private void UpdateFieldsFromTask(GptmdTask task)
{
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
addCompIonCheckBox.IsChecked = task.CommonParameters.AddCompIons;
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = fixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
fixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = variableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
variableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in localizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var mod in task.GptmdParameters.ListOfModsGptmd)
{
var theModType = gptmdModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
gptmdModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in variableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in fixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in gptmdModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(CalibrationTask task)
{
ProteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease; //protease needs to come first or recommended settings can overwrite the actual settings
MissedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxModsPerPeptideTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
MaxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
InitiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
MaxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
PrecursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
writeIndexMzmlCheckbox.IsChecked = task.CalibrationParameters.WriteIndexedMzml;
//writeIntermediateFilesCheckBox.IsChecked = task.CalibrationParameters.WriteIntermediateFiles;
MinScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in LocalizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(XLSearchTask task)
{
//Crosslink search para
//RbSearchCrosslink.IsChecked = !task.XlSearchParameters.SearchGlyco;
//RbSearchGlyco.IsChecked = task.XlSearchParameters.SearchGlyco;
cbCrosslinkers.SelectedItem = task.XlSearchParameters.Crosslinker;
ckbXLTopNum.IsChecked = task.XlSearchParameters.RestrictToTopNHits;
txtXLTopNum.Text = task.XlSearchParameters.CrosslinkSearchTopNum.ToString(CultureInfo.InvariantCulture);
ckbCrosslinkAtCleavageSite.IsChecked = task.XlSearchParameters.CrosslinkAtCleavageSite;
ckbQuenchH2O.IsChecked = task.XlSearchParameters.XlQuench_H2O;
ckbQuenchNH2.IsChecked = task.XlSearchParameters.XlQuench_NH2;
ckbQuenchTris.IsChecked = task.XlSearchParameters.XlQuench_Tris;
cbbXLprecusorMsTl.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
XLPrecusorMsTlTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinRatioTextBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
if (task.CommonParameters.ChildScanDissociationType != DissociationType.Unknown)
{
ChildScanDissociationTypeComboBox.SelectedItem = task.CommonParameters.ChildScanDissociationType.ToString();
}
checkBoxDecoy.IsChecked = task.XlSearchParameters.DecoyType != DecoyType.None;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
ckbPercolator.IsChecked = task.XlSearchParameters.WriteOutputForPercolator;
ckbPepXML.IsChecked = task.XlSearchParameters.WritePepXml;
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(SearchTask task)
{
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.SpecificProtease; //needs to be first, so nonspecific can override if necessary
classicSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Classic;
modernSearchRadioButton.IsChecked = task.SearchParameters.SearchType == SearchType.Modern;
//do these in if statements so as not to trigger the change
if (task.SearchParameters.SearchType == SearchType.NonSpecific && task.CommonParameters.DigestionParams.SearchModeType == CleavageSpecificity.None)
{
nonSpecificSearchRadioButton.IsChecked = true; //when this is changed it overrides the protease
if (task.CommonParameters.DigestionParams.SpecificProtease.Name.Equals("singleC") || task.CommonParameters.DigestionParams.SpecificProtease.Name.Equals("singleN"))
{
Protease nonspecific = ProteaseDictionary.Dictionary["non-specific"];
proteaseComboBox.SelectedItem = nonspecific;
}
else
{
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.SpecificProtease;
}
}
if (task.SearchParameters.SearchType == SearchType.NonSpecific && task.CommonParameters.DigestionParams.SearchModeType != CleavageSpecificity.None)
{
semiSpecificSearchRadioButton.IsChecked = true;
}
checkBoxParsimony.IsChecked = task.SearchParameters.DoParsimony;
checkBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
checkBoxNoQuant.IsChecked = !task.SearchParameters.DoQuantification;
checkBoxLFQ.IsChecked = task.SearchParameters.DoQuantification;
if (task.SearchParameters.SilacLabels != null && task.SearchParameters.SilacLabels.Count != 0)
{
checkBoxSILAC.IsChecked = true;
List <Proteomics.SilacLabel> labels = task.SearchParameters.SilacLabels;
foreach (Proteomics.SilacLabel label in labels)
{
SilacInfoForDataGrid infoToAdd = new SilacInfoForDataGrid(label);
if (label.AdditionalLabels != null)
{
foreach (Proteomics.SilacLabel additionalLabel in label.AdditionalLabels)
{
infoToAdd.AddAdditionalLabel(new SilacInfoForDataGrid(additionalLabel));
}
}
StaticSilacLabelsObservableCollection.Add(infoToAdd);
}
}
CheckBoxQuantifyUnlabeledForSilac.IsChecked = task.CommonParameters.DigestionParams.GeneratehUnlabeledProteinsForSilac;
peakFindingToleranceTextBox.Text = task.SearchParameters.QuantifyPpmTol.ToString(CultureInfo.InvariantCulture);
checkBoxMatchBetweenRuns.IsChecked = task.SearchParameters.MatchBetweenRuns;
checkBoxNormalize.IsChecked = task.SearchParameters.Normalize;
modPepsAreUnique.IsChecked = task.SearchParameters.ModPeptidesAreDifferent;
checkBoxHistogramAnalysis.IsChecked = task.SearchParameters.DoHistogramAnalysis;
histogramBinWidthTextBox.Text = task.SearchParameters.HistogramBinTolInDaltons.ToString(CultureInfo.InvariantCulture);
checkBoxTarget.IsChecked = task.SearchParameters.SearchTarget;
checkBoxDecoy.IsChecked = task.SearchParameters.DecoyType != DecoyType.None;
radioButtonReverseDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Reverse;
radioButtonSlideDecoy.IsChecked = task.SearchParameters.DecoyType == DecoyType.Slide;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxFragmentMassTextBox.Text = task.SearchParameters.MaxFragmentSize.ToString(CultureInfo.InvariantCulture); //put after max peptide length to allow for override of auto
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
MaxModNumTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
dissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
nTerminalIons.IsChecked = task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.Both || task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.N;
cTerminalIons.IsChecked = task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.Both || task.CommonParameters.DigestionParams.FragmentationTerminus == FragmentationTerminus.C;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
precursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
precursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
addCompIonCheckBox.IsChecked = task.CommonParameters.AddCompIons;
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
allAmbiguity.IsChecked = task.CommonParameters.ReportAllAmbiguity;
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
deltaScoreCheckBox.IsChecked = task.CommonParameters.UseDeltaScore;
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
NumberOfPeaksToKeepPerWindowTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinimumAllowedIntensityRatioToBasePeakTexBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
WindowWidthThomsonsTextBox.Text = task.CommonParameters.WindowWidthThomsons == double.MaxValue || !task.CommonParameters.WindowWidthThomsons.HasValue ? "" : task.CommonParameters.WindowWidthThomsons.Value.ToString(CultureInfo.InvariantCulture);
NumberOfWindowsTextBox.Text = task.CommonParameters.NumberOfWindows == int.MaxValue || !task.CommonParameters.NumberOfWindows.HasValue ? "" : task.CommonParameters.NumberOfWindows.Value.ToString(CultureInfo.InvariantCulture);
normalizePeaksInWindowCheckBox.IsChecked = task.CommonParameters.NormalizePeaksAccrossAllWindows;
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
if (task.CommonParameters.QValueOutputFilter < 1)
{
QValueTextBox.Text = task.CommonParameters.QValueOutputFilter.ToString(CultureInfo.InvariantCulture);
QValueCheckBox.IsChecked = true;
}
else
{
QValueTextBox.Text = "0.01";
QValueCheckBox.IsChecked = false;
}
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
ckbMzId.IsChecked = task.SearchParameters.WriteMzId;
writeDecoyCheckBox.IsChecked = task.SearchParameters.WriteDecoys;
writeContaminantCheckBox.IsChecked = task.SearchParameters.WriteContaminants;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in LocalizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
massDiffAcceptExact.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Exact;
massDiffAccept1mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.OneMM;
massDiffAccept2mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.TwoMM;
massDiffAccept3mm.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ThreeMM;
massDiffAccept187.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen;
massDiffAcceptOpen.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open;
massDiffAcceptCustom.IsChecked = task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom;
if (task.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Custom)
{
customkMdacTextBox.Text = task.SearchParameters.CustomMdac;
}
writePrunedDBCheckBox.IsChecked = task.SearchParameters.WritePrunedDatabase;
UpdateModSelectionGrid();
}
private void UpdateFieldsFromTask(GptmdTask task)
{
ProteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease; //protease needs to come first or recommended settings can overwrite the actual settings
UseProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
DeconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
DeconvolutionMaxAssumedChargeStateTextBox.Text = task.CommonParameters.DeconvolutionMaxAssumedChargeState.ToString();
MissedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
MaxModsPerPeptideTextBox.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
InitiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
ProductMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
ProductMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecursorMassToleranceTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
PrecursorMassToleranceComboBox.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
MinScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
MaxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
AddCompIonCheckBox.IsChecked = task.CommonParameters.AddCompIons;
MinVariantDepthTextBox.Text = task.CommonParameters.MinVariantDepth.ToString(CultureInfo.InvariantCulture);
MaxHeterozygousVariantsTextBox.Text = task.CommonParameters.MaxHeterozygousVariants.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
TrimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
TrimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
NumberOfPeaksToKeepPerWindowTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinimumAllowedIntensityRatioToBasePeakTexBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
ModTypeForTreeView theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var heh in LocalizeModTypeForTreeViewObservableCollection)
{
heh.Use = false;
}
foreach (var mod in task.GptmdParameters.ListOfModsGptmd)
{
ModTypeForTreeView theModType = GptmdModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
GptmdModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in GptmdModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
private void UpdateFieldsFromTask(GlycoSearchTask task)
{
RbtOGlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.OGlycanSearch;
RbtNGlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.NGlycanSearch;
Rbt_N_O_GlycoSearch.IsChecked = task._glycoSearchParameters.GlycoSearchType == EngineLayer.GlycoSearch.GlycoSearchType.N_O_GlycanSearch;
TbMaxOGlycanNum.Text = task._glycoSearchParameters.MaximumOGlycanAllowed.ToString(CultureInfo.InvariantCulture);
CkbOxoniumIonFilt.IsChecked = task._glycoSearchParameters.OxoniumIonFilt;
txtTopNum.Text = task._glycoSearchParameters.GlycoSearchTopNum.ToString(CultureInfo.InvariantCulture);
CmbOGlycanDatabase.SelectedItem = task._glycoSearchParameters.OGlycanDatabasefile;
CmbNGlycanDatabase.SelectedItem = task._glycoSearchParameters.NGlycanDatabasefile;
cbbPrecusorMsTl.SelectedIndex = task.CommonParameters.PrecursorMassTolerance is AbsoluteTolerance ? 0 : 1;
PrecusorMsTlTextBox.Text = task.CommonParameters.PrecursorMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
trimMs1.IsChecked = task.CommonParameters.TrimMs1Peaks;
trimMsMs.IsChecked = task.CommonParameters.TrimMsMsPeaks;
TopNPeaksTextBox.Text = task.CommonParameters.NumberOfPeaksToKeepPerWindow == int.MaxValue || !task.CommonParameters.NumberOfPeaksToKeepPerWindow.HasValue ? "" : task.CommonParameters.NumberOfPeaksToKeepPerWindow.Value.ToString(CultureInfo.InvariantCulture);
MinRatioTextBox.Text = task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak == double.MaxValue || !task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.HasValue ? "" : task.CommonParameters.MinimumAllowedIntensityRatioToBasePeak.Value.ToString(CultureInfo.InvariantCulture);
DissociationTypeComboBox.SelectedItem = task.CommonParameters.DissociationType.ToString();
ChildScanDissociationTypeComboBox.SelectedItem = "Null";
if (task.CommonParameters.MS2ChildScanDissociationType != DissociationType.Unknown)
{
ChildScanDissociationTypeComboBox.SelectedItem = task.CommonParameters.MS2ChildScanDissociationType.ToString();
}
CheckBoxDecoy.IsChecked = task._glycoSearchParameters.DecoyType != DecoyType.None;
RadioButtonReverseDecoy.IsChecked = task._glycoSearchParameters.DecoyType == DecoyType.Reverse;
RadioButtonSlideDecoy.IsChecked = task._glycoSearchParameters.DecoyType == DecoyType.Slide;
deconvolutePrecursors.IsChecked = task.CommonParameters.DoPrecursorDeconvolution;
useProvidedPrecursor.IsChecked = task.CommonParameters.UseProvidedPrecursorInfo;
missedCleavagesTextBox.Text = task.CommonParameters.DigestionParams.MaxMissedCleavages.ToString(CultureInfo.InvariantCulture);
MinPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MinPeptideLength.ToString(CultureInfo.InvariantCulture);
MaxPeptideLengthTextBox.Text = task.CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ? "" : task.CommonParameters.DigestionParams.MaxPeptideLength.ToString(CultureInfo.InvariantCulture);
proteaseComboBox.SelectedItem = task.CommonParameters.DigestionParams.Protease;
maxModificationIsoformsTextBox.Text = task.CommonParameters.DigestionParams.MaxModificationIsoforms.ToString(CultureInfo.InvariantCulture);
TxtBoxMaxModPerPep.Text = task.CommonParameters.DigestionParams.MaxModsForPeptide.ToString(CultureInfo.InvariantCulture);
initiatorMethionineBehaviorComboBox.SelectedIndex = (int)task.CommonParameters.DigestionParams.InitiatorMethionineBehavior;
productMassToleranceTextBox.Text = task.CommonParameters.ProductMassTolerance.Value.ToString(CultureInfo.InvariantCulture);
productMassToleranceComboBox.SelectedIndex = task.CommonParameters.ProductMassTolerance is AbsoluteTolerance ? 0 : 1;
minScoreAllowed.Text = task.CommonParameters.ScoreCutoff.ToString(CultureInfo.InvariantCulture);
numberOfDatabaseSearchesTextBox.Text = task.CommonParameters.TotalPartitions.ToString(CultureInfo.InvariantCulture);
maxThreadsTextBox.Text = task.CommonParameters.MaxThreadsToUsePerFile.ToString(CultureInfo.InvariantCulture);
CustomFragmentationWindow = new CustomFragmentationWindow(task.CommonParameters.CustomIons);
OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
foreach (var mod in task.CommonParameters.ListOfModsFixed)
{
var theModType = FixedModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var mod in task.CommonParameters.ListOfModsVariable)
{
var theModType = VariableModTypeForTreeViewObservableCollection.FirstOrDefault(b => b.DisplayName.Equals(mod.Item1));
if (theModType != null)
{
var theMod = theModType.Children.FirstOrDefault(b => b.ModName.Equals(mod.Item2));
if (theMod != null)
{
theMod.Use = true;
}
else
{
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
else
{
theModType = new ModTypeForTreeView(mod.Item1, true);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
theModType.Children.Add(new ModForTreeView("UNKNOWN MODIFICATION!", true, mod.Item2, true, theModType));
}
}
foreach (var ye in VariableModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
foreach (var ye in FixedModTypeForTreeViewObservableCollection)
{
ye.VerifyCheckState();
}
}
