public static bool ValidateAdductListTextBox(MessageBoxHelper helper, TextBox control, bool proteomic,
int minCharge, int maxCharge, out Adduct[] val)
{
val = proteomic ?
ArrayUtil.Parse(control.Text, Adduct.FromStringAssumeProtonated, TextUtil.SEPARATOR_CSV, new Adduct[0]) : // Treat "1" as protonated, proteomic [M+H]
ArrayUtil.Parse(control.Text, Adduct.FromStringAssumeChargeOnly, TextUtil.SEPARATOR_CSV, new Adduct[0]); // Treat "1" as [M+]
if (val.Length > 0 && val.All(adduct => TransitionFilter.IsChargeInRange(adduct, minCharge, maxCharge, proteomic)))
{
return(true);
}
string message;
if (proteomic)
{
message = Resources.TransitionSettingsControl_ValidateAdductListTextBox__0__must_contain_a_comma_separated_list_of_integers_describing_charge_states_between__1__and__2__;
}
else
{
message = Resources
.MessageBoxHelper_ValidateAdductListTextBox__0__must_contain_a_comma_separated_list_of_adducts_or_integers_describing_charge_states_with_absolute_values_from__1__to__2__;
}
helper.ShowTextBoxError(control, message, null, minCharge, maxCharge);
val = new Adduct[0];
return(false);
}
public TransitionSettings GetTransitionSettings(Form parent)
{
var helper = new MessageBoxHelper(parent);
TransitionSettings settings = SkylineWindow.DocumentUI.Settings.TransitionSettings;
// Validate and store filter settings
int[] precursorCharges;
if (!helper.ValidateNumberListTextBox(txtPrecursorCharges, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE, out precursorCharges))
{
return(null);
}
precursorCharges = precursorCharges.Distinct().ToArray();
int[] productCharges;
if (!helper.ValidateNumberListTextBox(txtIonCharges, Transition.MIN_PRODUCT_CHARGE, Transition.MAX_PRODUCT_CHARGE, out productCharges))
{
return(null);
}
productCharges = productCharges.Distinct().ToArray();
IonType[] types = IonTypes;
if (types.Length == 0)
{
helper.ShowTextBoxError(txtIonTypes, Resources.TransitionSettingsUI_OkDialog_Ion_types_must_contain_a_comma_separated_list_of_ion_types_a_b_c_x_y_z_and_p_for_precursor);
return(null);
}
types = types.Distinct().ToArray();
bool exclusionUseDIAWindow = cbExclusionUseDIAWindow.Visible && cbExclusionUseDIAWindow.Checked;
var filter = new TransitionFilter(precursorCharges, productCharges, types, settings.Filter.FragmentRangeFirstName, settings.Filter.FragmentRangeLastName,
settings.Filter.MeasuredIons, settings.Filter.PrecursorMzWindow, exclusionUseDIAWindow, settings.Filter.AutoSelect);
Helpers.AssignIfEquals(ref filter, settings.Filter);
// Validate and store library settings
double ionMatchTolerance;
if (!helper.ValidateDecimalTextBox(txtTolerance, TransitionLibraries.MIN_MATCH_TOLERANCE, TransitionLibraries.MAX_MATCH_TOLERANCE, out ionMatchTolerance))
{
return(null);
}
int ionCount = settings.Libraries.IonCount;
if (!helper.ValidateNumberTextBox(txtIonCount, TransitionLibraries.MIN_ION_COUNT, TransitionLibraries.MAX_ION_COUNT, out ionCount))
{
return(null);
}
TransitionLibraryPick pick = (settings.Libraries.Pick != TransitionLibraryPick.none) ? settings.Libraries.Pick : TransitionLibraryPick.all;
var libraries = new TransitionLibraries(ionMatchTolerance, ionCount, pick);
Helpers.AssignIfEquals(ref libraries, settings.Libraries);
return(new TransitionSettings(settings.Prediction, filter, libraries, settings.Integration, settings.Instrument, settings.FullScan));
}
public TransitionSettingsControl(IModifyDocumentContainer documentContainer)
{
_documentContainer = documentContainer;
InitializeComponent();
foreach (string item in TransitionFilter.GetStartFragmentFinderLabels())
{
comboRangeFrom.Items.Add(item);
}
foreach (string item in TransitionFilter.GetEndFragmentFinderLabels())
{
comboRangeTo.Items.Add(item);
}
SetFields(_documentContainer.Document.Settings.TransitionSettings);
PeptideIonTypes = PeptideIonTypes.Union(new[] { IonType.precursor, IonType.y }).ToArray(); // Add p, y if not already set
InitialPeptideIonTypes = PeptideIonTypes.ToArray();
}
private void Validate()
{
TransitionFilter.ValidateCharges(Resources.TransitionFilter_ProductCharges_Product_ion_charges, new[] { Charge },
Transition.MIN_PRODUCT_CHARGE, Transition.MAX_PRODUCT_CHARGE);
if (IsFragment)
{
if (string.IsNullOrEmpty(Fragment))
{
throw new InvalidDataException(Resources.MeasuredIon_Validate_Special_fragment_ions_must_have_at_least_one_fragmentation_residue);
}
AminoAcid.ValidateAAList(Fragment);
if (!string.IsNullOrEmpty(Restrict))
{
AminoAcid.ValidateAAList(Restrict);
}
if (!Terminus.HasValue)
{
throw new InvalidDataException(Resources.MeasuredIon_Validate_Special_fragment_ions_must_specify_the_terminal_side_of_the_amino_acid_residue_on_which_fragmentation_occurs);
}
if (MIN_MIN_FRAGMENT_LENGTH > MinFragmentLength || MinFragmentLength > MAX_MIN_FRAGMENT_LENGTH)
{
throw new InvalidDataException(string.Format(Resources.MeasuredIon_Validate_The_minimum_length__0__must_be_between__1__and__2__,
MinFragmentLength, MIN_MIN_FRAGMENT_LENGTH, MAX_MIN_FRAGMENT_LENGTH));
}
}
else
{
if (SettingsCustomIon.MonoisotopicMass == 0 || SettingsCustomIon.AverageMass == 0)
{
throw new InvalidDataException(Resources.MeasuredIon_Validate_Reporter_ions_must_specify_a_formula_or_valid_monoisotopic_and_average_masses);
}
if (SettingsCustomIon.MonoisotopicMass < MIN_REPORTER_MASS || SettingsCustomIon.AverageMass < MIN_REPORTER_MASS)
{
throw new InvalidDataException(string.Format(Resources.MeasuredIon_Validate_Reporter_ion_masses_must_be_greater_than_or_equal_to__0__, MIN_REPORTER_MASS));
}
if (SettingsCustomIon.MonoisotopicMass > MAX_REPORTER_MASS || SettingsCustomIon.AverageMass > MAX_REPORTER_MASS)
{
throw new InvalidDataException(string.Format(Resources.MeasuredIon_Validate_Reporter_ion_masses_must_be_less_than_or_equal_to__0__, MAX_REPORTER_MASS));
}
}
}
private void comboRangeTo_SelectedIndexChanged(object sender, EventArgs e)
{
// If nothing is checked yet, start with what is in the settings
if (!radioAll.Checked && !radioAllAndFiltered.Checked && !radioFiltered.Checked)
{
switch (Libraries.Pick)
{
case TransitionLibraryPick.all:
radioAll.Checked = true;
break;
case TransitionLibraryPick.all_plus:
radioAllAndFiltered.Checked = true;
break;
default:
radioFiltered.Checked = true;
break;
}
}
string fragmentRangeLastLabel = comboRangeTo.SelectedItem.ToString();
string fragmentRangeLastName = TransitionFilter.GetEndFragmentNameFromLabel(fragmentRangeLastLabel);
var countFinder = TransitionFilter.GetEndFragmentFinder(fragmentRangeLastName) as IEndCountFragmentFinder;
if (countFinder != null)
{
textIonCount.Text = countFinder.Count.ToString(LocalizationHelper.CurrentCulture);
if (!radioAllAndFiltered.Checked)
{
radioAll.Checked = true;
}
radioFiltered.Enabled = false;
}
else
{
textIonCount.Text = Libraries.IonCount.ToString(LocalizationHelper.CurrentCulture);
radioFiltered.Enabled = true;
}
}
public TransitionSettings GetTransitionSettings(Form parent)
{
var helper = new MessageBoxHelper(parent);
TransitionSettings settings = _documentContainer.Document.Settings.TransitionSettings;
// Validate and store filter settings
Adduct[] peptidePrecursorCharges;
if (!ValidateAdductListTextBox(helper, txtPeptidePrecursorCharges, true, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE, out peptidePrecursorCharges))
{
return(null);
}
peptidePrecursorCharges = peptidePrecursorCharges.Distinct().ToArray();
Adduct[] peptideProductCharges;
if (!ValidateAdductListTextBox(helper, txtPrecursorIonCharges, true, Transition.MIN_PRODUCT_CHARGE, Transition.MAX_PRODUCT_CHARGE, out peptideProductCharges))
{
return(null);
}
peptideProductCharges = peptideProductCharges.Distinct().ToArray();
IonType[] peptideIonTypes = PeptideIonTypes;
if (peptideIonTypes.Length == 0)
{
helper.ShowTextBoxError(txtIonTypes, Resources.TransitionSettingsUI_OkDialog_Ion_types_must_contain_a_comma_separated_list_of_ion_types_a_b_c_x_y_z_and_p_for_precursor);
return(null);
}
peptideIonTypes = peptideIonTypes.Distinct().ToArray();
bool exclusionUseDIAWindow = cbExclusionUseDIAWindow.Visible && cbExclusionUseDIAWindow.Checked;
var filter = new TransitionFilter(peptidePrecursorCharges, peptideProductCharges, peptideIonTypes,
settings.Filter.SmallMoleculePrecursorAdducts, settings.Filter.SmallMoleculeFragmentAdducts, settings.Filter.SmallMoleculeIonTypes,
settings.Filter.FragmentRangeFirstName, settings.Filter.FragmentRangeLastName,
settings.Filter.MeasuredIons, settings.Filter.PrecursorMzWindow, exclusionUseDIAWindow, settings.Filter.AutoSelect);
Helpers.AssignIfEquals(ref filter, settings.Filter);
// Validate and store library settings
double ionMatchTolerance;
if (!helper.ValidateDecimalTextBox(txtTolerance, TransitionLibraries.MIN_MATCH_TOLERANCE, TransitionLibraries.MAX_MATCH_TOLERANCE, out ionMatchTolerance))
{
return(null);
}
int minIonCount = settings.Libraries.MinIonCount;
if (string.IsNullOrEmpty(txtMinIonCount.Text))
{
minIonCount = 0;
}
else if (!helper.ValidateNumberTextBox(txtMinIonCount, 0, TransitionLibraries.MAX_ION_COUNT, out minIonCount))
{
return(null);
}
int ionCount = settings.Libraries.IonCount;
if (!helper.ValidateNumberTextBox(txtIonCount, TransitionLibraries.MIN_ION_COUNT, TransitionLibraries.MAX_ION_COUNT, out ionCount))
{
return(null);
}
if (minIonCount > ionCount)
{
helper.ShowTextBoxError(txtIonCount, string.Format(Resources.TransitionLibraries_DoValidate_Library_ion_count_value__0__must_not_be_less_than_min_ion_count_value__1__,
ionCount, minIonCount));
return(null);
}
TransitionLibraryPick pick = settings.Libraries.Pick != TransitionLibraryPick.none ? settings.Libraries.Pick : TransitionLibraryPick.all;
var libraries = new TransitionLibraries(ionMatchTolerance, minIonCount, ionCount, pick);
Helpers.AssignIfEquals(ref libraries, settings.Libraries);
return(new TransitionSettings(settings.Prediction, filter, libraries, settings.Integration, settings.Instrument, settings.FullScan));
}
private bool UpdateFullScanSettings()
{
var helper = new MessageBoxHelper(this);
// Validate and store MS1 full-scan settings
// If high resolution MS1 filtering is enabled, make sure precursor m/z type
// is monoisotopic and isotope enrichments are set
var precursorIsotopes = FullScanSettingsControl.PrecursorIsotopesCurrent;
var precursorAnalyzerType = FullScanSettingsControl.PrecursorMassAnalyzer;
var precursorMassType = TransitionSettings.Prediction.PrecursorMassType;
if (precursorIsotopes == FullScanPrecursorIsotopes.None)
{
if (WorkflowType != Workflow.dia)
{
MessageDlg.Show(this, Resources.ImportPeptideSearchDlg_UpdateFullScanSettings_Full_scan_MS1_filtering_must_be_enabled_in_order_to_import_a_peptide_search_);
return(false);
}
else if (FullScanSettingsControl.AcquisitionMethod == FullScanAcquisitionMethod.None)
{
MessageDlg.Show(this, Resources.ImportPeptideSearchDlg_UpdateFullScanSettings_Full_scan_MS1_or_MS_MS_filtering_must_be_enabled_in_order_to_import_a_peptide_search_);
return(false);
}
}
else if (precursorAnalyzerType != FullScanMassAnalyzerType.qit)
{
precursorMassType = MassType.Monoisotopic;
if (FullScanSettingsControl.Enrichments == null)
{
MessageDlg.Show(GetParentForm(this), Resources.TransitionSettingsUI_OkDialog_Isotope_enrichment_settings_are_required_for_MS1_filtering_on_high_resolution_mass_spectrometers);
return(false);
}
}
if (FullScanSettingsControl.IsolationScheme == null && FullScanSettingsControl.AcquisitionMethod == FullScanAcquisitionMethod.DIA)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_An_isolation_scheme_is_required_to_match_multiple_precursors);
return(false);
}
TransitionFilter filter = TransitionSettings.Filter;
if (FullScanSettingsControl.PrecursorChargesTextBox.Visible)
{
Adduct[] precursorCharges;
if (!TransitionSettingsControl.ValidateAdductListTextBox(helper, FullScanSettingsControl.PrecursorChargesTextBox, true, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE, out precursorCharges))
{
return(false);
}
precursorCharges = precursorCharges.Distinct().ToArray();
FullScanSettingsControl.PrecursorChargesString = TransitionFilter.AdductListToString(precursorCharges);
filter = TransitionSettings.Filter.ChangePeptidePrecursorCharges(precursorCharges);
}
if (WorkflowType == Workflow.dda && !filter.PeptideIonTypes.Contains(IonType.precursor))
{
filter = filter.ChangePeptideIonTypes(new[] { IonType.precursor });
}
if (!filter.AutoSelect)
{
filter = filter.ChangeAutoSelect(true);
}
Helpers.AssignIfEquals(ref filter, TransitionSettings.Filter);
if (FullScanSettingsControl.IsDIA() && filter.ExclusionUseDIAWindow)
{
if (FullScanSettingsControl.IsolationScheme.IsAllIons)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precusor_exclusion_when__All_Ions__is_selected_as_the_isolation_scheme___To_use_the_DIA_window_for_precusor_exclusion__change_the_isolation_scheme_in_the_Full_Scan_settings_);
return(false);
}
if (FullScanSettingsControl.IsolationScheme.FromResults)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precursor_exclusion_when_isolation_scheme_does_not_contain_prespecified_windows___Please_select_an_isolation_scheme_with_prespecified_windows_);
return(false);
}
}
TransitionFullScan fullScan;
if (!FullScanSettingsControl.ValidateFullScanSettings(helper, out fullScan))
{
return(false);
}
Helpers.AssignIfEquals(ref fullScan, TransitionSettings.FullScan);
var prediction = TransitionSettings.Prediction.ChangePrecursorMassType(precursorMassType);
Helpers.AssignIfEquals(ref prediction, TransitionSettings.Prediction);
TransitionSettings settings;
try
{
settings = new TransitionSettings(prediction, filter,
TransitionSettings.Libraries, TransitionSettings.Integration, TransitionSettings.Instrument, fullScan);
}
catch (Exception x)
{
MessageDlg.Show(this, x.Message);
return(false);
}
// Did user change the "use spectral libary ion mobility" values?
PeptidePrediction updatedPeptidePrediction;
bool peptidePredictionChanged = false;
try
{
updatedPeptidePrediction =
FullScanSettingsControl.UseSpectralLibraryIonMobilityValuesControl.ValidateNewSettings(true);
if (updatedPeptidePrediction == null)
{
return(false);
}
peptidePredictionChanged = !Equals(Document.Settings.PeptideSettings.Prediction, updatedPeptidePrediction);
}
catch (Exception)
{
return(false);
}
// Only update, if anything changed
if (Equals(settings, TransitionSettings) && !peptidePredictionChanged)
{
return(true);
}
ModifyDocumentNoUndo(doc => doc.ChangeSettings(doc.Settings.ChangeTransitionSettings(settings).ChangePeptideSettings(doc.Settings.PeptideSettings.ChangePrediction(updatedPeptidePrediction))));
_fullScanSettingsChanged = true;
return(true);
}
public TransitionSettingsUI(SkylineWindow parent)
{
InitializeComponent();
// Populate the fragment finder combo boxes
foreach (string item in TransitionFilter.GetStartFragmentFinderLabels())
{
comboRangeFrom.Items.Add(item);
}
foreach (string item in TransitionFilter.GetEndFragmentFinderLabels())
{
comboRangeTo.Items.Add(item);
}
_parent = parent;
_transitionSettings = _parent.DocumentUI.Settings.TransitionSettings;
// Initialize prediction settings
comboPrecursorMass.SelectedItem = Prediction.PrecursorMassType.GetLocalizedString();
comboIonMass.SelectedItem = Prediction.FragmentMassType.GetLocalizedString();
_driverCE = new SettingsListComboDriver <CollisionEnergyRegression>(comboCollisionEnergy,
Settings.Default.CollisionEnergyList);
string sel = (Prediction.CollisionEnergy == null ? null : Prediction.CollisionEnergy.Name);
_driverCE.LoadList(sel);
_driverDP = new SettingsListComboDriver <DeclusteringPotentialRegression>(comboDeclusterPotential,
Settings.Default.DeclusterPotentialList);
sel = (Prediction.DeclusteringPotential == null ? null : Prediction.DeclusteringPotential.Name);
_driverDP.LoadList(sel);
_driverCoV = new SettingsListComboDriver <CompensationVoltageParameters>(comboCompensationVoltage,
Settings.Default.CompensationVoltageList);
_driverCoV.LoadList(Prediction.CompensationVoltage == null ? null : Prediction.CompensationVoltage.Name);
_driverOptimizationLibrary = new SettingsListComboDriver <OptimizationLibrary>(comboOptimizationLibrary,
Settings.Default.OptimizationLibraryList);
_driverOptimizationLibrary.LoadList(Prediction.OptimizedLibrary == null ? null : Prediction.OptimizedLibrary.Name);
if (Prediction.OptimizedMethodType == OptimizedMethodType.None)
{
comboOptimizeType.SelectedIndex = 0;
}
else
{
cbUseOptimized.Checked = true;
comboOptimizeType.SelectedItem = Prediction.OptimizedMethodType.GetLocalizedString();
}
// Initialize filter settings
textPrecursorCharges.Text = Filter.PrecursorCharges.ToArray().ToString(", "); // Not L10N? Internationalization of comma?
textIonCharges.Text = Filter.ProductCharges.ToArray().ToString(", "); // Not L10N? Internationalization of comma?
textIonTypes.Text = TransitionFilter.ToStringIonTypes(Filter.IonTypes, true);
comboRangeFrom.SelectedItem = Filter.FragmentRangeFirst.Label;
comboRangeTo.SelectedItem = Filter.FragmentRangeLast.Label;
textExclusionWindow.Text = Filter.PrecursorMzWindow != 0
? Filter.PrecursorMzWindow.ToString(LocalizationHelper.CurrentCulture)
: string.Empty;
cbExclusionUseDIAWindow.Checked = Filter.ExclusionUseDIAWindow;
cbAutoSelect.Checked = Filter.AutoSelect;
_driverIons = new MeasuredIonListBoxDriver(listAlwaysAdd, Settings.Default.MeasuredIonList);
_driverIons.LoadList(Filter.MeasuredIons);
// Initialize library settings
cbLibraryPick.Checked = (Libraries.Pick != TransitionLibraryPick.none);
panelPick.Visible = cbLibraryPick.Checked;
textTolerance.Text = Libraries.IonMatchTolerance.ToString(LocalizationHelper.CurrentCulture);
textIonCount.Text = Libraries.IonCount.ToString(LocalizationHelper.CurrentCulture);
if (Libraries.Pick == TransitionLibraryPick.filter)
{
radioFiltered.Checked = true;
}
else if (Libraries.Pick == TransitionLibraryPick.all_plus)
{
radioAllAndFiltered.Checked = true;
}
// Initialize instrument settings
textMinMz.Text = Instrument.MinMz.ToString(LocalizationHelper.CurrentCulture);
textMaxMz.Text = Instrument.MaxMz.ToString(LocalizationHelper.CurrentCulture);
cbDynamicMinimum.Checked = Instrument.IsDynamicMin;
textMzMatchTolerance.Text = Instrument.MzMatchTolerance.ToString(LocalizationHelper.CurrentCulture);
if (Instrument.MaxTransitions.HasValue)
{
textMaxTrans.Text = Instrument.MaxTransitions.Value.ToString(LocalizationHelper.CurrentCulture);
}
if (Instrument.MaxInclusions.HasValue)
{
textMaxInclusions.Text = Instrument.MaxInclusions.Value.ToString(LocalizationHelper.CurrentCulture);
}
if (Instrument.MinTime.HasValue)
{
textMinTime.Text = Instrument.MinTime.Value.ToString(LocalizationHelper.CurrentCulture);
}
if (Instrument.MaxTime.HasValue)
{
textMaxTime.Text = Instrument.MaxTime.Value.ToString(LocalizationHelper.CurrentCulture);
}
// Initialize full-scan settings
FullScanSettingsControl = new FullScanSettingsControl(_parent)
{
Anchor = (AnchorStyles.Top | AnchorStyles.Left),
Location = new Point(0, 0),
Size = new Size(363, 491)
};
FullScanSettingsControl.IsolationSchemeChangedEvent += IsolationSchemeChanged;
tabFullScan.Controls.Add(FullScanSettingsControl);
// VISUAL:
// - Store the distance between the cbExclusionDIAWindow and the lower end of the box (to use as margin later)
// - Shift the cbExclusionDIAWindow down (it is only higher in the designer for better manipulation)
_lower_margin = groupBox1.Height - textExclusionWindow.Location.Y - textExclusionWindow.Height;
int pixelShift = cbExclusionUseDIAWindow.Location.Y - lbPrecursorMzWindow.Location.Y;
cbExclusionUseDIAWindow.Location = new Point(cbExclusionUseDIAWindow.Location.X, cbExclusionUseDIAWindow.Location.Y - pixelShift);
DoIsolationSchemeChanged();
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
// Validate and store prediction settings
string massType = comboPrecursorMass.SelectedItem.ToString();
MassType precursorMassType = MassTypeExtension.GetEnum(massType);
massType = comboIonMass.SelectedItem.ToString();
MassType fragmentMassType = MassTypeExtension.GetEnum(massType);
string nameCE = comboCollisionEnergy.SelectedItem.ToString();
CollisionEnergyRegression collisionEnergy =
Settings.Default.GetCollisionEnergyByName(nameCE);
string nameDP = comboDeclusterPotential.SelectedItem.ToString();
DeclusteringPotentialRegression declusteringPotential =
Settings.Default.GetDeclusterPotentialByName(nameDP);
string nameCoV = comboCompensationVoltage.SelectedItem.ToString();
CompensationVoltageParameters compensationVoltage =
Settings.Default.GetCompensationVoltageByName(nameCoV);
string nameOptLib = comboOptimizationLibrary.SelectedItem.ToString();
OptimizationLibrary optimizationLibrary =
Settings.Default.GetOptimizationLibraryByName(nameOptLib);
OptimizedMethodType optimizedMethodType = OptimizedMethodType.None;
if (cbUseOptimized.Checked)
{
optimizedMethodType = OptimizedMethodTypeExtension.GetEnum(comboOptimizeType.SelectedItem.ToString());
}
TransitionPrediction prediction = new TransitionPrediction(precursorMassType,
fragmentMassType, collisionEnergy,
declusteringPotential,
compensationVoltage,
optimizationLibrary,
optimizedMethodType);
Helpers.AssignIfEquals(ref prediction, Prediction);
// Validate and store filter settings
int[] precursorCharges;
int min = TransitionGroup.MIN_PRECURSOR_CHARGE;
int max = TransitionGroup.MAX_PRECURSOR_CHARGE;
if (!helper.ValidateNumberListTextBox(tabControl1, (int)TABS.Filter, textPrecursorCharges,
min, max, out precursorCharges))
{
return;
}
precursorCharges = precursorCharges.Distinct().ToArray();
int[] productCharges;
min = Transition.MIN_PRODUCT_CHARGE;
max = Transition.MAX_PRODUCT_CHARGE;
if (!helper.ValidateNumberListTextBox(tabControl1, (int)TABS.Filter, textIonCharges,
min, max, out productCharges))
{
return;
}
productCharges = productCharges.Distinct().ToArray();
IonType[] types = TransitionFilter.ParseTypes(textIonTypes.Text, new IonType[0]);
if (types.Length == 0)
{
helper.ShowTextBoxError(tabControl1, (int)TABS.Filter, textIonTypes,
Resources.TransitionSettingsUI_OkDialog_Ion_types_must_contain_a_comma_separated_list_of_ion_types_a_b_c_x_y_z_and_p_for_precursor);
return;
}
types = types.Distinct().ToArray();
double exclusionWindow = 0;
if (!string.IsNullOrEmpty(textExclusionWindow.Text) &&
!Equals(textExclusionWindow.Text, exclusionWindow.ToString(LocalizationHelper.CurrentCulture)))
{
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Filter, textExclusionWindow,
TransitionFilter.MIN_EXCLUSION_WINDOW, TransitionFilter.MAX_EXCLUSION_WINDOW, out exclusionWindow))
{
return;
}
}
string fragmentRangeFirst = TransitionFilter.GetStartFragmentNameFromLabel(comboRangeFrom.SelectedItem.ToString());
string fragmentRangeLast = TransitionFilter.GetEndFragmentNameFromLabel(comboRangeTo.SelectedItem.ToString());
var measuredIons = _driverIons.Chosen;
bool autoSelect = cbAutoSelect.Checked;
bool exclusionUseDIAWindow = FullScanSettingsControl.IsDIA() && cbExclusionUseDIAWindow.Checked;
var filter = new TransitionFilter(precursorCharges, productCharges, types,
fragmentRangeFirst, fragmentRangeLast, measuredIons,
exclusionWindow, exclusionUseDIAWindow, autoSelect);
Helpers.AssignIfEquals(ref filter, Filter);
// Validate and store library settings
TransitionLibraryPick pick = TransitionLibraryPick.none;
if (cbLibraryPick.Checked)
{
if (radioAll.Checked)
{
pick = TransitionLibraryPick.all;
}
else if (radioAllAndFiltered.Checked)
{
pick = TransitionLibraryPick.all_plus;
}
else
{
pick = TransitionLibraryPick.filter;
}
}
double ionMatchTolerance;
double minTol = TransitionLibraries.MIN_MATCH_TOLERANCE;
double maxTol = TransitionLibraries.MAX_MATCH_TOLERANCE;
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Library, textTolerance,
minTol, maxTol, out ionMatchTolerance))
{
return;
}
int ionCount = Libraries.IonCount;
if (pick != TransitionLibraryPick.none)
{
min = TransitionLibraries.MIN_ION_COUNT;
max = TransitionLibraries.MAX_ION_COUNT;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Library, textIonCount,
min, max, out ionCount))
{
return;
}
}
TransitionLibraries libraries = new TransitionLibraries(ionMatchTolerance, ionCount, pick);
Helpers.AssignIfEquals(ref libraries, Libraries);
// This dialog does not yet change integration settings
TransitionIntegration integration = _transitionSettings.Integration;
// Validate and store instrument settings
int minMz;
min = TransitionInstrument.MIN_MEASUREABLE_MZ;
max = TransitionInstrument.MAX_MEASURABLE_MZ - TransitionInstrument.MIN_MZ_RANGE;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMinMz, min, max, out minMz))
{
return;
}
int maxMz;
min = minMz + TransitionInstrument.MIN_MZ_RANGE;
max = TransitionInstrument.MAX_MEASURABLE_MZ;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxMz, min, max, out maxMz))
{
return;
}
bool isDynamicMin = cbDynamicMinimum.Checked;
double mzMatchTolerance;
minTol = TransitionInstrument.MIN_MZ_MATCH_TOLERANCE;
maxTol = TransitionInstrument.MAX_MZ_MATCH_TOLERANCE;
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Instrument, textMzMatchTolerance,
minTol, maxTol, out mzMatchTolerance))
{
return;
}
int?maxTrans = null;
if (!string.IsNullOrEmpty(textMaxTrans.Text))
{
int maxTransTemp;
min = TransitionInstrument.MIN_TRANSITION_MAX;
max = TransitionInstrument.MAX_TRANSITION_MAX;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxTrans,
min, max, out maxTransTemp))
{
return;
}
maxTrans = maxTransTemp;
}
int?maxInclusions = null;
if (!string.IsNullOrEmpty(textMaxInclusions.Text))
{
int maxInclusionsTemp;
min = TransitionInstrument.MIN_INCLUSION_MAX;
max = TransitionInstrument.MAX_INCLUSION_MAX;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxInclusions,
min, max, out maxInclusionsTemp))
{
return;
}
maxInclusions = maxInclusionsTemp;
}
int?minTime = null, maxTime = null;
min = TransitionInstrument.MIN_TIME;
max = TransitionInstrument.MAX_TIME;
if (!string.IsNullOrEmpty(textMinTime.Text))
{
int minTimeTemp;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMinTime,
min, max, out minTimeTemp))
{
return;
}
minTime = minTimeTemp;
}
if (!string.IsNullOrEmpty(textMaxTime.Text))
{
int maxTimeTemp;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxTime,
min, max, out maxTimeTemp))
{
return;
}
maxTime = maxTimeTemp;
}
if (minTime.HasValue && maxTime.HasValue && maxTime.Value - minTime.Value < TransitionInstrument.MIN_TIME_RANGE)
{
helper.ShowTextBoxError(tabControl1, (int)TABS.Instrument, textMaxTime,
string.Format(Resources.TransitionSettingsUI_OkDialog_The_allowable_retention_time_range__0__to__1__must_be_at_least__2__minutes_apart,
minTime, maxTime, TransitionInstrument.MIN_TIME_RANGE));
return;
}
TransitionInstrument instrument = new TransitionInstrument(minMz,
maxMz, isDynamicMin, mzMatchTolerance, maxTrans, maxInclusions, minTime, maxTime);
Helpers.AssignIfEquals(ref instrument, Instrument);
// Validate and store full-scan settings
// If high resolution MS1 filtering is enabled, make sure precursor m/z type
// is monoisotopic and isotope enrichments are set
FullScanPrecursorIsotopes precursorIsotopes = PrecursorIsotopesCurrent;
FullScanMassAnalyzerType precursorAnalyzerType = PrecursorMassAnalyzer;
if (precursorIsotopes != FullScanPrecursorIsotopes.None &&
precursorAnalyzerType != FullScanMassAnalyzerType.qit)
{
if (precursorMassType != MassType.Monoisotopic)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_High_resolution_MS1_filtering_requires_use_of_monoisotopic_precursor_masses);
tabControl1.SelectedIndex = (int)TABS.Prediction;
comboPrecursorMass.Focus();
return;
}
if (FullScanSettingsControl.Enrichments == null)
{
tabControl1.SelectedIndex = (int)TABS.FullScan;
MessageDlg.Show(GetParentForm(this), Resources.TransitionSettingsUI_OkDialog_Isotope_enrichment_settings_are_required_for_MS1_filtering_on_high_resolution_mass_spectrometers);
FullScanSettingsControl.ComboEnrichmentsSetFocus();
return;
}
}
IsolationScheme isolationScheme = FullScanSettingsControl.IsolationScheme;
FullScanAcquisitionMethod acquisitionMethod = AcquisitionMethod;
if (isolationScheme == null && acquisitionMethod == FullScanAcquisitionMethod.DIA)
{
tabControl1.SelectedIndex = (int)TABS.FullScan;
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_An_isolation_scheme_is_required_to_match_multiple_precursors);
FullScanSettingsControl.ComboIsolationSchemeSetFocus();
return;
}
if (isolationScheme != null && isolationScheme.WindowsPerScan.HasValue && !maxInclusions.HasValue)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Before_performing_a_multiplexed_DIA_scan_the_instrument_s_firmware_inclusion_limit_must_be_specified);
tabControl1.SelectedIndex = (int)TABS.Instrument;
textMaxInclusions.Focus();
return;
}
if (FullScanSettingsControl.IsDIA() && cbExclusionUseDIAWindow.Checked)
{
if (FullScanSettingsControl.IsolationScheme.IsAllIons)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precusor_exclusion_when__All_Ions__is_selected_as_the_isolation_scheme___To_use_the_DIA_window_for_precusor_exclusion__change_the_isolation_scheme_in_the_Full_Scan_settings_);
tabControl1.SelectedIndex = (int)TABS.Filter;
cbExclusionUseDIAWindow.Focus();
return;
}
if (FullScanSettingsControl.IsolationScheme.FromResults)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precursor_exclusion_when_isolation_scheme_does_not_contain_prespecified_windows___Please_select_an_isolation_scheme_with_prespecified_windows_);
tabControl1.SelectedIndex = (int)TABS.Filter;
cbExclusionUseDIAWindow.Focus();
return;
}
}
TransitionFullScan fullScan;
if (!FullScanSettingsControl.ValidateFullScanSettings(helper, out fullScan, tabControl1, (int)TABS.FullScan))
{
return;
}
Helpers.AssignIfEquals(ref fullScan, FullScan);
TransitionSettings settings = new TransitionSettings(prediction,
filter, libraries, integration, instrument, fullScan);
// Only update, if anything changed
if (!Equals(settings, _transitionSettings))
{
if (!_parent.ChangeSettingsMonitored(this, Resources.TransitionSettingsUI_OkDialog_Changing_transition_settings,
s => s.ChangeTransitionSettings(settings)))
{
return;
}
_transitionSettings = settings;
}
DialogResult = DialogResult.OK;
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
// Validate and store prediction settings
string massType = comboPrecursorMass.SelectedItem.ToString();
MassType precursorMassType = MassTypeExtension.GetEnum(massType);
massType = comboIonMass.SelectedItem.ToString();
MassType fragmentMassType = MassTypeExtension.GetEnum(massType);
string nameCE = comboCollisionEnergy.SelectedItem.ToString();
CollisionEnergyRegression collisionEnergy =
Settings.Default.GetCollisionEnergyByName(nameCE);
string nameDP = comboDeclusterPotential.SelectedItem.ToString();
DeclusteringPotentialRegression declusteringPotential =
Settings.Default.GetDeclusterPotentialByName(nameDP);
string nameCoV = comboCompensationVoltage.SelectedItem.ToString();
CompensationVoltageParameters compensationVoltage =
Settings.Default.GetCompensationVoltageByName(nameCoV);
string nameOptLib = comboOptimizationLibrary.SelectedItem.ToString();
OptimizationLibrary optimizationLibrary =
Settings.Default.GetOptimizationLibraryByName(nameOptLib);
OptimizedMethodType optimizedMethodType = OptimizedMethodType.None;
if (cbUseOptimized.Checked)
{
optimizedMethodType = OptimizedMethodTypeExtension.GetEnum(comboOptimizeType.SelectedItem.ToString());
}
TransitionPrediction prediction = new TransitionPrediction(precursorMassType,
fragmentMassType, collisionEnergy,
declusteringPotential,
compensationVoltage,
optimizationLibrary,
optimizedMethodType);
Helpers.AssignIfEquals(ref prediction, Prediction);
// Validate and store filter settings
int[] precursorCharges;
int min = TransitionGroup.MIN_PRECURSOR_CHARGE;
int max = TransitionGroup.MAX_PRECURSOR_CHARGE;
if (!helper.ValidateNumberListTextBox(tabControl1, (int) TABS.Filter, textPrecursorCharges,
min, max, out precursorCharges))
return;
precursorCharges = precursorCharges.Distinct().ToArray();
int[] productCharges;
min = Transition.MIN_PRODUCT_CHARGE;
max = Transition.MAX_PRODUCT_CHARGE;
if (!helper.ValidateNumberListTextBox(tabControl1, (int) TABS.Filter, textIonCharges,
min, max, out productCharges))
return;
productCharges = productCharges.Distinct().ToArray();
IonType[] types = TransitionFilter.ParseTypes(textIonTypes.Text, new IonType[0]);
if (types.Length == 0)
{
helper.ShowTextBoxError(tabControl1, (int) TABS.Filter, textIonTypes,
Resources.TransitionSettingsUI_OkDialog_Ion_types_must_contain_a_comma_separated_list_of_ion_types_a_b_c_x_y_z_and_p_for_precursor);
return;
}
types = types.Distinct().ToArray();
double exclusionWindow = 0;
if (!string.IsNullOrEmpty(textExclusionWindow.Text) &&
!Equals(textExclusionWindow.Text, exclusionWindow.ToString(LocalizationHelper.CurrentCulture)))
{
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Filter, textExclusionWindow,
TransitionFilter.MIN_EXCLUSION_WINDOW, TransitionFilter.MAX_EXCLUSION_WINDOW, out exclusionWindow))
{
return;
}
}
string fragmentRangeFirst = TransitionFilter.GetStartFragmentNameFromLabel(comboRangeFrom.SelectedItem.ToString());
string fragmentRangeLast = TransitionFilter.GetEndFragmentNameFromLabel(comboRangeTo.SelectedItem.ToString());
var measuredIons = _driverIons.Chosen;
bool autoSelect = cbAutoSelect.Checked;
bool exclusionUseDIAWindow = FullScanSettingsControl.IsDIA() && cbExclusionUseDIAWindow.Checked;
var filter = new TransitionFilter(precursorCharges, productCharges, types,
fragmentRangeFirst, fragmentRangeLast, measuredIons,
exclusionWindow, exclusionUseDIAWindow, autoSelect);
Helpers.AssignIfEquals(ref filter, Filter);
// Validate and store library settings
TransitionLibraryPick pick = TransitionLibraryPick.none;
if (cbLibraryPick.Checked)
{
if (radioAll.Checked)
pick = TransitionLibraryPick.all;
else if (radioAllAndFiltered.Checked)
pick = TransitionLibraryPick.all_plus;
else
pick = TransitionLibraryPick.filter;
}
double ionMatchTolerance;
double minTol = TransitionLibraries.MIN_MATCH_TOLERANCE;
double maxTol = TransitionLibraries.MAX_MATCH_TOLERANCE;
if (!helper.ValidateDecimalTextBox(tabControl1, (int) TABS.Library, textTolerance,
minTol, maxTol, out ionMatchTolerance))
return;
int ionCount = Libraries.IonCount;
if (pick != TransitionLibraryPick.none)
{
min = TransitionLibraries.MIN_ION_COUNT;
max = TransitionLibraries.MAX_ION_COUNT;
if (!helper.ValidateNumberTextBox(tabControl1, (int) TABS.Library, textIonCount,
min, max, out ionCount))
return;
}
TransitionLibraries libraries = new TransitionLibraries(ionMatchTolerance, ionCount, pick);
Helpers.AssignIfEquals(ref libraries, Libraries);
// This dialog does not yet change integration settings
TransitionIntegration integration = _transitionSettings.Integration;
// Validate and store instrument settings
int minMz;
min = TransitionInstrument.MIN_MEASUREABLE_MZ;
max = TransitionInstrument.MAX_MEASURABLE_MZ - TransitionInstrument.MIN_MZ_RANGE;
if (!helper.ValidateNumberTextBox(tabControl1, (int) TABS.Instrument, textMinMz, min, max, out minMz))
return;
int maxMz;
min = minMz + TransitionInstrument.MIN_MZ_RANGE;
max = TransitionInstrument.MAX_MEASURABLE_MZ;
if (!helper.ValidateNumberTextBox(tabControl1, (int) TABS.Instrument, textMaxMz, min, max, out maxMz))
return;
bool isDynamicMin = cbDynamicMinimum.Checked;
double mzMatchTolerance;
minTol = TransitionInstrument.MIN_MZ_MATCH_TOLERANCE;
maxTol = TransitionInstrument.MAX_MZ_MATCH_TOLERANCE;
if (!helper.ValidateDecimalTextBox(tabControl1, (int) TABS.Instrument, textMzMatchTolerance,
minTol, maxTol, out mzMatchTolerance))
return;
int? maxTrans = null;
if (!string.IsNullOrEmpty(textMaxTrans.Text))
{
int maxTransTemp;
min = TransitionInstrument.MIN_TRANSITION_MAX;
max = TransitionInstrument.MAX_TRANSITION_MAX;
if (!helper.ValidateNumberTextBox(tabControl1, (int) TABS.Instrument, textMaxTrans,
min, max, out maxTransTemp))
return;
maxTrans = maxTransTemp;
}
int? maxInclusions = null;
if (!string.IsNullOrEmpty(textMaxInclusions.Text))
{
int maxInclusionsTemp;
min = TransitionInstrument.MIN_INCLUSION_MAX;
max = TransitionInstrument.MAX_INCLUSION_MAX;
if (!helper.ValidateNumberTextBox(tabControl1, (int) TABS.Instrument, textMaxInclusions,
min, max, out maxInclusionsTemp))
return;
maxInclusions = maxInclusionsTemp;
}
int? minTime = null, maxTime = null;
min = TransitionInstrument.MIN_TIME;
max = TransitionInstrument.MAX_TIME;
if (!string.IsNullOrEmpty(textMinTime.Text))
{
int minTimeTemp;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMinTime,
min, max, out minTimeTemp))
return;
minTime = minTimeTemp;
}
if (!string.IsNullOrEmpty(textMaxTime.Text))
{
int maxTimeTemp;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxTime,
min, max, out maxTimeTemp))
return;
maxTime = maxTimeTemp;
}
if (minTime.HasValue && maxTime.HasValue && maxTime.Value - minTime.Value < TransitionInstrument.MIN_TIME_RANGE)
{
helper.ShowTextBoxError(tabControl1, (int) TABS.Instrument, textMaxTime,
string.Format(Resources.TransitionSettingsUI_OkDialog_The_allowable_retention_time_range__0__to__1__must_be_at_least__2__minutes_apart,
minTime, maxTime, TransitionInstrument.MIN_TIME_RANGE));
return;
}
TransitionInstrument instrument = new TransitionInstrument(minMz,
maxMz, isDynamicMin, mzMatchTolerance, maxTrans, maxInclusions, minTime, maxTime);
Helpers.AssignIfEquals(ref instrument, Instrument);
// Validate and store full-scan settings
// If high resolution MS1 filtering is enabled, make sure precursor m/z type
// is monoisotopic and isotope enrichments are set
FullScanPrecursorIsotopes precursorIsotopes = PrecursorIsotopesCurrent;
FullScanMassAnalyzerType precursorAnalyzerType = PrecursorMassAnalyzer;
if (precursorIsotopes != FullScanPrecursorIsotopes.None &&
precursorAnalyzerType != FullScanMassAnalyzerType.qit)
{
if (precursorMassType != MassType.Monoisotopic)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_High_resolution_MS1_filtering_requires_use_of_monoisotopic_precursor_masses);
tabControl1.SelectedIndex = (int)TABS.Prediction;
comboPrecursorMass.Focus();
return;
}
if (FullScanSettingsControl.Enrichments == null)
{
tabControl1.SelectedIndex = (int) TABS.FullScan;
MessageDlg.Show(GetParentForm(this), Resources.TransitionSettingsUI_OkDialog_Isotope_enrichment_settings_are_required_for_MS1_filtering_on_high_resolution_mass_spectrometers);
FullScanSettingsControl.ComboEnrichmentsSetFocus();
return;
}
}
IsolationScheme isolationScheme = FullScanSettingsControl.IsolationScheme;
FullScanAcquisitionMethod acquisitionMethod = AcquisitionMethod;
if (isolationScheme == null && acquisitionMethod == FullScanAcquisitionMethod.DIA)
{
tabControl1.SelectedIndex = (int)TABS.FullScan;
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_An_isolation_scheme_is_required_to_match_multiple_precursors);
FullScanSettingsControl.ComboIsolationSchemeSetFocus();
return;
}
if (isolationScheme != null && isolationScheme.WindowsPerScan.HasValue && !maxInclusions.HasValue)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Before_performing_a_multiplexed_DIA_scan_the_instrument_s_firmware_inclusion_limit_must_be_specified);
tabControl1.SelectedIndex = (int)TABS.Instrument;
textMaxInclusions.Focus();
return;
}
if (FullScanSettingsControl.IsDIA() && cbExclusionUseDIAWindow.Checked)
{
if (FullScanSettingsControl.IsolationScheme.IsAllIons)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precusor_exclusion_when__All_Ions__is_selected_as_the_isolation_scheme___To_use_the_DIA_window_for_precusor_exclusion__change_the_isolation_scheme_in_the_Full_Scan_settings_);
tabControl1.SelectedIndex = (int)TABS.Filter;
cbExclusionUseDIAWindow.Focus();
return;
}
if (FullScanSettingsControl.IsolationScheme.FromResults)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precursor_exclusion_when_isolation_scheme_does_not_contain_prespecified_windows___Please_select_an_isolation_scheme_with_prespecified_windows_);
tabControl1.SelectedIndex = (int)TABS.Filter;
cbExclusionUseDIAWindow.Focus();
return;
}
}
TransitionFullScan fullScan;
if (!FullScanSettingsControl.ValidateFullScanSettings(helper, out fullScan, tabControl1, (int)TABS.FullScan))
return;
Helpers.AssignIfEquals(ref fullScan, FullScan);
TransitionSettings settings = new TransitionSettings(prediction,
filter, libraries, integration, instrument, fullScan);
// Only update, if anything changed
if (!Equals(settings, _transitionSettings))
{
if (!_parent.ChangeSettingsMonitored(this, Resources.TransitionSettingsUI_OkDialog_Changing_transition_settings,
s => s.ChangeTransitionSettings(settings)))
{
return;
}
_transitionSettings = settings;
}
DialogResult = DialogResult.OK;
}
public TransitionSettings GetTransitionSettings(Form parent)
{
var helper = new MessageBoxHelper(parent);
TransitionSettings settings = SkylineWindow.DocumentUI.Settings.TransitionSettings;
// Validate and store filter settings
int[] precursorCharges;
if (!helper.ValidateNumberListTextBox(txtPrecursorCharges, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE, out precursorCharges))
return null;
precursorCharges = precursorCharges.Distinct().ToArray();
int[] productCharges;
if (!helper.ValidateNumberListTextBox(txtIonCharges, Transition.MIN_PRODUCT_CHARGE, Transition.MAX_PRODUCT_CHARGE, out productCharges))
return null;
productCharges = productCharges.Distinct().ToArray();
IonType[] types = IonTypes;
if (types.Length == 0)
{
helper.ShowTextBoxError(txtIonTypes, Resources.TransitionSettingsUI_OkDialog_Ion_types_must_contain_a_comma_separated_list_of_ion_types_a_b_c_x_y_z_and_p_for_precursor);
return null;
}
types = types.Distinct().ToArray();
bool exclusionUseDIAWindow = cbExclusionUseDIAWindow.Visible && cbExclusionUseDIAWindow.Checked;
var filter = new TransitionFilter(precursorCharges, productCharges, types, settings.Filter.FragmentRangeFirstName, settings.Filter.FragmentRangeLastName,
settings.Filter.MeasuredIons, settings.Filter.PrecursorMzWindow, exclusionUseDIAWindow, settings.Filter.AutoSelect);
Helpers.AssignIfEquals(ref filter, settings.Filter);
// Validate and store library settings
double ionMatchTolerance;
if (!helper.ValidateDecimalTextBox(txtTolerance, TransitionLibraries.MIN_MATCH_TOLERANCE, TransitionLibraries.MAX_MATCH_TOLERANCE, out ionMatchTolerance))
return null;
int ionCount = settings.Libraries.IonCount;
if (!helper.ValidateNumberTextBox(txtIonCount, TransitionLibraries.MIN_ION_COUNT, TransitionLibraries.MAX_ION_COUNT, out ionCount))
return null;
TransitionLibraryPick pick = (settings.Libraries.Pick != TransitionLibraryPick.none) ? settings.Libraries.Pick : TransitionLibraryPick.all;
var libraries = new TransitionLibraries(ionMatchTolerance, ionCount, pick);
Helpers.AssignIfEquals(ref libraries, settings.Libraries);
return new TransitionSettings(settings.Prediction, filter, libraries, settings.Integration, settings.Instrument, settings.FullScan);
}
