private void CheckIfNumber(object sender, TextCompositionEventArgs e)
{
e.Handled = !GlobalGuiSettings.CheckIsNumber(e.Text);
}
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()];
string separationType = SeparationTypeComboBox.SelectedItem.ToString();
DissociationType ms2childDissociationType = DissociationType.Unknown;
if (MS2ChildScanDissociationTypeComboBox.SelectedItem.ToString() != "Null")
{
ms2childDissociationType = GlobalVariables.AllSupportedDissociationTypes[MS2ChildScanDissociationTypeComboBox.SelectedItem.ToString()];
}
DissociationType ms3childDissociationType = DissociationType.Unknown;
if (MS3ChildScanDissociationTypeComboBox.SelectedItem.ToString() != "Null")
{
ms3childDissociationType = GlobalVariables.AllSupportedDissociationTypes[MS3ChildScanDissociationTypeComboBox.SelectedItem.ToString()];
}
CustomFragmentationWindow.Close();
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.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,
separationType: separationType,
ms2childScanDissociationType: ms2childDissociationType,
ms3childScanDissociationType: ms3childDissociationType,
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 SaveButton_Click(object sender, RoutedEventArgs e)
{
CleavageSpecificity searchModeType = CleavageSpecificity.Full; //classic and modern by default
if (semiSpecificSearchRadioButton.IsChecked.Value) //semi
{
searchModeType = CleavageSpecificity.Semi;
}
else if (nonSpecificSearchRadioButton.IsChecked.Value) //non
{
searchModeType = CleavageSpecificity.None;
}
//else it's the default of full
if (searchModeType != CleavageSpecificity.Full)
{
if (((Protease)proteaseComboBox.SelectedItem).Name.Contains("non-specific"))
{
searchModeType = CleavageSpecificity.None; //prevents an accidental semi attempt of a non-specific protease
if (cTerminalIons.IsChecked.Value)
{
Protease singleC = ProteaseDictionary.Dictionary["singleC"];
proteaseComboBox.SelectedItem = singleC;
}
else //we're not allowing no ion types. It must have N if it doesn't have C.
{
Protease singleN = ProteaseDictionary.Dictionary["singleN"];
proteaseComboBox.SelectedItem = singleN;
}
}
if (!addCompIonCheckBox.IsChecked.Value)
{
MessageBox.Show("Warning: Complementary ions are strongly recommended when using this algorithm.");
}
//only use N or C termini, not both
if (cTerminalIons.IsChecked.Value)
{
nTerminalIons.IsChecked = false;
}
else
{
nTerminalIons.IsChecked = true;
}
}
if (!GlobalGuiSettings.CheckTaskSettingsValidity(precursorMassToleranceTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
peakFindingToleranceTextBox.Text, histogramBinWidthTextBox.Text, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text,
MinimumAllowedIntensityRatioToBasePeakTexBox.Text, WindowWidthThomsonsTextBox.Text, NumberOfWindowsTextBox.Text, numberOfDatabaseSearchesTextBox.Text, MaxModNumTextBox.Text, MaxFragmentMassTextBox.Text, QValueTextBox.Text))
{
return;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[dissociationTypeComboBox.SelectedItem.ToString()];
CustomFragmentationWindow.Close();
FragmentationTerminus fragmentationTerminus = FragmentationTerminus.Both;
if (nTerminalIons.IsChecked.Value && !cTerminalIons.IsChecked.Value)
{
fragmentationTerminus = FragmentationTerminus.N;
}
else if (!nTerminalIons.IsChecked.Value && cTerminalIons.IsChecked.Value)
{
fragmentationTerminus = FragmentationTerminus.C;
}
else if (!nTerminalIons.IsChecked.Value && !cTerminalIons.IsChecked.Value) //why would you want this
{
fragmentationTerminus = FragmentationTerminus.None;
MessageBox.Show("Warning: No ion types were selected. MetaMorpheus will be unable to search MS/MS spectra.");
}
//else both
int maxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int minPeptideLengthValue = (int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int maxPeptideLengthValue = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MinVariantDepth = int.Parse(MinVariantDepthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxHeterozygousVariants = int.Parse(MaxHeterozygousVariantsTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxModificationIsoformsValue = (int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture));
int maxModsForPeptideValue = (int.Parse(MaxModNumTextBox.Text, CultureInfo.InvariantCulture));
InitiatorMethionineBehavior initiatorMethionineBehavior = ((InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex);
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: maxMissedCleavages,
minPeptideLength: minPeptideLengthValue,
maxPeptideLength: maxPeptideLengthValue,
maxModificationIsoforms: maxModificationIsoformsValue,
initiatorMethionineBehavior: initiatorMethionineBehavior,
maxModsForPeptides: maxModsForPeptideValue,
searchModeType: searchModeType,
fragmentationTerminus: fragmentationTerminus,
generateUnlabeledProteinsForSilac: CheckBoxQuantifyUnlabeledForSilac.IsChecked.Value);
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 (precursorMassToleranceComboBox.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
TheTask.SearchParameters.MaxFragmentSize = Double.Parse(MaxFragmentMassTextBox.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)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
bool TrimMs1Peaks = trimMs1.IsChecked.Value;
bool TrimMsMsPeaks = trimMsMs.IsChecked.Value;
int?numPeaksToKeep = null;
if (int.TryParse(NumberOfPeaksToKeepPerWindowTextBox.Text, out int numberOfPeaksToKeeep))
{
numPeaksToKeep = numberOfPeaksToKeeep;
}
double?minimumAllowedIntensityRatioToBasePeak = null;
if (double.TryParse(MinimumAllowedIntensityRatioToBasePeakTexBox.Text, out double minimumAllowedIntensityRatio))
{
minimumAllowedIntensityRatioToBasePeak = minimumAllowedIntensityRatio;
}
double?windowWidthThompsons = null;
if (double.TryParse(WindowWidthThomsonsTextBox.Text, out double windowWidth))
{
windowWidthThompsons = windowWidth;
}
int?numberOfWindows = null;
if (int.TryParse(NumberOfWindowsTextBox.Text, out int numWindows))
{
numberOfWindows = numWindows;
}
bool normalizePeaksAccrossAllWindows = normalizePeaksInWindowCheckBox.IsChecked.Value;
bool parseMaxThreadsPerFile = !maxThreadsTextBox.Text.Equals("") && (int.Parse(maxThreadsTextBox.Text) <= Environment.ProcessorCount && int.Parse(maxThreadsTextBox.Text) > 0);
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "SearchTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
useDeltaScore: deltaScoreCheckBox.IsChecked.Value,
reportAllAmbiguity: allAmbiguity.IsChecked.Value,
deconvolutionMaxAssumedChargeState: int.Parse(DeconvolutionMaxAssumedChargeStateTextBox.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
dissociationType: dissociationType,
precursorMassTolerance: PrecursorMassTolerance,
productMassTolerance: ProductMassTolerance,
digestionParams: digestionParamsToSave,
trimMs1Peaks: TrimMs1Peaks,
trimMsMsPeaks: TrimMsMsPeaks,
numberOfPeaksToKeepPerWindow: numPeaksToKeep,
minimumAllowedIntensityRatioToBasePeak: minimumAllowedIntensityRatioToBasePeak,
windowWidthThomsons: windowWidthThompsons,
numberOfWindows: numberOfWindows, //maybe change this some day
normalizePeaksAccrossAllWindows: normalizePeaksAccrossAllWindows, //maybe change this some day
addCompIons: addCompIonCheckBox.IsChecked.Value,
qValueOutputFilter: QValueCheckBox.IsChecked.Value ? double.Parse(QValueTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
minVariantDepth: MinVariantDepth,
maxHeterozygousVariants: MaxHeterozygousVariants);
if (classicSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Classic;
}
else if (modernSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Modern;
}
else //both semi and nonspecific are termed "nonspecific", because they both contain at least one nonspecific cleavage and they share the same algorithm
{
TheTask.SearchParameters.SearchType = SearchType.NonSpecific;
}
TheTask.SearchParameters.DoParsimony = checkBoxParsimony.IsChecked.Value;
TheTask.SearchParameters.NoOneHitWonders = checkBoxNoOneHitWonders.IsChecked.Value;
TheTask.SearchParameters.DoQuantification = !checkBoxNoQuant.IsChecked.Value;
//SilacLabel deconvolution
{
if (StaticSilacLabelsObservableCollection.Count == 0)
{
TheTask.SearchParameters.SilacLabels = null;
}
else
{
List <Proteomics.SilacLabel> labelsToSave = new List <Proteomics.SilacLabel>();
foreach (SilacInfoForDataGrid info in StaticSilacLabelsObservableCollection)
{
Proteomics.SilacLabel labelToAdd = info.SilacLabel[0];
//This is needed to prevent double adding of additional labels.
//A quick test is to create a silac condition with two labels, save, reopen the task, save, and reopen again.
//Without this line, the second label will be doubled (K+8)&(R+10)&(R+10)
if (labelToAdd.AdditionalLabels != null)
{
labelToAdd.AdditionalLabels.Clear();
}
for (int infoIndex = 1; infoIndex < info.SilacLabel.Count; infoIndex++)
{
labelToAdd.AddAdditionalSilacLabel(info.SilacLabel[infoIndex]);
}
labelsToSave.Add(labelToAdd);
}
TheTask.SearchParameters.SilacLabels = labelsToSave;
}
}
TheTask.SearchParameters.Normalize = checkBoxNormalize.IsChecked.Value;
TheTask.SearchParameters.MatchBetweenRuns = checkBoxMatchBetweenRuns.IsChecked.Value;
TheTask.SearchParameters.ModPeptidesAreDifferent = modPepsAreUnique.IsChecked.Value;
TheTask.SearchParameters.QuantifyPpmTol = double.Parse(peakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.SearchTarget = checkBoxTarget.IsChecked.Value;
TheTask.SearchParameters.WriteMzId = ckbMzId.IsChecked.Value;
TheTask.SearchParameters.WriteDecoys = writeDecoyCheckBox.IsChecked.Value;
TheTask.SearchParameters.WriteContaminants = writeContaminantCheckBox.IsChecked.Value;
//TheTask.SearchParameters.OutPepXML = ckbPepXML.IsChecked.Value;
if (checkBoxDecoy.IsChecked.Value)
{
if (radioButtonReverseDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Reverse;
}
else //if (radioButtonSlideDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Slide;
}
}
else
{
TheTask.SearchParameters.DecoyType = DecoyType.None;
}
if (massDiffAcceptExact.IsChecked.HasValue && massDiffAcceptExact.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Exact;
}
if (massDiffAccept1mm.IsChecked.HasValue && massDiffAccept1mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.OneMM;
}
if (massDiffAccept2mm.IsChecked.HasValue && massDiffAccept2mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.TwoMM;
}
if (massDiffAccept3mm.IsChecked.HasValue && massDiffAccept3mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ThreeMM;
}
if (massDiffAccept187.IsChecked.HasValue && massDiffAccept187.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ModOpen;
}
if (massDiffAcceptOpen.IsChecked.HasValue && massDiffAcceptOpen.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Open;
}
if (massDiffAcceptCustom.IsChecked.HasValue && massDiffAcceptCustom.IsChecked.Value)
{
try
{
MassDiffAcceptor customMassDiffAcceptor = SearchTask.GetMassDiffAcceptor(null, MassDiffAcceptorType.Custom, customkMdacTextBox.Text);
}
catch (Exception ex)
{
MessageBox.Show("Could not parse custom mass difference acceptor: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Error);
return;
}
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Custom;
TheTask.SearchParameters.CustomMdac = customkMdacTextBox.Text;
}
//determine if semi or nonspecific with a specific protease.
if (searchModeType == CleavageSpecificity.Semi || protease.CleavageSpecificity == CleavageSpecificity.Semi)
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific, FdrCategory.SemiSpecific
};
}
else if (searchModeType == CleavageSpecificity.None && protease.CleavageSpecificity != CleavageSpecificity.None)
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific, FdrCategory.SemiSpecific, FdrCategory.NonSpecific
};
}
else
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific
};
}
// displays warning if classic search is enabled with an open search mode
if (TheTask.SearchParameters.SearchType == SearchType.Classic &&
(TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen || TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open))
{
MessageBoxResult result = MessageBox.Show("Modern Search mode is recommended when conducting open precursor mass searches to reduce search time.\n\n" +
"Continue anyway?", "Modern search recommended", MessageBoxButton.OKCancel);
if (result == MessageBoxResult.Cancel)
{
return;
}
}
TheTask.SearchParameters.DoHistogramAnalysis = checkBoxHistogramAnalysis.IsChecked.Value;
TheTask.SearchParameters.HistogramBinTolInDaltons = double.Parse(histogramBinWidthTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.WritePrunedDatabase = writePrunedDBCheckBox.IsChecked.Value;
SetModSelectionForPrunedDB();
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
string fieldNotUsed = "1";
if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
MaxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text, MinimumAllowedIntensityRatioToBasePeakTexBox.Text, null, null, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed))
{
return;
}
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 minVariantDepth = int.Parse(MinVariantDepthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxHeterozygousVariants = int.Parse(MaxHeterozygousVariantsTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxModificationIsoforms = int.Parse(MaxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture);
int maxModsPerPeptide = int.Parse(MaxModsPerPeptideTextBox.Text, CultureInfo.InvariantCulture);
InitiatorMethionineBehavior initiatorMethionineBehavior = (InitiatorMethionineBehavior)InitiatorMethionineBehaviorComboBox.SelectedIndex;
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
CustomFragmentationWindow.Close();
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 (PrecursorMassToleranceComboBox.SelectedIndex == 0)
{
precursorMassTolerance = new AbsoluteTolerance(double.Parse(PrecursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
precursorMassTolerance = new PpmTolerance(double.Parse(PrecursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
List <(string, string)> 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)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
bool TrimMs1Peaks = TrimMs1.IsChecked.Value;
bool TrimMsMsPeaks = TrimMsMs.IsChecked.Value;
int?numPeaksToKeep = null;
if (!string.IsNullOrWhiteSpace(NumberOfPeaksToKeepPerWindowTextBox.Text))
{
if (int.TryParse(NumberOfPeaksToKeepPerWindowTextBox.Text, out int numberOfPeaksToKeeep))
{
numPeaksToKeep = numberOfPeaksToKeeep;
}
else
{
MessageBox.Show("The value that you entered for number of peaks to keep is not acceptable. Try again.");
return;
}
}
double?minimumAllowedIntensityRatioToBasePeak = null;
if (!string.IsNullOrWhiteSpace(MinimumAllowedIntensityRatioToBasePeakTexBox.Text))
{
if (double.TryParse(MinimumAllowedIntensityRatioToBasePeakTexBox.Text, out double minimumAllowedIntensityRatio))
{
minimumAllowedIntensityRatioToBasePeak = minimumAllowedIntensityRatio;
}
else
{
MessageBox.Show("The value that you entered for minimum allowed intensity ratio to keep is not acceptable. Try again.");
return;
}
}
List <(string, string)> 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)));
}
bool parseMaxThreadsPerFile = int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) <= Environment.ProcessorCount && int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) > 0;
CommonParameters commonParamsToSave = new CommonParameters(
useProvidedPrecursorInfo: UseProvidedPrecursor.IsChecked.Value,
deconvolutionMaxAssumedChargeState: int.Parse(DeconvolutionMaxAssumedChargeStateTextBox.Text, CultureInfo.InvariantCulture),
doPrecursorDeconvolution: DeconvolutePrecursors.IsChecked.Value,
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "GPTMDTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(MaxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
digestionParams: new DigestionParams(
protease: protease.Name,
maxMissedCleavages: maxMissedCleavages,
minPeptideLength: minPeptideLength,
maxPeptideLength: maxPeptideLength,
maxModificationIsoforms: maxModificationIsoforms,
maxModsForPeptides: maxModsPerPeptide,
initiatorMethionineBehavior: initiatorMethionineBehavior),
dissociationType: dissociationType,
scoreCutoff: double.Parse(MinScoreAllowed.Text, CultureInfo.InvariantCulture),
precursorMassTolerance: precursorMassTolerance,
productMassTolerance: productMassTolerance,
trimMs1Peaks: TrimMs1Peaks,
trimMsMsPeaks: TrimMsMsPeaks,
numberOfPeaksToKeepPerWindow: numPeaksToKeep,
minimumAllowedIntensityRatioToBasePeak: minimumAllowedIntensityRatioToBasePeak,
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
addCompIons: AddCompIonCheckBox.IsChecked.Value,
minVariantDepth: minVariantDepth,
maxHeterozygousVariants: maxHeterozygousVariants);
TheTask.GptmdParameters.ListOfModsGptmd = new List <(string, string)>();
foreach (var heh in gptmdModTypeForTreeViewObservableCollection)
{
TheTask.GptmdParameters.ListOfModsGptmd.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
string fieldNotUsed = "1";
if (!GlobalGuiSettings.CheckTaskSettingsValidity(precursorMassToleranceTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed))
{
return;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
int MaxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, 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 MinVariantDepth = int.Parse(MinVariantDepthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxHeterozygousVariants = int.Parse(MaxHeterozygousVariantsTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxModificationIsoforms = int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture);
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[DissociationTypeComboBox.SelectedItem.ToString()];
CustomFragmentationWindow.Close();
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: MaxMissedCleavages,
minPeptideLength: MinPeptideLength,
maxPeptideLength: MaxPeptideLength,
maxModificationIsoforms: MaxModificationIsoforms);
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)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
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)));
}
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 (precursorMassToleranceComboBox.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
bool parseMaxThreadsPerFile = int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) <= Environment.ProcessorCount && int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) > 0;
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "CalibrateTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
digestionParams: digestionParamsToSave,
dissociationType: dissociationType,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
productMassTolerance: ProductMassTolerance,
precursorMassTolerance: PrecursorMassTolerance,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
minVariantDepth: MinVariantDepth,
maxHeterozygousVariants: MaxHeterozygousVariants);
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
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;
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
if (nonSpecificSearchRadioButton1.IsChecked.Value || semiSpecificSearchRadioButton.IsChecked.Value)
{
if ((bCheckBox.IsChecked.Value || cCheckBox.IsChecked.Value) && (yCheckBox.IsChecked.Value || zdotCheckBox.IsChecked.Value))
{
//MessageBox.Show("Only ion types from a single terminus are allowed for this search algorithm. \ne.g. b- and/or c-ions OR y- and/or zdot-ions. \nC-terminal ions (y and/or zdot) will be chosen by default.");
bCheckBox.IsChecked = false;
cCheckBox.IsChecked = false;
}
if (((Protease)proteaseComboBox.SelectedItem).Name.Contains("non-specific"))
{
proteaseComboBox.SelectedItem = proteaseComboBox.Items.CurrentItem;
if ((bCheckBox.IsChecked.Value || cCheckBox.IsChecked.Value))
{
for (int i = 0; i < proteaseComboBox.Items.Count; i++)
{
if (((Protease)proteaseComboBox.Items[i]).Name.Equals("singleN"))
{
proteaseComboBox.SelectedItem = proteaseComboBox.Items[i];
break;
}
}
}
else
{
for (int i = 0; i < proteaseComboBox.Items.Count; i++)
{
if (((Protease)proteaseComboBox.Items[i]).Name.Equals("singleC"))
{
proteaseComboBox.SelectedItem = proteaseComboBox.Items[i];
break;
}
}
}
}
if (((Protease)proteaseComboBox.SelectedItem).Name.Contains("semi-trypsin"))
{
proteaseComboBox.Items.MoveCurrentToFirst();
proteaseComboBox.SelectedItem = proteaseComboBox.Items.CurrentItem;
while (!((Protease)proteaseComboBox.SelectedItem).Name.Equals("trypsin"))
{
proteaseComboBox.Items.MoveCurrentToNext();
proteaseComboBox.SelectedItem = proteaseComboBox.Items.CurrentItem;
}
}
if (!addCompIonCheckBox.IsChecked.Value)
{
MessageBox.Show("Warning: Complementary ions are strongly recommended when using this algorithm.");
}
}
if (!GlobalGuiSettings.CheckTaskSettingsValidity(precursorMassToleranceTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
peakFindingToleranceTextBox.Text, histogramBinWidthTextBox.Text, DeconvolutionMaxAssumedChargeStateTextBox.Text, TopNPeaksTextBox.Text,
MinRatioTextBox.Text, numberOfDatabaseSearchesTextBox.Text, MaxModNumTextBox.Text, MaxFragmentMassTextBox.Text, QValueTextBox.Text))
{
return;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
bool semiProteaseDigestion = (semiSpecificSearchRadioButton.IsChecked.Value && ((Protease)proteaseComboBox.SelectedItem).CleavageSpecificity != CleavageSpecificity.SingleN && ((Protease)proteaseComboBox.SelectedItem).CleavageSpecificity != CleavageSpecificity.SingleC);
TerminusType terminusTypeSemiProtease = (bCheckBox.IsChecked.Value || cCheckBox.IsChecked.Value ? TerminusType.N : TerminusType.C);
int maxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int minPeptideLengthValue = (int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int maxPeptideLengthValue = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int maxModificationIsoformsValue = (int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture));
int maxModsForPeptideValue = (int.Parse(MaxModNumTextBox.Text, CultureInfo.InvariantCulture));
InitiatorMethionineBehavior initiatorMethionineBehavior = ((InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex);
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
semiProteaseDigestion: semiProteaseDigestion,
terminusTypeSemiProtease: terminusTypeSemiProtease,
maxMissedCleavages: maxMissedCleavages,
minPeptideLength: minPeptideLengthValue,
maxPeptideLength: maxPeptideLengthValue,
maxModificationIsoforms: maxModificationIsoformsValue,
initiatorMethionineBehavior: initiatorMethionineBehavior,
maxModsForPeptides: maxModsForPeptideValue);
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 (precursorMassToleranceComboBox.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
TheTask.SearchParameters.MaxFragmentSize = Double.Parse(MaxFragmentMassTextBox.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)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
bool TrimMs1Peaks = trimMs1.IsChecked.Value;
bool TrimMsMsPeaks = trimMsMs.IsChecked.Value;
int TopNpeaks = int.Parse(TopNPeaksTextBox.Text);
double MinRatio = double.Parse(MinRatioTextBox.Text);
bool parseMaxThreadsPerFile = !maxThreadsTextBox.Text.Equals("") && (int.Parse(maxThreadsTextBox.Text) <= Environment.ProcessorCount && int.Parse(maxThreadsTextBox.Text) > 0);
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "SearchTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
useDeltaScore: deltaScoreCheckBox.IsChecked.Value,
reportAllAmbiguity: allAmbiguity.IsChecked.Value,
deconvolutionMaxAssumedChargeState: int.Parse(DeconvolutionMaxAssumedChargeStateTextBox.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
calculateEValue: eValueCheckBox.IsChecked.Value,
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
bIons: bCheckBox.IsChecked.Value,
yIons: yCheckBox.IsChecked.Value,
cIons: cCheckBox.IsChecked.Value,
zDotIons: zdotCheckBox.IsChecked.Value,
precursorMassTolerance: PrecursorMassTolerance,
productMassTolerance: ProductMassTolerance,
digestionParams: digestionParamsToSave,
trimMs1Peaks: TrimMs1Peaks,
trimMsMsPeaks: TrimMsMsPeaks,
topNpeaks: TopNpeaks,
minRatio: MinRatio,
addCompIons: addCompIonCheckBox.IsChecked.Value,
qValueOutputFilter: QValueCheckBox.IsChecked.Value ? double.Parse(QValueTextBox.Text, CultureInfo.InvariantCulture) : double.PositiveInfinity);
if (classicSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Classic;
}
else if (modernSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Modern;
}
else //if (nonSpecificSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.NonSpecific;
}
TheTask.SearchParameters.DoParsimony = checkBoxParsimony.IsChecked.Value;
TheTask.SearchParameters.NoOneHitWonders = checkBoxNoOneHitWonders.IsChecked.Value;
TheTask.SearchParameters.DoQuantification = checkBoxQuantification.IsChecked.Value;
TheTask.SearchParameters.Normalize = checkBoxNormalize.IsChecked.Value;
TheTask.SearchParameters.MatchBetweenRuns = checkBoxMatchBetweenRuns.IsChecked.Value;
TheTask.SearchParameters.ModPeptidesAreDifferent = modPepsAreUnique.IsChecked.Value;
TheTask.SearchParameters.QuantifyPpmTol = double.Parse(peakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.SearchTarget = checkBoxTarget.IsChecked.Value;
TheTask.SearchParameters.WriteMzId = ckbMzId.IsChecked.Value;
//TheTask.SearchParameters.OutPepXML = ckbPepXML.IsChecked.Value;
if (checkBoxDecoy.IsChecked.Value)
{
if (radioButtonReverseDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Reverse;
}
else //if (radioButtonSlideDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Slide;
}
}
else
{
TheTask.SearchParameters.DecoyType = DecoyType.None;
}
if (massDiffAcceptExact.IsChecked.HasValue && massDiffAcceptExact.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Exact;
}
if (massDiffAccept1mm.IsChecked.HasValue && massDiffAccept1mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.OneMM;
}
if (massDiffAccept2mm.IsChecked.HasValue && massDiffAccept2mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.TwoMM;
}
if (massDiffAccept3mm.IsChecked.HasValue && massDiffAccept3mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ThreeMM;
}
if (massDiffAccept187.IsChecked.HasValue && massDiffAccept187.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ModOpen;
}
if (massDiffAcceptOpen.IsChecked.HasValue && massDiffAcceptOpen.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Open;
}
if (massDiffAcceptCustom.IsChecked.HasValue && massDiffAcceptCustom.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Custom;
TheTask.SearchParameters.CustomMdac = customkMdacTextBox.Text;
}
// displays warning if classic search is enabled with an open search mode
if (TheTask.SearchParameters.SearchType == SearchType.Classic &&
(TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen || TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open))
{
MessageBoxResult result = MessageBox.Show("We recommend using Modern Search mode when conducting open precursor mass searches to reduce search time.\n\n" +
"Continue anyway?", "Modern search recommended", MessageBoxButton.OKCancel);
if (result == MessageBoxResult.Cancel)
{
return;
}
}
TheTask.SearchParameters.DoHistogramAnalysis = checkBoxHistogramAnalysis.IsChecked.Value;
TheTask.SearchParameters.HistogramBinTolInDaltons = double.Parse(histogramBinWidthTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.WritePrunedDatabase = writePrunedDBCheckBox.IsChecked.Value;
SetModSelectionForPrunedDB();
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
// 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;
}
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, numberOfDatabaseSearchesTextBox.Text, fieldNotUsed, fieldNotUsed, fieldNotUsed))
{
return;
}
TheTask.XlSearchParameters.CrosslinkSearchTop = ckbXLTopNum.IsChecked.Value;
TheTask.XlSearchParameters.CrosslinkSearchTopNum = int.Parse(txtXLTopNum.Text, CultureInfo.InvariantCulture);
//TheTask.XlSearchParameters.CrosslinkSearchWithAllBeta = ckbSearchWithXLAllBeta.IsChecked.Value;
TheTask.XlSearchParameters.CrosslinkerType = (CrosslinkerType)cbCrosslinker.SelectedIndex;
//TheTask.XlSearchParameters.FragmentationType = (FragmentaionType)cbFragmentation.SelectedIndex;
if (cbbXLprecusorMsTl.SelectedIndex == 0)
{
TheTask.XlSearchParameters.XlPrecusorMsTl = new AbsoluteTolerance(double.Parse(XLPrecusorMsTlTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
TheTask.XlSearchParameters.XlPrecusorMsTl = new PpmTolerance(double.Parse(XLPrecusorMsTlTextBox.Text, CultureInfo.InvariantCulture));
}
TheTask.XlSearchParameters.XlCharge_2_3 = ckbCharge_2_3.IsChecked.Value;
TheTask.XlSearchParameters.XlCharge_2_3_PrimeFragment = ckbCharge_2_3_PrimeFragments.IsChecked.Value;
TheTask.XlSearchParameters.XlQuench_H2O = ckbQuenchH2O.IsChecked.Value;
TheTask.XlSearchParameters.XlQuench_NH2 = ckbQuenchNH2.IsChecked.Value;
TheTask.XlSearchParameters.XlQuench_Tris = ckbQuenchTris.IsChecked.Value;
if (TheTask.XlSearchParameters.CrosslinkerType == CrosslinkerType.UserDefined)
{
TheTask.XlSearchParameters.UdXLkerName = txtUdXLKerName.Text;
TheTask.XlSearchParameters.UdXLkerCleavable = ckbUdXLkerCleavable.IsChecked.Value;
TheTask.XlSearchParameters.UdXLkerResidues = txtUdXLkerAminoAcids.Text;
TheTask.XlSearchParameters.UdXLkerResidues2 = txtUdXLkerAminoAcids2.Text;
TheTask.XlSearchParameters.UdXLkerLongMass = string.IsNullOrEmpty(txtUdXLkerLongMass.Text) ? (double?)null : double.Parse(txtUdXLkerLongMass.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.UdXLkerShortMass = string.IsNullOrEmpty(txtUdXLkerShortMass.Text) ? (double?)null : double.Parse(txtUdXLkerShortMass.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.UdXLkerTotalMass = string.IsNullOrEmpty(txtUdXLkerTotalMs.Text) ? (double?)null : double.Parse(txtUdXLkerTotalMs.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.UdXLkerLoopMass = string.IsNullOrEmpty(txtUdXLkerLoopMass.Text) ? (double?)null : double.Parse(txtUdXLkerLoopMass.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.UdXLkerDeadendMassH2O = string.IsNullOrEmpty(txtUdXLkerDeadendH2O.Text) ? (double?)null : double.Parse(txtUdXLkerDeadendH2O.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.UdXLkerDeadendMassNH2 = string.IsNullOrEmpty(txtUdXLkerDeadendNH2.Text) ? (double?)null : double.Parse(txtUdXLkerDeadendNH2.Text, CultureInfo.InvariantCulture);
TheTask.XlSearchParameters.UdXLkerDeadendMassTris = string.IsNullOrEmpty(txtUdXLkerDeadendTris.Text) ? (double?)null : double.Parse(txtUdXLkerDeadendTris.Text, CultureInfo.InvariantCulture);
}
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));
}
TheTask.XlSearchParameters.XlOutPercolator = ckbPercolator.IsChecked.Value;
TheTask.XlSearchParameters.XlOutPepXML = ckbPepXML.IsChecked.Value;
TheTask.XlSearchParameters.XlOutAll = ckbAllResults.IsChecked.Value;
TheTask.XlSearchParameters.XlOutCrosslink = ckbCrosslink.IsChecked.Value;
//TheTask.UseProvidedPrecursorInfo = useProvidedPrecursor.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.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 : "XLSearchTask",
productMassTolerance: ProductMassTolerance,
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
digestionParams: digestionParamsToSave,
trimMs1Peaks: trimMs1.IsChecked.Value,
trimMsMsPeaks: trimMsMs.IsChecked.Value,
topNpeaks: int.Parse(TopNPeaksTextBox.Text),
minRatio: double.Parse(MinRatioTextBox.Text),
bIons: bCheckBox.IsChecked.Value,
yIons: yCheckBox.IsChecked.Value,
cIons: cCheckBox.IsChecked.Value,
zDotIons: zdotCheckBox.IsChecked.Value,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
listOfModsVariable: listOfModsVariable,
listOfModsFixed: listOfModsFixed);
TheTask.CommonParameters = commonParamsToSave;
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;
}
