolerance,
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable);
TheTask.NeoParameters = neoParameters;
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
