private void SaveButton_Click(object sender, RoutedEventArgs e)
{
string fieldNotUsed = "1";
if (!GlobalGuiSettings.CheckTaskSettingsValidity(XLPrecusorMsTlTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, fieldNotUsed, fieldNotUsed, fieldNotUsed))
{
return;
}
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
DissociationType childDissociationType = DissociationType.Unknown;
if (ChildScanDissociationTypeComboBox.SelectedItem != null)
{
childDissociationType = GlobalVariables.AllSupportedDissociationTypes[ChildScanDissociationTypeComboBox.SelectedItem.ToString()];
}
CustomFragmentationWindow.Close();
//TheTask.XlSearchParameters.SearchGlyco = RbSearchGlyco.IsChecked.Value;
//TheTask.XlSearchParameters.SearchGlycoWithBgYgIndex = CkbSearchGlycoWithBgYgIndex.IsChecked.Value;
TheTask.XlSearchParameters.RestrictToTopNHits = ckbXLTopNum.IsChecked.Value;
TheTask.XlSearchParameters.CrosslinkSearchTopNum = int.Parse(txtXLTopNum.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.CrosslinkAtCleavageSite = ckbCrosslinkAtCleavageSite.IsChecked.Value;
TheTask.XlSearchParameters.Crosslinker = (Crosslinker)cbCrosslinkers.SelectedItem;
TheTask.XlSearchParameters.XlQuench_H2O = ckbQuenchH2O.IsChecked.Value;
TheTask.XlSearchParameters.XlQuench_NH2 = ckbQuenchNH2.IsChecked.Value;
TheTask.XlSearchParameters.XlQuench_Tris = ckbQuenchTris.IsChecked.Value;
TheTask.XlSearchParameters.DecoyType = checkBoxDecoy.IsChecked.Value ? DecoyType.Reverse : DecoyType.None;
Protease protease = (Protease)proteaseComboBox.SelectedItem;
int MaxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MinPeptideLength = (int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MaxPeptideLength = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MaxModificationIsoforms = (int.Parse(maxModificationIsoformsTextBox.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);
Tolerance ProductMassTolerance;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance PrecursorMassTolerance;
if (cbbXLprecusorMsTl.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(XLPrecusorMsTlTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(XLPrecusorMsTlTextBox.Text, CultureInfo.InvariantCulture));
}
TheTask.XlSearchParameters.WriteOutputForPercolator = ckbPercolator.IsChecked.Value;
TheTask.XlSearchParameters.WritePepXml = ckbPepXML.IsChecked.Value;
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.ModName)));
}
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.ModName)));
}
CommonParameters commonParamsToSave = new CommonParameters(
precursorMassTolerance: PrecursorMassTolerance,
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "XLSearchTask",
productMassTolerance: ProductMassTolerance,
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
digestionParams: digestionParamsToSave,
trimMs1Peaks: trimMs1.IsChecked.Value,
trimMsMsPeaks: trimMsMs.IsChecked.Value,
numberOfPeaksToKeepPerWindow: int.Parse(TopNPeaksTextBox.Text),
minimumAllowedIntensityRatioToBasePeak: double.Parse(MinRatioTextBox.Text, CultureInfo.InvariantCulture),
dissociationType: dissociationType,
childScanDissociationType: childDissociationType,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
listOfModsVariable: listOfModsVariable,
listOfModsFixed: listOfModsFixed,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down");
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
private void CancelButton_Click(object sender, RoutedEventArgs e)
{
DialogResult = false;
CustomFragmentationWindow.Close();
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
string fieldNotUsed = "1";
if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecusorMsTlTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, TopNPeaksTextBox.Text, MinRatioTextBox.Text, null, null, numberOfDatabaseSearchesTextBox.Text, TxtBoxMaxModPerPep.Text, fieldNotUsed, fieldNotUsed))
{
return;
}
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
DissociationType childDissociationType = DissociationType.Unknown;
if (ChildScanDissociationTypeComboBox.SelectedItem.ToString() != "Null")
{
childDissociationType = GlobalVariables.AllSupportedDissociationTypes[ChildScanDissociationTypeComboBox.SelectedItem.ToString()];
}
CustomFragmentationWindow.Close();
if (RbtOGlycoSearch.IsChecked.Value)
{
TheTask._glycoSearchParameters.GlycoSearchType = EngineLayer.GlycoSearch.GlycoSearchType.OGlycanSearch;
}
else if (RbtNGlycoSearch.IsChecked.Value)
{
TheTask._glycoSearchParameters.GlycoSearchType = EngineLayer.GlycoSearch.GlycoSearchType.NGlycanSearch;
}
else if (Rbt_N_O_GlycoSearch.IsChecked.Value)
{
TheTask._glycoSearchParameters.GlycoSearchType = EngineLayer.GlycoSearch.GlycoSearchType.N_O_GlycanSearch;
}
TheTask._glycoSearchParameters.OGlycanDatabasefile = CmbOGlycanDatabase.SelectedItem.ToString();
TheTask._glycoSearchParameters.NGlycanDatabasefile = CmbNGlycanDatabase.SelectedItem.ToString();
TheTask._glycoSearchParameters.GlycoSearchTopNum = int.Parse(txtTopNum.Text, CultureInfo.InvariantCulture);
TheTask._glycoSearchParameters.MaximumOGlycanAllowed = int.Parse(TbMaxOGlycanNum.Text, CultureInfo.InvariantCulture);
TheTask._glycoSearchParameters.OxoniumIonFilt = CkbOxoniumIonFilt.IsChecked.Value;
if (CheckBoxDecoy.IsChecked.Value)
{
if (RadioButtonReverseDecoy.IsChecked.Value)
{
TheTask._glycoSearchParameters.DecoyType = DecoyType.Reverse;
}
else //if (radioButtonSlideDecoy.IsChecked.Value)
{
TheTask._glycoSearchParameters.DecoyType = DecoyType.Slide;
}
}
else
{
TheTask._glycoSearchParameters.DecoyType = DecoyType.None;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
int MaxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MinPeptideLength = (int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MaxPeptideLength = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MaxModificationIsoforms = (int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture));
int MaxModPerPep = (int.Parse(TxtBoxMaxModPerPep.Text, CultureInfo.InvariantCulture));
InitiatorMethionineBehavior InitiatorMethionineBehavior = ((InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex);
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: MaxMissedCleavages,
minPeptideLength: MinPeptideLength,
maxPeptideLength: MaxPeptideLength,
maxModificationIsoforms: MaxModificationIsoforms,
maxModsForPeptides: MaxModPerPep,
initiatorMethionineBehavior: InitiatorMethionineBehavior);
Tolerance ProductMassTolerance;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance PrecursorMassTolerance;
if (cbbPrecusorMsTl.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(PrecusorMsTlTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(PrecusorMsTlTextBox.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.ModName)));
}
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.ModName)));
}
CommonParameters commonParamsToSave = new CommonParameters(
precursorMassTolerance: PrecursorMassTolerance,
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "GlycoSearchTask",
productMassTolerance: ProductMassTolerance,
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
digestionParams: digestionParamsToSave,
trimMs1Peaks: trimMs1.IsChecked.Value,
trimMsMsPeaks: trimMsMs.IsChecked.Value,
numberOfPeaksToKeepPerWindow: int.Parse(TopNPeaksTextBox.Text),
minimumAllowedIntensityRatioToBasePeak: double.Parse(MinRatioTextBox.Text, CultureInfo.InvariantCulture),
dissociationType: dissociationType,
ms2childScanDissociationType: childDissociationType,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
maxThreadsToUsePerFile: int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture),
listOfModsVariable: listOfModsVariable,
listOfModsFixed: listOfModsFixed,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down");
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
