public void OkDialog() { var helper = new MessageBoxHelper(this); var charge = 0; if (textCharge.Visible && !helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge)) { return; } if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue) { helper.ShowTextBoxError(textRetentionTimeWindow, Resources.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_); return; } Charge = charge; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty if (string.IsNullOrEmpty(_formulaBox.Formula)) { // Can the text fields be understood as mz? if (!_formulaBox.ValidateAverageText(helper)) { return; } if (!_formulaBox.ValidateMonoText(helper)) { return; } } var formula = _formulaBox.Formula; var monoMass = _formulaBox.MonoMass ?? 0; var averageMass = _formulaBox.AverageMass ?? 0; if (monoMass < CustomIon.MIN_MASS || averageMass < CustomIon.MIN_MASS) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format(Resources.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__, CustomIon.MIN_MASS)); return; } if (monoMass > CustomIon.MAX_MASS || averageMass > CustomIon.MAX_MASS) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format(Resources.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__, CustomIon.MAX_MASS)); return; } if ((_transitionSettings != null) && (!_transitionSettings.IsMeasurablePrecursor(BioMassCalc.CalculateIonMz(monoMass, charge)) || !_transitionSettings.IsMeasurablePrecursor(BioMassCalc.CalculateIonMz(averageMass, charge)))) { _formulaBox.ShowTextBoxErrorFormula(helper, Resources.SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_); return; } if (!string.IsNullOrEmpty(_formulaBox.Formula)) { try { ResultCustomIon = new DocNodeCustomIon(formula, textName.Text); } catch (InvalidDataException x) { _formulaBox.ShowTextBoxErrorFormula(helper, x.Message); return; } } else { ResultCustomIon = new DocNodeCustomIon(monoMass, averageMass, textName.Text); } // Did user change the list of heavy labels? if (_driverLabelType != null) { PeptideModifications modifications = new PeptideModifications( _peptideSettings.Modifications.StaticModifications, _peptideSettings.Modifications.MaxVariableMods, _peptideSettings.Modifications.MaxNeutralLosses, _driverLabelType.GetHeavyModifications(), // This is the only thing the user may have altered _peptideSettings.Modifications.InternalStandardTypes); var settings = _peptideSettings.ChangeModifications(modifications); // Only update if anything changed if (!Equals(settings, _peptideSettings)) { SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings); if (!_parent.ChangeSettings(newSettings, true)) { return; } _peptideSettings = newSettings.PeptideSettings; } } // See if this combination of charge and label would conflict with any existing transition groups if (_existingIds != null && _existingIds.Any(t => { var transitionGroup = t as TransitionGroup; return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) && Equals(transitionGroup.PrecursorCharge, Charge) && !ReferenceEquals(t, _initialId)); })) { helper.ShowTextBoxError(textName, Resources.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_charge_and_label_type_already_exists_, textName.Text); return; } // See if this would conflict with any existing transitions if (_existingIds != null && (_existingIds.Any(t => { var transition = t as Transition; return(transition != null && ((transition.Charge == Charge) && Equals(transition.CustomIon, ResultCustomIon)) && !ReferenceEquals(t, _initialId)); }))) { helper.ShowTextBoxError(textName, Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text); return; } DialogResult = DialogResult.OK; }
private MeasuredIon ValidateCustomIon(string name) { var helper = new MessageBoxHelper(this); string formula = _formulaBox.Formula.ToString(LocalizationHelper.CurrentCulture); var charge = ValidateCharge(); if (!charge.HasValue) { return(null); } double monoMass; double avgMass; if (!string.IsNullOrEmpty(formula)) { // Mass is specified by chemical formula try { monoMass = SequenceMassCalc.ParseModMass(BioMassCalc.MONOISOTOPIC, formula); avgMass = SequenceMassCalc.ParseModMass(BioMassCalc.AVERAGE, formula); } catch (ArgumentException x) { helper.ShowTextBoxError(_formulaBox, x.Message); return(null); } } else if (_formulaBox.MonoMass != null || _formulaBox.AverageMass != null) { // Mass is specified by combination of mz and charge formula = null; if (!_formulaBox.ValidateMonoText(helper)) { return(null); } if (!_formulaBox.ValidateAverageText(helper)) { return(null); } _formulaBox.Charge = charge; // This provokes calculation of mass from displayed mz values monoMass = _formulaBox.MonoMass.Value; avgMass = _formulaBox.AverageMass.Value; } else { // User hasn't fully specified either way _formulaBox.ShowTextBoxErrorFormula(helper, Resources.EditMeasuredIonDlg_OkDialog_Please_specify_a_formula_or_constant_masses); return(null); } if (MeasuredIon.MIN_REPORTER_MASS > monoMass || MeasuredIon.MIN_REPORTER_MASS > avgMass) { _formulaBox.ShowTextBoxErrorMonoMass(helper, string.Format(Resources.EditMeasuredIonDlg_OkDialog_Reporter_ion_masses_must_be_less_than_or_equal_to__0__, MeasuredIon.MAX_REPORTER_MASS)); return(null); } if (monoMass > MeasuredIon.MAX_REPORTER_MASS || avgMass > MeasuredIon.MAX_REPORTER_MASS) { _formulaBox.ShowTextBoxErrorAverageMass(helper, string.Format(Resources.EditMeasuredIonDlg_OkDialog_Reporter_ion_masses_must_be_less_than_or_equal_to__0__, MeasuredIon.MAX_REPORTER_MASS)); return(null); } return(new MeasuredIon(name, formula, monoMass, avgMass, charge.Value)); }
public void OkDialog() { var helper = new MessageBoxHelper(this); string name; if (!helper.ValidateNameTextBox(_editing ? (Control)textName : comboMod, out name)) { return; } // Allow updating the original modification if (!_editing || !Equals(name, Modification.Name)) { if (!ModNameAvailable(name)) { helper.ShowTextBoxError(_editing ? (Control)textName : comboMod, Resources.EditStaticModDlg_OkDialog_The_modification__0__already_exists, name); return; } } string aas = comboAA.Text; if (string.IsNullOrEmpty(aas)) { aas = null; } else { // Use the cleanest possible format. var sb = new StringBuilder(); foreach (string aaPart in aas.Split(SEPARATOR_AA)) { string aa = aaPart.Trim(); if (aa.Length == 0) { continue; } if (sb.Length > 0) { sb.Append(", "); // Not L10N } sb.Append(aa); } } string termString = comboTerm.SelectedItem.ToString(); ModTerminus?term = null; if (!string.IsNullOrEmpty(termString)) { term = (ModTerminus)Enum.Parse(typeof(ModTerminus), termString); } if (cbVariableMod.Checked && aas == null && term == null) { MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Variable_modifications_must_specify_amino_acid_or_terminus); comboAA.Focus(); return; } string formula = null; double? monoMass = null; double? avgMass = null; LabelAtoms labelAtoms = LabelAtoms.None; if (cbChemicalFormula.Checked) { formula = Formula; } else { labelAtoms = LabelAtoms; } // Get the losses to know whether any exist below IList <FragmentLoss> losses = null; if (listNeutralLosses.Items.Count > 0) { losses = Losses.ToArray(); } if (!string.IsNullOrEmpty(formula)) { try { SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, formula, SequenceMassCalc.MassPrecision); } catch (ArgumentException x) { _formulaBox.ShowTextBoxErrorFormula(helper, x.Message); return; } } else if (labelAtoms == LabelAtoms.None) { formula = null; // Allow formula and both masses to be empty, if losses are present if (NotZero(_formulaBox.MonoMass) || NotZero(_formulaBox.AverageMass) || losses == null) { // TODO: Maximum and minimum masses should be formalized and applied everywhere double mass; if (!_formulaBox.ValidateMonoText(helper, -1500, 5000, out mass)) { return; } monoMass = mass; if (!_formulaBox.ValidateAverageText(helper, -1500, 5000, out mass)) { return; } avgMass = mass; } // Loss-only modifications may not be variable else if (cbVariableMod.Checked) { MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_The_variable_checkbox_only_applies_to_precursor_modification_Product_ion_losses_are_inherently_variable); cbVariableMod.Focus(); return; } } else if (aas == null && term.HasValue) { MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Labeled_atoms_on_terminal_modification_are_not_valid); return; } RelativeRT relativeRT = RelativeRT.Matching; if (comboRelativeRT.Visible && comboRelativeRT.SelectedItem != null) { relativeRT = RelativeRTExtension.GetEnum(comboRelativeRT.SelectedItem.ToString()); } // Store state of the chemical formula checkbox for next use. if (cbChemicalFormula.Visible) { Settings.Default.ShowHeavyFormula = _formulaBox.FormulaVisible; } var newMod = new StaticMod(name, aas, term, cbVariableMod.Checked, formula, labelAtoms, relativeRT, monoMass, avgMass, losses); foreach (StaticMod mod in _existing) { if (newMod.Equivalent(mod) && !(_editing && mod.Equals(_originalModification))) { if (DialogResult.OK == MultiButtonMsgDlg.Show( this, TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_an_existing_modification_with_the_same_settings, string.Format("'{0}'.", mod.Name), // Not L10N string.Empty, Resources.EditStaticModDlg_OkDialog_Continue), MultiButtonMsgDlg.BUTTON_OK)) { Modification = newMod; DialogResult = DialogResult.OK; } return; } } var uniMod = UniMod.GetModification(name, IsStructural); // If the modification name is not found in Unimod, check if there exists a modification in Unimod that matches // the dialog modification, and prompt the user to to use the Unimod modification instead. if (uniMod == null) { var matchingMod = UniMod.FindMatchingStaticMod(newMod, IsStructural); if (matchingMod != null && (ModNameAvailable(matchingMod.Name) || (_editing && Equals(matchingMod.Name, Modification.Name)))) { var result = MultiButtonMsgDlg.Show( this, TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_a_Unimod_modification_with_the_same_settings, string.Empty, string.Format(Resources.EditStaticModDlg_OkDialog_Click__Unimod__to_use_the_name___0___, matchingMod.Name), string.Format(Resources.EditStaticModDlg_OkDialog_Click__Custom__to_use_the_name___0___, name)), Resources.EditStaticModDlg_OkDialog_Unimod, Resources.EditStaticModDlg_OkDialog_Custom, true); if (result == DialogResult.Yes) { newMod = matchingMod.MatchVariableAndLossInclusion(newMod); // Unimod } if (result == DialogResult.Cancel) { return; } } } else { // If the dialog modification matches the modification of the same name in Unimod, // use the UnimodId. if (newMod.Equivalent(uniMod)) { newMod = uniMod.MatchVariableAndLossInclusion(newMod); } else { // Finally, if the modification name is found in Unimod, but the modification in Unimod does not // match the dialog modification, prompt the user to use the Unimod modification definition instead. if (DialogResult.OK != MultiButtonMsgDlg.Show( this, TextUtil.LineSeparate(string.Format(Resources.EditStaticModDlg_OkDialog_This_modification_does_not_match_the_Unimod_specifications_for___0___, name), string.Empty, Resources.EditStaticModDlg_OkDialog_Use_non_standard_settings_for_this_name), MultiButtonMsgDlg.BUTTON_OK)) { return; } } } _modification = newMod; DialogResult = DialogResult.OK; }
private MeasuredIon ValidateCustomIon(string name) { var helper = new MessageBoxHelper(this); string formula = (_formulaBox.NeutralFormula ?? string.Empty).ToString(LocalizationHelper.CurrentCulture); var charge = ValidateCharge(); if (!charge.HasValue) { return(null); } double monoMass; double avgMass; if (!string.IsNullOrEmpty(formula)) { // Mass is specified by chemical formula try { monoMass = SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, formula, SequenceMassCalc.MassPrecision); avgMass = SequenceMassCalc.FormulaMass(BioMassCalc.AVERAGE, formula, SequenceMassCalc.MassPrecision); } catch (ArgumentException x) { helper.ShowTextBoxError(_formulaBox, x.Message); return(null); } } else if (_formulaBox.MonoMass != null || _formulaBox.AverageMass != null) { // Mass is specified by combination of mz and charge formula = null; if (!_formulaBox.ValidateMonoText(helper)) { return(null); } if (!_formulaBox.ValidateAverageText(helper)) { return(null); } // CONSIDER(bspratt): should we switch to using adducts instead of baking ions into formula? _formulaBox.Adduct = Adduct.FromChargeNoMass(charge.Value); // This provokes calculation of mass from displayed mz values monoMass = _formulaBox.MonoMass.Value; avgMass = _formulaBox.AverageMass.Value; } else { // User hasn't fully specified either way _formulaBox.ShowTextBoxErrorFormula(helper, Resources.EditMeasuredIonDlg_OkDialog_Please_specify_a_formula_or_constant_masses); return(null); } if (MeasuredIon.MIN_REPORTER_MASS > monoMass || MeasuredIon.MIN_REPORTER_MASS > avgMass) { _formulaBox.ShowTextBoxErrorMonoMass(helper, string.Format(Resources.EditMeasuredIonDlg_OkDialog_Reporter_ion_masses_must_be_less_than_or_equal_to__0__, MeasuredIon.MAX_REPORTER_MASS)); return(null); } if (monoMass > MeasuredIon.MAX_REPORTER_MASS || avgMass > MeasuredIon.MAX_REPORTER_MASS) { _formulaBox.ShowTextBoxErrorAverageMass(helper, string.Format(Resources.EditMeasuredIonDlg_OkDialog_Reporter_ion_masses_must_be_less_than_or_equal_to__0__, MeasuredIon.MAX_REPORTER_MASS)); return(null); } return(new MeasuredIon(name, formula, monoMass, avgMass, Adduct.FromChargeNoMass(charge.Value))); // Charge-only adduct: user is assumed to have placed ion elements in formula }
public void OkDialog() { var helper = new MessageBoxHelper(this); var charge = 0; if (textCharge.Visible && !helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge)) { return; } var adduct = Adduct.NonProteomicProtonatedFromCharge(charge); if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue) { helper.ShowTextBoxError(textRetentionTimeWindow, Resources .Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_); return; } if (Adduct.IsEmpty || Adduct.AdductCharge != adduct.AdductCharge) { Adduct = adduct; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty } if (string.IsNullOrEmpty(_formulaBox.NeutralFormula)) { // Can the text fields be understood as mz? if (!_formulaBox.ValidateAverageText(helper)) { return; } if (!_formulaBox.ValidateMonoText(helper)) { return; } } var monoMass = new TypedMass(_formulaBox.MonoMass ?? 0, MassType.Monoisotopic); var averageMass = new TypedMass(_formulaBox.AverageMass ?? 0, MassType.Average); if (monoMass < CustomMolecule.MIN_MASS || averageMass < CustomMolecule.MIN_MASS) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format( Resources .EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__, CustomMolecule.MIN_MASS)); return; } if (monoMass > CustomMolecule.MAX_MASS || averageMass > CustomMolecule.MAX_MASS) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format( Resources .EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__, CustomMolecule.MAX_MASS)); return; } if ((_transitionSettings != null) && (!_transitionSettings.IsMeasurablePrecursor( adduct.MzFromNeutralMass(monoMass, MassType.Monoisotopic)) || !_transitionSettings.IsMeasurablePrecursor(adduct.MzFromNeutralMass(averageMass, MassType.Average)))) { _formulaBox.ShowTextBoxErrorFormula(helper, Resources .SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_); return; } if (_usageMode == UsageMode.precursor) { // Only the adduct should be changing SetResult(_resultCustomMolecule, Adduct); } else if (!string.IsNullOrEmpty(_formulaBox.NeutralFormula)) { try { var name = textName.Text; if (string.IsNullOrEmpty(name)) { name = _formulaBox.NeutralFormula; // Clip off any adduct description } SetResult(new CustomMolecule(_formulaBox.NeutralFormula, name), Adduct); } catch (InvalidDataException x) { _formulaBox.ShowTextBoxErrorFormula(helper, x.Message); return; } } else { SetResult(new CustomMolecule(monoMass, averageMass, textName.Text), Adduct); } // Did user change the list of heavy labels? if (_driverLabelType != null) { PeptideModifications modifications = new PeptideModifications( _peptideSettings.Modifications.StaticModifications, _peptideSettings.Modifications.MaxVariableMods, _peptideSettings.Modifications.MaxNeutralLosses, _driverLabelType.GetHeavyModifications(), // This is the only thing the user may have altered _peptideSettings.Modifications.InternalStandardTypes); var settings = _peptideSettings.ChangeModifications(modifications); // Only update if anything changed if (!Equals(settings, _peptideSettings)) { SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings); if (!_parent.ChangeSettings(newSettings, true)) { return; } _peptideSettings = newSettings.PeptideSettings; } } // See if this combination of charge and label would conflict with any existing transition groups if (_existingIds != null && _existingIds.Any(t => { var transitionGroup = t as TransitionGroup; return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) && Equals(transitionGroup.PrecursorAdduct.AsFormula(), Adduct .AsFormula()) && // Compare AsFormula so proteomic and non-proteomic protonation are seen as same thing !ReferenceEquals(t, _initialId)); })) { helper.ShowTextBoxError(textName, Resources .EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_adduct_and_label_type_already_exists_, textName.Text); return; } // See if this would conflict with any existing transitions if (_existingIds != null && (_existingIds.Any(t => { var transition = t as Transition; return(transition != null && (Equals(transition.Adduct.AsFormula(), Adduct.AsFormula()) && Equals(transition.CustomIon, ResultCustomMolecule)) && !ReferenceEquals(t, _initialId)); }))) { helper.ShowTextBoxError(textName, Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text); return; } DialogResult = DialogResult.OK; }
public void OkDialog() { var helper = new MessageBoxHelper(this); string formulaLoss = _formulaBox.Formula; double?monoLoss = null; double?avgLoss = null; if (!string.IsNullOrEmpty(formulaLoss)) { try { double massMono = SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, formulaLoss, SequenceMassCalc.MassPrecision); double massAverage = SequenceMassCalc.FormulaMass(BioMassCalc.AVERAGE, formulaLoss, SequenceMassCalc.MassPrecision); if (FragmentLoss.MIN_LOSS_MASS > massMono || FragmentLoss.MIN_LOSS_MASS > massAverage) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format(Resources.EditFragmentLossDlg_OkDialog_Neutral_loss_masses_must_be_greater_than_or_equal_to__0__, FragmentLoss.MIN_LOSS_MASS)); return; } if (massMono > FragmentLoss.MAX_LOSS_MASS || massAverage > FragmentLoss.MAX_LOSS_MASS) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format(Resources.EditFragmentLossDlg_OkDialog_Neutral_loss_masses_must_be_less_than_or_equal_to__0__, FragmentLoss.MAX_LOSS_MASS)); return; } } catch (ArgumentException x) { _formulaBox.ShowTextBoxErrorFormula(helper, x.Message); return; } } else if (_formulaBox.MonoMass != null || _formulaBox.AverageMass != null) { formulaLoss = null; double mass; if (!_formulaBox.ValidateMonoText(helper, FragmentLoss.MIN_LOSS_MASS, FragmentLoss.MAX_LOSS_MASS, out mass)) { return; } monoLoss = mass; if (!_formulaBox.ValidateAverageText(helper, FragmentLoss.MIN_LOSS_MASS, FragmentLoss.MAX_LOSS_MASS, out mass)) { return; } avgLoss = mass; } else { _formulaBox.ShowTextBoxErrorFormula(helper, Resources.EditFragmentLossDlg_OkDialog_Please_specify_a_formula_or_constant_masses); return; } // Make sure the new loss does not already exist. var loss = new FragmentLoss(formulaLoss, monoLoss, avgLoss, Inclusion); if (_existing.Contains(loss)) { MessageDlg.Show(this, string.Format(Resources.EditFragmentLossDlg_OkDialog_The_loss__0__already_exists, loss)); return; } Loss = loss; DialogResult = DialogResult.OK; }
public void OkDialog() { var helper = new MessageBoxHelper(this); var charge = 0; if (textCharge.Visible && !helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge)) { return; } var adduct = Adduct.NonProteomicProtonatedFromCharge(charge); if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue) { helper.ShowTextBoxError(textRetentionTimeWindow, Resources .Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_); return; } if (Adduct.IsEmpty || Adduct.AdductCharge != adduct.AdductCharge) { Adduct = adduct; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty } if (string.IsNullOrEmpty(_formulaBox.NeutralFormula)) { // Can the text fields be understood as mz? if (!_formulaBox.ValidateAverageText(helper)) { return; } if (!_formulaBox.ValidateMonoText(helper)) { return; } } var monoMass = new TypedMass(_formulaBox.MonoMass ?? 0, MassType.Monoisotopic); var averageMass = new TypedMass(_formulaBox.AverageMass ?? 0, MassType.Average); if (monoMass < CustomMolecule.MIN_MASS || averageMass < CustomMolecule.MIN_MASS) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format( Resources .EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__, CustomMolecule.MIN_MASS)); return; } if (monoMass > CustomMolecule.MAX_MASS || averageMass > CustomMolecule.MAX_MASS) { _formulaBox.ShowTextBoxErrorFormula(helper, string.Format( Resources .EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__, CustomMolecule.MAX_MASS)); return; } if ((_transitionSettings != null) && (!_transitionSettings.IsMeasurablePrecursor( adduct.MzFromNeutralMass(monoMass, MassType.Monoisotopic)) || !_transitionSettings.IsMeasurablePrecursor(adduct.MzFromNeutralMass(averageMass, MassType.Average)))) { _formulaBox.ShowTextBoxErrorFormula(helper, Resources .SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_); return; } // Ion mobility value must have ion mobility units if (textIonMobility.Visible && IonMobility.HasValue) { if (IonMobilityUnits == eIonMobilityUnits.none) { helper.ShowTextBoxError(textIonMobility, Resources.EditCustomMoleculeDlg_OkDialog_Please_specify_the_ion_mobility_units_); comboBoxIonMobilityUnits.Focus(); return; } if (IonMobility.Value == 0 || (IonMobility.Value < 0 && !IonMobilityFilter.AcceptNegativeMobilityValues(IonMobilityUnits))) { helper.ShowTextBoxError(textIonMobility, string.Format(Resources.SmallMoleculeTransitionListReader_ReadPrecursorOrProductColumns_Invalid_ion_mobility_value__0_, IonMobility)); textIonMobility.Focus(); return; } } if (_usageMode == UsageMode.precursor) { // Only the adduct should be changing SetResult(_resultCustomMolecule, Adduct); } else if (!string.IsNullOrEmpty(_formulaBox.NeutralFormula)) { try { var name = textName.Text; if (string.IsNullOrEmpty(name)) { name = _formulaBox.NeutralFormula; // Clip off any adduct description } SetResult(new CustomMolecule(_formulaBox.NeutralFormula, name), Adduct); } catch (InvalidDataException x) { _formulaBox.ShowTextBoxErrorFormula(helper, x.Message); return; } } else { SetResult(new CustomMolecule(monoMass, averageMass, textName.Text), Adduct); } // Did user change the list of heavy labels? if (_driverLabelType != null) { // This is the only thing the user may have altered var newHeavyMods = _driverLabelType.GetHeavyModifications().ToArray(); if (!ArrayUtil.EqualsDeep(newHeavyMods, _peptideSettings.Modifications.HeavyModifications)) { var labelTypes = _peptideSettings.Modifications.InternalStandardTypes.Where(t => newHeavyMods.Any(m => Equals(m.LabelType, t))).ToArray(); if (labelTypes.Length == 0) { labelTypes = new[] { newHeavyMods.First().LabelType } } ; PeptideModifications modifications = new PeptideModifications( _peptideSettings.Modifications.StaticModifications, _peptideSettings.Modifications.MaxVariableMods, _peptideSettings.Modifications.MaxNeutralLosses, newHeavyMods, labelTypes); var settings = _peptideSettings.ChangeModifications(modifications); SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings); if (!_parent.ChangeSettings(newSettings, true)) { // Not expected, since we checked for a change before calling // Otherwise, this is very confusing. The form just refuses to go away // We would prefer to get an unhandled exception and fix this Assume.Fail(); return; } _peptideSettings = newSettings.PeptideSettings; } } // See if this combination of charge and label would conflict with any existing transition groups if (_existingIds != null && _existingIds.Any(t => { var transitionGroup = t as TransitionGroup; return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) && Equals(transitionGroup.PrecursorAdduct.AsFormula(), Adduct .AsFormula()) && // Compare AsFormula so proteomic and non-proteomic protonation are seen as same thing !ReferenceEquals(t, _initialId)); })) { helper.ShowTextBoxError(textName, Resources .EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_adduct_and_label_type_already_exists_, textName.Text); return; } // See if this would conflict with any existing transitions if (_existingIds != null && (_existingIds.Any(t => { var transition = t as Transition; return(transition != null && (Equals(transition.Adduct.AsFormula(), Adduct.AsFormula()) && Equals(transition.CustomIon, ResultCustomMolecule)) && !ReferenceEquals(t, _initialId)); }))) { helper.ShowTextBoxError(textName, Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text); return; } DialogResult = DialogResult.OK; }