public void AddModification(StaticMod mod, ModType type)
{
if (mod == null)
{
return;
}
ImportPeptideSearch.UserDefinedTypedMods.Add(mod);
PeptideSettings newPeptideSettings = SkylineWindow.Document.Settings.PeptideSettings;
var newMods = new List <StaticMod>(
(type == ModType.structural ? newPeptideSettings.Modifications.StaticModifications : newPeptideSettings.Modifications.HeavyModifications)
)
{
mod
};
newPeptideSettings = (type == ModType.structural)
? newPeptideSettings.ChangeModifications(newPeptideSettings.Modifications.ChangeStaticModifications(newMods))
: newPeptideSettings.ChangeModifications(newPeptideSettings.Modifications.ChangeHeavyModifications(newMods));
SkylineWindow.ChangeSettings(SkylineWindow.Document.Settings.ChangePeptideSettings(newPeptideSettings), true,
string.Format(Resources.MatchModificationsControl_AddModification_Add__0__modification__1_, type, mod.Name));
SkylineWindow.Document.Settings.UpdateDefaultModifications(false);
FillLists(SkylineWindow.Document);
}
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);
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;
}
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;
}