public void Refresh()
{
if (websocket.IsConnected)
{
MidiObserver.Display(EMidiOBSItemType.ReloadOBSData, EMidiOBSOutputType.Off, -1, -1, true);
var studiomode = websocket.StudioModeEnabled();
Mode = studiomode ? 2 : 1;
OutputStatus = websocket.GetStreamingStatus();
CurrentTransition = websocket.GetCurrentTransition();
LoadSources();
LoadScenesAndSources();
LoadTransitions();
if (studiomode)
{
ActivePScene = -1;
var pscene = websocket.GetPreviewScene();
ActivePSceneName = pscene.Name;
for (int i = 0; i < Scenes.Count(); i++)
{
if (Scenes[i].Name == ActivePSceneName)
{
ActivePScene = i;
}
}
}
MidiObserver.Display(EMidiOBSItemType.ReloadOBSData, EMidiOBSOutputType.On, -1, -1, true);
MidiObserver.RenderSurface();
}
}
private bool UpdateTransitionSettings()
{
TransitionSettings newTransitionSettings = TransitionSettingsControl.GetTransitionSettings(this);
if (newTransitionSettings == null)
{
return(false);
}
TransitionSettingsControl.SetFields(newTransitionSettings);
// Only update, if anything changed
Helpers.AssignIfEquals(ref newTransitionSettings, TransitionSettings);
if (Equals(newTransitionSettings, TransitionSettings))
{
return(true);
}
if (SkylineWindow.ChangeSettings(SkylineWindow.DocumentUI.Settings.ChangeTransitionSettings(newTransitionSettings), true))
{
_transitionSettingsChanged = true;
return(true);
}
return(false);
}
void Transition(TransitionSettings transitionSettings, TransitionModeType transitionMode)
{
if (transitionMode == TransitionModeType.In && TransitionInConfig.OnTransitionStart != null)
{
TransitionInConfig.OnTransitionStart.Invoke();
}
else if (transitionMode == TransitionModeType.Out && TransitionOutConfig.OnTransitionStart != null)
{
TransitionOutConfig.OnTransitionStart.Invoke();
}
// set new transition id to stop all old transitions.
_activeTransitionId = Guid.NewGuid().ToString();
_transitionSettings = transitionSettings;
TransitionMode = transitionMode;
// get the easing function - will be null for unsupported types.
_easingFunction = TweenMethods.GetEasingFunction(_transitionSettings.TransitionType);
// if delay and duration are both zero then just set end state, otherwise run the transition.
if (Mathf.Approximately(_transitionSettings.Delay, 0) && Mathf.Approximately(_transitionSettings.Duration, 0))
{
SetProgress(1);
SetAmount(_endFloat);
}
else
{
SetProgress(0);
StartCoroutine(TransitionInternal(_activeTransitionId, transitionMode));
}
}
public static TransitionFilterAndLibrariesSettings GetDefault(TransitionSettings transitionSettings)
{
return(new TransitionFilterAndLibrariesSettings(transitionSettings.Filter.PeptidePrecursorChargesString,
transitionSettings.Filter.PeptideProductChargesString,
transitionSettings.Filter.PeptideIonTypesString, transitionSettings.Filter.ExclusionUseDIAWindow,
transitionSettings.Libraries.IonMatchTolerance, transitionSettings.Libraries.MinIonCount,
transitionSettings.Libraries.IonCount));
}
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 static TransitionFilterAndLibrariesSettings GetDefault(TransitionSettings transitionSettings)
{
return(new TransitionFilterAndLibrariesSettings(transitionSettings.Filter.PeptidePrecursorChargesString,
transitionSettings.Filter.PeptideProductChargesString,
transitionSettings.Filter.PeptideIonTypesString, transitionSettings.Filter.ExclusionUseDIAWindow,
transitionSettings.Libraries.IonMatchTolerance, transitionSettings.Libraries.MinIonCount,
transitionSettings.Libraries.IonCount, transitionSettings.Filter.FragmentRangeFirst.Label,
transitionSettings.Filter.FragmentRangeLast.Label, transitionSettings.Instrument.MinMz,
transitionSettings.Instrument.MaxMz));
}
public FragmentFilter(TransitionSettings transitionSettings, IEnumerable <Adduct> rankedAdducts, IEnumerable <IonType> rankedIonTypes)
{
TransitionSettings = transitionSettings;
FragmentMatchCount = TransitionSettings.Libraries.IonCount;
LibraryPick = TransitionSettings.Libraries.Pick;
AdductsToDisplay = RankedAdducts = ImmutableList.ValueOf(rankedAdducts);
IonTypesToDisplay = RankedIonTypes = ImmutableList.ValueOf(rankedIonTypes);
RankedCharges = ImmutableList.ValueOf(RankedAdducts.Select(adduct => Math.Abs(adduct.AdductCharge)).Distinct());
UseFilter = true;
}
public void SetFields(TransitionSettings settings)
{
PeptidePrecursorCharges = settings.Filter.PeptidePrecursorCharges.ToArray();
PeptideIonCharges = settings.Filter.PeptideProductCharges.ToArray();
PeptideIonTypes = settings.Filter.PeptideIonTypes.ToArray();
ExclusionUseDIAWindow = settings.Filter.ExclusionUseDIAWindow;
IonMatchTolerance = settings.Libraries.IonMatchTolerance;
MinIonCount = settings.Libraries.MinIonCount;
IonCount = settings.Libraries.IonCount;
}
private bool ApplyRanking(RankingState rankingState, double ionMz, MatchedFragmentIon match, bool filter, int start, int end, double startMz, ref RankedMI rankedMI)
{
// Avoid ranking precursor ions without losses, if the precursor isotopes will
// not be taken from product ions
if (!ExcludePrecursorIsotopes || match.IonType != IonType.precursor || match.Losses != null)
{
int offset = OrdinalToOffset(match.IonType, match.Ordinal);
var type = match.IonType;
if (filter)
{
if (TargetInfoObj.LookupMods == null || !TargetInfoObj.LookupMods.HasCrosslinks)
{
if (!TransitionSettings.Accept(Sequence, MoleculeMassesObj.precursorMz, type, offset, ionMz, start,
end, startMz))
{
return(false);
}
}
}
if (rankingState.matchAll)
{
if (MinMz > ionMz || ionMz > MaxMz)
{
return(false);
}
if (!RankTypes.Contains(type))
{
return(false);
}
if (RankLimit.HasValue && rankingState.Ranked >= RankLimit)
{
return(false);
}
if (type != IonType.precursor)
{
// CONSIDER(bspratt) we may eventually want adduct-level control for small molecules, not just abs charge
if (!RankCharges.Contains(Math.Abs(match.Charge.AdductCharge)))
{
return(false);
}
}
}
rankedMI = rankedMI.ChangeRank(rankingState.RankNext());
return(true);
}
return(false);
}
public TransitionSettingsControl(SkylineWindow skylineWindow)
{
SkylineWindow = skylineWindow;
TransitionSettings settings = SkylineWindow.DocumentUI.Settings.TransitionSettings;
InitializeComponent();
PrecursorCharges = settings.Filter.PrecursorCharges.ToArray();
IonCharges = settings.Filter.ProductCharges.ToArray();
IonTypes = settings.Filter.IonTypes.Union(new[] { IonType.precursor, IonType.y }).ToArray(); // Add p, y if not already set
ExclusionUseDIAWindow = settings.Filter.ExclusionUseDIAWindow;
IonMatchTolerance = settings.Libraries.IonMatchTolerance;
IonCount = settings.Libraries.IonCount;
}
public void SetFields(TransitionSettings settings)
{
PeptidePrecursorCharges = settings.Filter.PeptidePrecursorCharges.ToArray();
PeptideIonCharges = settings.Filter.PeptideProductCharges.ToArray();
PeptideIonTypes = settings.Filter.PeptideIonTypes.ToArray();
ExclusionUseDIAWindow = settings.Filter.ExclusionUseDIAWindow;
IonMatchTolerance = settings.Libraries.IonMatchTolerance;
MinIonCount = settings.Libraries.MinIonCount;
IonCount = settings.Libraries.IonCount;
IonRangeFrom = settings.Filter.FragmentRangeFirst.Label;
IonRangeTo = settings.Filter.FragmentRangeLast.Label;
MinIonMz = settings.Instrument.MinMz;
MaxIonMz = settings.Instrument.MaxMz;
}
public void OBSCurrentTransitionInfo_BuildFromJSON()
{
string transitionName = "Transition name éèïöü";
int duration = 2000;
var data = new JObject();
data.Add("name", transitionName);
data.Add("duration", duration);
var transitionInfo = new TransitionSettings(data);
Assert.AreEqual(transitionName, transitionInfo.Name);
Assert.AreEqual(duration, transitionInfo.Duration);
}
private SOBSTransition _translateActiveTransition(TransitionSettings input)
{
SOBSTransition transition = new SOBSTransition();
transition.Name = input.Name;
transition.Id = _uidFromString(input.Name);
for (int i = 0; i < Transitions.Count; i++)
{
if (Transitions[i].Id == transition.Id)
{
transition.Index = i;
}
}
return(transition);
}
public void Transition(TransitionSettings transitionSettings, Vector3 startAmount, Vector3 endAmount, TransitionModeType transitionMode)
{
// if this transition should not run then return immediately
if (transitionSettings.TransitionType == TransitionHelper.TransitionType.none)
{
return;
}
// save transition values
_targetType = TargetTypeEnum.Vector3;
_startVector3 = startAmount;
_endVector3 = endAmount;
// start transition
Transition(transitionSettings, transitionMode);
}
private bool UpdateTransitionSettings()
{
TransitionSettings newTransitionSettings = TransitionSettingsControl.GetTransitionSettings(this);
if (newTransitionSettings == null)
{
return(false);
}
TransitionSettingsControl.SetFields(newTransitionSettings);
// Only update, if anything changed
Helpers.AssignIfEquals(ref newTransitionSettings, TransitionSettings);
if (Equals(newTransitionSettings, TransitionSettings))
{
return(true);
}
ModifyDocumentNoUndo(doc => doc.ChangeSettings(doc.Settings.ChangeTransitionSettings(newTransitionSettings)));
_transitionSettingsChanged = true;
return(true);
}
private void InitializeComponent()
{
AvaloniaXamlLoader.Load(this);
if (Environment.OSVersion.Platform == PlatformID.Win32NT)
{
this.ExtendClientAreaToDecorationsHint = true;
this.ExtendClientAreaTitleBarHeightHint = -1;
this.ExtendClientAreaChromeHints = Avalonia.Platform.ExtendClientAreaChromeHints.NoChrome;
this.TransparencyLevelHint = WindowTransparencyLevel.AcrylicBlur;
this.Background = new SolidColorBrush(Colors.Transparent);
}
WindowTitle = "SingleWindow";
Transition = new TransitionSettings(TransitionSettings.EnterTransitions.SlideLeft, TimeSpan.FromMilliseconds(250));
BackKey = Key.Escape;
m_Container = this.FindControl <Grid>("m_Container");
m_TitleBar = this.FindControl <Controls.TitleBar>("m_TitleBar");
Closing += OnWindowClosing;
KeyDown += OnKeyDown;
}
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 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 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));
}
/// <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 void ReporterIonTest()
{
// Test the code that updates old-style formulas
Assert.AreEqual("C5C'H13N2", BioMassCalc.AddH("C5C'H12N2"));
Assert.AreEqual("CO2H", BioMassCalc.AddH("CO2"));
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(10))); // H2O2 is not very heavy!
IdentityPath path;
SrmDocument docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8));
const string formula = "H2O2"; // This was H2O, but that falls below mz=10 at z > 1
const string hydrogenPeroxide = "Hydrogen Perxoide";
var reporterIons = new[] { new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.SINGLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.DOUBLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.TRIPLY_PROTONATED), MeasuredIonList.NTERM_PROLINE };
SrmDocument docReporterIon = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(reporterIons)));
AssertEx.IsDocumentTransitionCount(docReporterIon, 7);
//Check With Monoisotopic
var mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = docReporterIon.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Check with Average
TransitionPrediction predSettings =
docReporterIon.Settings.TransitionSettings.Prediction.ChangeFragmentMassType(MassType.Average);
TransitionSettings tranSettings = docReporterIon.Settings.TransitionSettings.ChangePrediction(predSettings);
SrmSettings srmSettings = docReporterIon.Settings.ChangeTransitionSettings(tranSettings);
SrmDocument averageDocument = docReporterIon.ChangeSettings(srmSettings);
mass = BioMassCalc.AVERAGE.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = averageDocument.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Make sure the rest of the transitions aren't reporter ions
for (int i = 3; i < 7; i++)
{
Transition tran = docReporterIon.MoleculeTransitions.ElementAt(i).Transition;
Assert.AreNotEqual(tran.CustomIon, reporterIons);
}
var optionalIon = new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.SINGLY_PROTONATED, true);
SrmDocument optionalDoc = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { optionalIon })));
Assert.AreEqual(3, optionalDoc.PeptideTransitionCount);
optionalDoc = optionalDoc.ChangeSettings(optionalDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(false) })));
AssertEx.IsDocumentTransitionCount(optionalDoc, 4);
Assert.AreEqual(optionalIon.ChangeIsOptional(false).SettingsCustomIon,
optionalDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
optionalDoc =
optionalDoc.ChangeSettings(
optionalDoc.Settings.ChangeTransitionFilter(
filter => filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(true) })));
TransitionGroupDocNode nodeGroup = optionalDoc.MoleculeTransitionGroups.ElementAt(0);
var filteredNodes =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, true)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
var unfilteredNodes =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, false)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
Assert.AreEqual(0, filteredNodes.Count());
Assert.AreEqual(1, unfilteredNodes.Count());
}
/// <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;
}
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 SrmSettings ChangeTransitionSettings(TransitionSettings prop)
{
// If changing to only MS1 filtering, make sure Integrat All is on
if (IsOnlyMsEnabled(prop.FullScan) && !IsOnlyMsEnabled(TransitionSettings.FullScan))
{
if (!prop.Integration.IsIntegrateAll)
prop = prop.ChangeIntegration(prop.Integration.ChangeIntegrateAll(true));
}
SrmSettings settings = ChangeProp(ImClone(this), im => im.TransitionSettings = prop);
if (prop.Prediction.PrecursorMassType != TransitionSettings.Prediction.PrecursorMassType)
settings.CreatePrecursorMassCalcs();
if (prop.Prediction.FragmentMassType != TransitionSettings.Prediction.FragmentMassType)
settings.CreateFragmentMassCalcs();
return settings;
}
/// <summary>
/// Makes sure settings loaded from XML are complete, and uses default
/// values where anything is missing.
/// </summary>
private void ValidateLoad()
{
SrmSettings defaults = SrmSettingsList.GetDefault();
PeptideSettings defPep = defaults.PeptideSettings;
if (PeptideSettings == null)
PeptideSettings = defPep;
else
{
PeptideSettings = PeptideSettings.MergeDefaults(defPep);
}
TransitionSettings defTran = defaults.TransitionSettings;
if (TransitionSettings == null)
TransitionSettings = defTran;
else
{
TransitionPrediction prediction = TransitionSettings.Prediction;
// Backward compatibility: handle the move of RetentionTime
// from TransitionSettings to PeptideSettings after v0.1.0.0
if (TransitionSettings.Prediction == null)
prediction = defTran.Prediction;
else if (prediction.RetentionTime != null)
{
if (PeptideSettings.Prediction != null && // Make Resharper happy
PeptideSettings.Prediction.RetentionTime == null)
{
PeptideSettings = PeptideSettings.ChangePrediction(
new PeptidePrediction(prediction.RetentionTime));
}
prediction = new TransitionPrediction(prediction);
}
TransitionFilter filter = TransitionSettings.Filter ?? defTran.Filter;
TransitionLibraries libraries = TransitionSettings.Libraries ?? defTran.Libraries;
TransitionIntegration integration = TransitionSettings.Integration ?? defTran.Integration;
TransitionInstrument instrument = TransitionSettings.Instrument ?? defTran.Instrument;
TransitionFullScan fullScan = TransitionSettings.FullScan ?? defTran.FullScan;
// Backward compatibility with v2.1, get a RT filter length from peptide prediction settings
if (fullScan.RetentionTimeFilterType == RetentionTimeFilterType.scheduling_windows &&
fullScan.RetentionTimeFilterLength == 0 &&
PeptideSettings.Prediction != null)
{
double rtFilterLen = 0;
if (PeptideSettings.Prediction.UseMeasuredRTs)
{
rtFilterLen = PeptideSettings.Prediction.MeasuredRTWindow.Value / 2;
}
else if (PeptideSettings.Prediction.RetentionTime != null)
{
rtFilterLen = PeptideSettings.Prediction.RetentionTime.TimeWindow / 2;
}
if (rtFilterLen > 0)
{
fullScan = fullScan.ChangeRetentionTimeFilter(fullScan.RetentionTimeFilterType, rtFilterLen);
}
}
TransitionSettings transitionSettings = new TransitionSettings(prediction,
filter,
libraries,
integration,
instrument,
fullScan);
// If the above null checks result in a changed PeptideSettings object,
// then use the changed version.
if (!Equals(TransitionSettings, transitionSettings))
TransitionSettings = transitionSettings;
}
// Initialize mass calculators
CreatePrecursorMassCalcs();
CreateFragmentMassCalcs();
}
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 override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
reader.ReadStartElement();
PeptideSettings = reader.DeserializeElement<PeptideSettings>();
TransitionSettings = reader.DeserializeElement<TransitionSettings>();
// 10.23.12 -- The order of <measured_results> and <data_settings> has been switched to enable parsing (in Panorama)
// of all annotation definitions before reading any replicate annotations in <measured_results>.
// We want Skyline to be able to read older documents where <measured_results> come before <data_settings>
if (reader.IsStartElement(new XmlElementHelper<MeasuredResults>().ElementNames[0]))
{
MeasuredResults = reader.DeserializeElement<MeasuredResults>();
DataSettings = reader.DeserializeElement<DataSettings>() ?? DataSettings.DEFAULT;
}
else
{
DataSettings = reader.DeserializeElement<DataSettings>() ?? DataSettings.DEFAULT;
MeasuredResults = reader.DeserializeElement<MeasuredResults>();
}
DocumentRetentionTimes = reader.DeserializeElement<DocumentRetentionTimes>() ?? DocumentRetentionTimes.EMPTY;
reader.ReadEndElement();
ValidateLoad();
}
/// <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, UsageMode usageMode, string title, Identity initialId,
IEnumerable <Identity> existingIds, int minCharge, int maxCharge,
SrmSettings settings, CustomMolecule molecule, Adduct defaultCharge,
ExplicitTransitionGroupValues explicitTransitionGroupAttributes,
ExplicitTransitionValues explicitTransitionAttributes,
ExplicitRetentionTimeInfo explicitRetentionTime,
IsotopeLabelType defaultIsotopeLabelType)
{
Text = title;
_parent = parent;
_initialId = initialId;
_existingIds = existingIds;
_minCharge = minCharge;
_maxCharge = maxCharge;
_transitionSettings = settings != null ? settings.TransitionSettings : null;
_peptideSettings = settings != null ? settings.PeptideSettings : null;
_resultAdduct = Adduct.EMPTY;
_resultCustomMolecule = molecule;
_usageMode = usageMode;
var enableFormulaEditing = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.moleculeEdit ||
usageMode == UsageMode.fragment;
var enableAdductEditing = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.precursor ||
usageMode == UsageMode.fragment;
var suggestOnlyAdductsWithMass = usageMode != UsageMode.fragment;
var needExplicitTransitionValues = usageMode == UsageMode.fragment;
var needExplicitTransitionGroupValues = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.precursor;
InitializeComponent();
NameText = molecule == null ? String.Empty : molecule.Name;
textName.Enabled = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.moleculeEdit ||
usageMode == UsageMode.fragment; // Can user edit name?
var needOptionalValuesBox = explicitRetentionTime != null || explicitTransitionGroupAttributes != null || explicitTransitionAttributes != null;
if (!needExplicitTransitionValues)
{
labelCollisionEnergy.Visible = false;
textCollisionEnergy.Visible = false;
labelSLens.Visible = false;
textSLens.Visible = false;
labelConeVoltage.Visible = false;
textConeVoltage.Visible = false;
labelIonMobilityHighEnergyOffset.Visible = false;
textIonMobilityHighEnergyOffset.Visible = false;
labelDeclusteringPotential.Visible = false;
textDeclusteringPotential.Visible = false;
}
if (!needExplicitTransitionGroupValues)
{
labelCCS.Visible = false;
textBoxCCS.Visible = false;
labelIonMobility.Visible = false;
textIonMobility.Visible = false;
labelIonMobilityUnits.Visible = false;
comboBoxIonMobilityUnits.Visible = false;
}
var heightDelta = 0;
// Initialise the ion mobility units dropdown with L10N values
foreach (eIonMobilityUnits t in Enum.GetValues(typeof(eIonMobilityUnits)))
{
comboBoxIonMobilityUnits.Items.Add(IonMobilityFilter.IonMobilityUnitsL10NString(t));
}
if (needOptionalValuesBox)
{
var newHeight = groupBoxOptionalValues.Height;
var movers = new List <Control>();
int offset = 0;
if (!needExplicitTransitionGroupValues && !needExplicitTransitionValues)
{
// We blanked out everything but the retention time
newHeight = labelCollisionEnergy.Location.Y;
}
else if (!needExplicitTransitionGroupValues)
{
// We need to shift transition-level items up to where retention time was
movers.AddRange(new Control[] {
textCollisionEnergy, labelCollisionEnergy, textDeclusteringPotential, labelDeclusteringPotential, textSLens,
labelSLens, textConeVoltage, labelConeVoltage, textIonMobilityHighEnergyOffset, labelIonMobilityHighEnergyOffset
});
labelIonMobilityHighEnergyOffset.Location = labelIonMobility.Location;
textIonMobilityHighEnergyOffset.Location = textIonMobility.Location;
offset = labelCollisionEnergy.Location.Y - labelRetentionTime.Location.Y;
newHeight = textBoxCCS.Location.Y;
}
else if (!needExplicitTransitionValues)
{
// We need to shift precursor-level items up to where retention time was
movers.AddRange(new Control[] { textBoxCCS, labelCCS, textIonMobility,
labelIonMobility, comboBoxIonMobilityUnits, labelIonMobilityUnits });
offset = labelIonMobility.Location.Y - (explicitRetentionTime == null ? labelRetentionTime.Location.Y : labelCollisionEnergy.Location.Y);
newHeight = explicitRetentionTime == null ? textSLens.Location.Y : textIonMobility.Location.Y;
}
foreach (var mover in movers)
{
mover.Anchor = AnchorStyles.Left | AnchorStyles.Top;
mover.Location = new Point(mover.Location.X, mover.Location.Y - offset);
}
heightDelta = groupBoxOptionalValues.Height - newHeight;
groupBoxOptionalValues.Height = newHeight;
}
ResultExplicitTransitionGroupValues = new ExplicitTransitionGroupValues(explicitTransitionGroupAttributes);
ResultExplicitTransitionValues = new ExplicitTransitionValues(explicitTransitionAttributes);
string labelAverage = !defaultCharge.IsEmpty
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_mass_;
string labelMono = !defaultCharge.IsEmpty
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_mass_;
var defaultFormula = molecule == null ? string.Empty : molecule.Formula;
var transition = initialId as Transition;
FormulaBox.EditMode editMode;
if (enableAdductEditing && !enableFormulaEditing)
{
editMode = FormulaBox.EditMode.adduct_only;
}
else if (!enableAdductEditing && enableFormulaEditing)
{
editMode = FormulaBox.EditMode.formula_only;
}
else
{
editMode = FormulaBox.EditMode.formula_and_adduct;
}
string formulaBoxLabel;
if (defaultCharge.IsEmpty)
{
formulaBoxLabel = Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_Chemi_cal_formula_;
}
else if (editMode == FormulaBox.EditMode.adduct_only)
{
var prompt = defaultFormula;
if (string.IsNullOrEmpty(defaultFormula) && molecule != null)
{
// Defined by mass only
prompt = molecule.ToString();
}
formulaBoxLabel = string.Format(Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_Addu_ct_for__0__,
prompt);
}
else
{
formulaBoxLabel = Resources.EditMeasuredIonDlg_EditMeasuredIonDlg_Ion__chemical_formula_;
}
double?averageMass = null;
double?monoMass = null;
if (transition != null && string.IsNullOrEmpty(defaultFormula) && transition.IsCustom())
{
averageMass = transition.CustomIon.AverageMass;
monoMass = transition.CustomIon.MonoisotopicMass;
}
else if (molecule != null)
{
averageMass = molecule.AverageMass;
monoMass = molecule.MonoisotopicMass;
}
_formulaBox =
new FormulaBox(false, // Not proteomic, so offer Cl and Br in atoms popup
formulaBoxLabel,
labelAverage,
labelMono,
defaultCharge,
editMode,
suggestOnlyAdductsWithMass)
{
NeutralFormula = defaultFormula,
AverageMass = averageMass,
MonoMass = monoMass,
Location = new Point(textName.Left, textName.Bottom + 12)
};
_formulaBox.ChargeChange += (sender, args) =>
{
if (!_formulaBox.Adduct.IsEmpty)
{
Adduct = _formulaBox.Adduct;
var revisedFormula = _formulaBox.NeutralFormula + Adduct.AdductFormula;
if (!Equals(revisedFormula, _formulaBox.Formula))
{
_formulaBox.Formula = revisedFormula;
}
if (string.IsNullOrEmpty(_formulaBox.NeutralFormula) && averageMass.HasValue)
{
_formulaBox.AverageMass = averageMass;
_formulaBox.MonoMass = monoMass;
}
}
};
Controls.Add(_formulaBox);
_formulaBox.TabIndex = 2;
_formulaBox.Enabled = enableFormulaEditing || enableAdductEditing;
Adduct = defaultCharge;
var needCharge = !Adduct.IsEmpty;
textCharge.Visible = labelCharge.Visible = needCharge;
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;
}
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(PeptideSettingsUI.LabelTypeComboDriver.UsageType.InternalStandardPicker, comboIsotopeLabelType,
settings.PeptideSettings.Modifications, null, null, null, null)
{
SelectedName = defaultIsotopeLabelType.Name
};
}
else
{
comboIsotopeLabelType.Visible = false;
labelIsotopeLabelType.Visible = false;
}
Height -= heightDelta;
}
