private void AddAdditionalButton_Click(object sender, RoutedEventArgs e)
{
if (ValidateClick())
{
//save current label
SilacLabel savedLabel = new SilacLabel(AminoAcid, '\0', ChemicalFormula.Text, Convert.ToDouble(MassDifference.Text));
SilacLabelStorageForMultiLabeledConditions = new SilacInfoForDataGrid(savedLabel);
//open a new window to allow for more mods on this condition
var dialog = new SilacModificationWindow();
if (dialog.ShowDialog() == true)
{
char originalAminoAcid = SilacLabelStorageForMultiLabeledConditions.SilacLabel[0].OriginalAminoAcid;
//As you loop throught this, the process looks something like addAdditional->addAdditional->Save (for 3 labels).
//But the saving actually happens as Save->add->add by storing the list of labels in each dialog.SilacLabel
//So you need to search against the dialog.silacLabel instead of the storage, which is only temporarily populated at the end.
if (dialog.SilacLabel.SilacLabel.Any(x => x.OriginalAminoAcid == originalAminoAcid))
{
MessageBox.Show("The amino acid '" + originalAminoAcid.ToString() + "' was labeled multiple times for this condition. Please try again.");
CancelSilacButton_Click(sender, e);
}
else
{
SilacLabelStorageForMultiLabeledConditions.AddAdditionalLabel(dialog.SilacLabel);
SaveSilacLabelsButton_Click(sender, e);
}
}
}
}
private void SaveSilacLabelsButton_Click(object sender, RoutedEventArgs e)
{
if (ValidateClick())
{
SilacLabel = SilacLabelStorageForMultiLabeledConditions ?? //use if labels have been added
new SilacInfoForDataGrid(new SilacLabel(AminoAcid, '\0', ChemicalFormula.Text, Convert.ToDouble(MassDifference.Text)), DetermineExperimentType());
DialogResult = true;
}
}
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();
}
public void AddAdditionalLabel(SilacInfoForDataGrid label)
{
SilacLabel.AddRange(label.SilacLabel);
LabelFormula.AddRange(label.LabelFormula);
AminoAcidLabels += " & " + label.AminoAcidLabels;
}
