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;
}
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 &&
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)
{
int[] precursorCharges;
if (!helper.ValidateNumberListTextBox(FullScanSettingsControl.PrecursorChargesTextBox, TransitionGroup.MIN_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE, out precursorCharges))
return false;
precursorCharges = precursorCharges.Distinct().ToArray();
filter = TransitionSettings.Filter.ChangePrecursorCharges(precursorCharges);
}
if (WorkflowType == Workflow.dda && !filter.IonTypes.Contains(IonType.precursor))
filter = filter.ChangeIonTypes(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;
}
// Only update, if anything changed
if (!Equals(settings, TransitionSettings))
{
SrmSettings newSettings = SkylineWindow.DocumentUI.Settings.ChangeTransitionSettings(settings);
if (!SkylineWindow.ChangeSettings(newSettings, true))
{
return false;
}
}
// MS1 filtering must be enabled
if (!FullScan.IsEnabledMs)
{
MessageDlg.Show(this, Resources.ImportPeptideSearchDlg_UpdateFullScanSettings_Full_scan_MS1_filtering_must_be_enabled_in_order_to_import_a_peptide_search_);
return false;
}
return true;
}
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);
}