public SrmSettings(string name, PeptideSettings peptideSettings, TransitionSettings transitionSettings, DataSettings dataSettings, DocumentRetentionTimes documentRetentionTimes)
: base(name)
{
PeptideSettings = peptideSettings;
TransitionSettings = transitionSettings;
DataSettings = dataSettings;
DocumentRetentionTimes = documentRetentionTimes;
// Create cached calculator instances
CreatePrecursorMassCalcs();
CreateFragmentMassCalcs();
}
public SrmSettings ChangePeptideSettings(PeptideSettings prop)
{
SrmSettings settings = ChangeProp(ImClone(this), im => im.PeptideSettings = prop);
// If modifications have change, then new mass calculators are needed.
if (!Equals(prop.Modifications, PeptideSettings.Modifications))
{
settings.CreatePrecursorMassCalcs();
settings.CreateFragmentMassCalcs();
}
return settings;
}
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;
}
/// <summary>
/// For creating at the Molecule level (create molecule and first transition group) or modifying at the transition level
/// Null values imply "don't ask user for this"
/// </summary>
public EditCustomMoleculeDlg(SkylineWindow parent, string title, Identity initialId, IEnumerable<Identity> existingIds, int minCharge, int maxCharge,
SrmSettings settings, string defaultName, string defaultFormula, int? defaultCharge, ExplicitTransitionGroupValues explicitAttributes,
ExplicitRetentionTimeInfo explicitRetentionTime,
IsotopeLabelType defaultIsotopeLabelType, bool enableFormulaEditing = true)
{
Text = title;
_parent = parent;
_initialId = initialId;
_existingIds = existingIds;
_minCharge = minCharge;
_maxCharge = maxCharge;
_transitionSettings = settings != null ? settings.TransitionSettings : null;
_peptideSettings = settings != null ? settings.PeptideSettings : null;
InitializeComponent();
NameText = defaultName;
var needOptionalValuesBox = explicitRetentionTime != null || explicitAttributes != null;
var heightDelta = 0;
if (explicitAttributes == null)
{
ResultExplicitTransitionGroupValues = null;
labelCollisionEnergy.Visible = false;
textCollisionEnergy.Visible = false;
labelSLens.Visible = false;
textSLens.Visible = false;
labelCompensationVoltage.Visible = false;
textCompensationVoltage.Visible = false;
labelConeVoltage.Visible = false;
textConeVoltage.Visible = false;
labelDriftTimeHighEnergyOffsetMsec.Visible = false;
textDriftTimeHighEnergyOffsetMsec.Visible = false;
labelDriftTimeMsec.Visible = false;
textDriftTimeMsec.Visible = false;
if (needOptionalValuesBox)
{
// We blanked out everything but the retention time
var vmargin = labelRetentionTime.Location.Y;
var newHeight = textRetentionTime.Location.Y + textRetentionTime.Height + vmargin;
heightDelta = groupBoxOptionalValues.Height - newHeight;
groupBoxOptionalValues.Height = newHeight;
}
}
else
{
ResultExplicitTransitionGroupValues = new ExplicitTransitionGroupValues(explicitAttributes);
}
string labelAverage = defaultCharge.HasValue
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_mass_;
string labelMono = defaultCharge.HasValue
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_mass_;
_formulaBox =
new FormulaBox(Resources.EditMeasuredIonDlg_EditMeasuredIonDlg_Ion__chemical_formula_,
labelAverage,
labelMono,
defaultCharge)
{
Formula = defaultFormula,
Location = new Point(textName.Left, textName.Bottom + 12)
};
Controls.Add(_formulaBox);
_formulaBox.TabIndex = 2;
_formulaBox.Enabled = enableFormulaEditing;
bool needCharge = defaultCharge.HasValue;
textCharge.Visible = labelCharge.Visible = needCharge;
Charge = defaultCharge ?? 0;
if (needOptionalValuesBox && !needCharge)
{
heightDelta += groupBoxOptionalValues.Location.Y - labelCharge.Location.Y;
groupBoxOptionalValues.Location = new Point(groupBoxOptionalValues.Location.X, labelCharge.Location.Y);
}
if (explicitRetentionTime == null)
{
// Don't ask user for retetention times
RetentionTime = null;
RetentionTimeWindow = null;
labelRetentionTime.Visible = false;
labelRetentionTimeWindow.Visible = false;
textRetentionTime.Visible = false;
textRetentionTimeWindow.Visible = false;
if (needOptionalValuesBox)
{
var rtHeight = labelCollisionEnergy.Location.Y - labelRetentionTimeWindow.Location.Y;
groupBoxOptionalValues.Height -= rtHeight;
heightDelta += rtHeight;
}
}
else
{
RetentionTime = explicitRetentionTime.RetentionTime;
RetentionTimeWindow = explicitRetentionTime.RetentionTimeWindow;
}
if (!needOptionalValuesBox)
{
groupBoxOptionalValues.Visible = false;
heightDelta = groupBoxOptionalValues.Height;
}
// Initialize label
if (settings != null && defaultIsotopeLabelType != null)
{
_driverLabelType = new PeptideSettingsUI.LabelTypeComboDriver(comboIsotopeLabelType,
settings.PeptideSettings.Modifications, null, null, null, null)
{
SelectedName = defaultIsotopeLabelType.Name
};
}
else
{
comboIsotopeLabelType.Visible = false;
labelIsotopeLabelType.Visible = false;
}
Height -= heightDelta;
}
public Digestion GetDigestion(ProteomeDb proteomeDb, PeptideSettings peptideSettings)
{
return proteomeDb.GetDigestion(peptideSettings.Enzyme.Name);
}
public bool HasDigestion(PeptideSettings peptideSettings)
{
return DigestionNames.Contains(peptideSettings.Enzyme.Name);
}
public PeptideSettingsUI(SkylineWindow parent, LibraryManager libraryManager)
{
InitializeComponent();
btnUpdateIonMobilityLibraries.Visible = false; // TODO: ion mobility libraries are more complex than initially thought - put this off until after summer 2014 release
_parent = parent;
_libraryManager = libraryManager;
_peptideSettings = parent.DocumentUI.Settings.PeptideSettings;
// Initialize digestion settings
_driverEnzyme = new SettingsListComboDriver<Enzyme>(comboEnzyme, Settings.Default.EnzymeList);
_driverEnzyme.LoadList(_peptideSettings.Enzyme.GetKey());
for (int i = DigestSettings.MIN_MISSED_CLEAVAGES; i <= DigestSettings.MAX_MISSED_CLEAVAGES; i++)
comboMissedCleavages.Items.Add(i.ToString(CultureInfo.InvariantCulture));
comboMissedCleavages.SelectedItem = Digest.MaxMissedCleavages.ToString(LocalizationHelper.CurrentCulture);
if (comboMissedCleavages.SelectedIndex < 0)
comboMissedCleavages.SelectedIndex = 0;
cbRaggedEnds.Checked = Digest.ExcludeRaggedEnds;
// Initialize prediction settings
_driverRT = new SettingsListComboDriver<RetentionTimeRegression>(comboRetentionTime, Settings.Default.RetentionTimeList);
string sel = (Prediction.RetentionTime == null ? null : Prediction.RetentionTime.Name);
_driverRT.LoadList(sel);
cbUseMeasuredRT.Checked = textMeasureRTWindow.Enabled = Prediction.UseMeasuredRTs;
if (Prediction.MeasuredRTWindow.HasValue)
textMeasureRTWindow.Text = Prediction.MeasuredRTWindow.Value.ToString(LocalizationHelper.CurrentCulture);
_driverDT = new SettingsListComboDriver<DriftTimePredictor>(comboDriftTimePredictor, Settings.Default.DriftTimePredictorList);
string selDT = (Prediction.DriftTimePredictor == null ? null : Prediction.DriftTimePredictor.Name);
_driverDT.LoadList(selDT);
cbUseSpectralLibraryDriftTimes.Checked = textSpectralLibraryDriftTimesResolvingPower.Enabled = Prediction.UseLibraryDriftTimes;
if (Prediction.LibraryDriftTimesResolvingPower.HasValue)
textSpectralLibraryDriftTimesResolvingPower.Text = Prediction.LibraryDriftTimesResolvingPower.Value.ToString(LocalizationHelper.CurrentCulture);
// Initialize filter settings
_driverExclusion = new SettingsListBoxDriver<PeptideExcludeRegex>(listboxExclusions, Settings.Default.PeptideExcludeList);
_driverExclusion.LoadList(null, Filter.Exclusions);
textExcludeAAs.Text = Filter.ExcludeNTermAAs.ToString(LocalizationHelper.CurrentCulture);
textMaxLength.Text = Filter.MaxPeptideLength.ToString(LocalizationHelper.CurrentCulture);
textMinLength.Text = Filter.MinPeptideLength.ToString(LocalizationHelper.CurrentCulture);
cbAutoSelect.Checked = Filter.AutoSelect;
// Initialize spectral library settings
_driverLibrary = new SettingsListBoxDriver<LibrarySpec>(listLibraries, Settings.Default.SpectralLibraryList);
IList<LibrarySpec> listLibrarySpecs = Libraries.LibrarySpecs;
_driverLibrary.LoadList(null, listLibrarySpecs);
_driverBackgroundProteome = new SettingsListComboDriver<BackgroundProteomeSpec>(comboBackgroundProteome, Settings.Default.BackgroundProteomeList);
_driverBackgroundProteome.LoadList(_peptideSettings.BackgroundProteome.Name);
panelPick.Visible = listLibrarySpecs.Count > 0;
btnExplore.Enabled = listLibraries.Items.Count > 0;
comboMatching.SelectedIndex = (int) Libraries.Pick;
_lastRankId = Libraries.RankId;
_lastPeptideCount = Libraries.PeptideCount.HasValue
? Libraries.PeptideCount.Value.ToString(LocalizationHelper.CurrentCulture)
: null;
UpdateRanks(null);
// Initialize modification settings
_driverStaticMod = new SettingsListBoxDriver<StaticMod>(listStaticMods, Settings.Default.StaticModList);
_driverStaticMod.LoadList(null, Modifications.StaticModifications);
_driverHeavyMod = new SettingsListBoxDriver<StaticMod>(listHeavyMods, Settings.Default.HeavyModList);
_driverLabelType = new LabelTypeComboDriver(comboLabelType, Modifications, _driverHeavyMod,
labelStandardType, comboStandardType, listStandardTypes);
textMaxVariableMods.Text = Modifications.MaxVariableMods.ToString(LocalizationHelper.CurrentCulture);
textMaxNeutralLosses.Text = Modifications.MaxNeutralLosses.ToString(LocalizationHelper.CurrentCulture);
// Initialize peak scoring settings.
_driverPeakScoringModel = new SettingsListComboDriver<PeakScoringModelSpec>(comboPeakScoringModel, Settings.Default.PeakScoringModelList);
var peakScoringModel = _peptideSettings.Integration.PeakScoringModel;
_driverPeakScoringModel.LoadList(peakScoringModel != null ? peakScoringModel.Name : null);
IsShowLibraryExplorer = false;
tabControl1.TabPages.Remove(tabIntegration);
comboNormalizationMethod.Items.AddRange(
NormalizationMethod.ListNormalizationMethods(parent.DocumentUI).ToArray());
comboNormalizationMethod.SelectedItem = _peptideSettings.Quantification.NormalizationMethod;
comboWeighting.Items.AddRange(RegressionWeighting.All.Cast<object>().ToArray());
comboWeighting.SelectedItem = _peptideSettings.Quantification.RegressionWeighting;
comboRegressionFit.Items.AddRange(RegressionFit.All.Cast<object>().ToArray());
comboRegressionFit.SelectedItem = _peptideSettings.Quantification.RegressionFit;
comboQuantMsLevel.SelectedIndex = Math.Max(0, _quantMsLevels.IndexOf(_peptideSettings.Quantification.MsLevel));
tbxQuantUnits.Text = _peptideSettings.Quantification.Units;
}
public void ShowViewLibraryDlg(string libName = null)
{
CheckDisposed();
// Validate new settings without showing message boxes
PeptideSettings settings = ValidateNewSettings(false);
// Only update, if anything changed
if (!Equals(settings, _peptideSettings))
{
var result = MultiButtonMsgDlg.Show(
this,
Resources.PeptideSettingsUI_ShowViewLibraryDlg_Peptide_settings_have_been_changed_Save_changes,
MultiButtonMsgDlg.BUTTON_YES,
MultiButtonMsgDlg.BUTTON_NO,
true);
switch (result)
{
case DialogResult.Yes:
// If settings are null, then validation failed the first time
if (settings == null)
{
// Show the error this time
ValidateNewSettings(true);
return;
}
SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings);
if (_parent.ChangeSettings(newSettings, true))
{
_peptideSettings = settings;
}
break;
case DialogResult.No:
break;
case DialogResult.Cancel:
return;
}
}
IsShowLibraryExplorer = true;
DialogResult = DialogResult.OK;
var index = _parent.OwnedForms.IndexOf(form => form is ViewLibraryDlg);
if (index == -1)
{
// Selected library name should be the ListBox selected item if possible, else the first checked item,
// else the empty string.
if (libName == null)
{
libName = _driverLibrary.ListBox.SelectedItem != null
? _driverLibrary.ListBox.SelectedItem.ToString()
: (_driverLibrary.CheckedNames.Any() ? _driverLibrary.CheckedNames[0] : string.Empty);
}
var viewLibraryDlg = new ViewLibraryDlg(_libraryManager, libName, _parent) { Owner = Owner };
viewLibraryDlg.Show();
}
}
public void OkDialog()
{
PeptideSettings settings = ValidateNewSettings(true);
if (settings == null)
return;
// Only update, if anything changed
if (!Equals(settings, _peptideSettings))
{
if (!_parent.ChangeSettingsMonitored(this, Resources.PeptideSettingsUI_OkDialog_Changing_peptide_settings,
s => s.ChangePeptideSettings(settings)))
{
return;
}
_peptideSettings = settings;
}
DialogResult = DialogResult.OK;
}
public PeptideSettings MergeDefaults(PeptideSettings defPep)
{
PeptideSettings newPeptideSettings = ImClone(this);
newPeptideSettings.Enzyme = newPeptideSettings.Enzyme ?? defPep.Enzyme;
newPeptideSettings.DigestSettings = newPeptideSettings.DigestSettings ?? defPep.DigestSettings;
newPeptideSettings.Prediction = newPeptideSettings.Prediction ?? defPep.Prediction;
newPeptideSettings.Filter = newPeptideSettings.Filter ?? defPep.Filter;
newPeptideSettings.Libraries = newPeptideSettings.Libraries ?? defPep.Libraries;
newPeptideSettings.BackgroundProteome = newPeptideSettings.BackgroundProteome ?? defPep.BackgroundProteome;
newPeptideSettings.Modifications = newPeptideSettings.Modifications ?? defPep.Modifications;
newPeptideSettings.Integration = newPeptideSettings.Integration ?? defPep.Integration;
return Equals(newPeptideSettings, this) ? this : newPeptideSettings;
}
public bool Equals(PeptideSettings obj)
{
if (ReferenceEquals(null, obj)) return false;
if (ReferenceEquals(this, obj)) return true;
return Equals(obj.Enzyme, Enzyme) &&
Equals(obj.DigestSettings, DigestSettings) &&
Equals(obj.Prediction, Prediction) &&
Equals(obj.Filter, Filter) &&
Equals(obj.Libraries, Libraries) &&
Equals(obj.Modifications, Modifications) &&
Equals(obj.Integration, Integration) &&
Equals(obj.BackgroundProteome, BackgroundProteome) &&
Equals(obj.Quantification, Quantification);
}