public PrecursorTextId(SignedMz precursorMz, IonMobilityFilter ionMobilityFilter, Target target, ChromExtractor extractor) : this()
{
PrecursorMz = precursorMz;
IonMobility = ionMobilityFilter ?? IonMobilityFilter.EMPTY;
Target = target;
Extractor = extractor;
}
// Used by TransitionGroupDocNode.AddChromInfo to aggregate ion mobility information from all transitions
public TransitionGroupIonMobilityInfo AddIonMobilityFilterInfo(IonMobilityFilter ionMobility, bool isMs1)
{
var val = Equals(ionMobility.IonMobilityExtractionWindowWidth, IonMobilityWindow) ? this : ChangeProp(ImClone(this), im => im.IonMobilityWindow = ionMobility.IonMobilityExtractionWindowWidth);
if (ionMobility.IonMobility.Units != IonMobilityUnits && ionMobility.IonMobility.Units != MsDataFileImpl.eIonMobilityUnits.none)
{
val = ChangeProp(ImClone(val), im => im.IonMobilityUnits = ionMobility.IonMobility.Units);
}
// Filling in MS1 or MS2 data, or just more of what we already know
if (isMs1)
{
// We expect these all to be the same for MS1, but can't assert that here because we
// may be in the process of re-import with a different filter setting.
val = Equals(ionMobility.IonMobility.Mobility, val.IonMobilityMS1) ? val : ChangeProp(ImClone(val), im => im.IonMobilityMS1 = ionMobility.IonMobility.Mobility);
}
else
{
// We expect these all to be the same for MS/MS, but can't assert that here because we
// may be in the process of re-import with a different filter setting.
val = Equals(ionMobility.IonMobility.Mobility, val.IonMobilityFragment) ? val : ChangeProp(ImClone(val), im => im.IonMobilityFragment = ionMobility.IonMobility.Mobility);
}
if (ionMobility.CollisionalCrossSectionSqA.HasValue && !Equals(ionMobility.CollisionalCrossSectionSqA, val.CollisionalCrossSection))
{
val = ChangeProp(ImClone(val), im => im.CollisionalCrossSection = ionMobility.CollisionalCrossSectionSqA);
}
return(val);
}
public EditDriftTimePredictorDlg(IEnumerable <IonMobilityPredictor> existing)
{
_existing = existing;
_showRegressions = true;
InitializeComponent();
foreach (eIonMobilityUnits units in Enum.GetValues(typeof(eIonMobilityUnits)))
{
if (units != eIonMobilityUnits.none) // Don't present "none" as an option
{
comboBoxIonMobilityUnits.Items.Add(IonMobilityFilter.IonMobilityUnitsL10NString(units));
}
}
_smallMoleculeUI = Program.MainWindow.Document.HasSmallMolecules || Program.MainWindow.ModeUI != SrmDocument.DOCUMENT_TYPE.proteomic;
if (_smallMoleculeUI)
{
gridMeasuredDriftTimes.Columns[COLUMN_SEQUENCE].HeaderText = Resources.EditDriftTimePredictorDlg_EditDriftTimePredictorDlg_Molecule;
gridMeasuredDriftTimes.Columns[COLUMN_CHARGE].HeaderText = Resources.EditDriftTimePredictorDlg_EditDriftTimePredictorDlg_Adduct;
}
var targetResolver = TargetResolver.MakeTargetResolver(Program.ActiveDocumentUI);
MeasuredDriftTimeSequence.TargetResolver = targetResolver;
// TODO: ion mobility libraries are more complex than initially thought - leave these conversions to the mass spec vendors for now
labelIonMobilityLibrary.Visible = comboLibrary.Visible = false;
Icon = Resources.Skyline;
_driverIonMobilityLibraryListComboDriver = new SettingsListComboDriver <IonMobilityLibrarySpec>(comboLibrary, Settings.Default.IonMobilityLibraryList);
_driverIonMobilityLibraryListComboDriver.LoadList(null);
UpdateControls();
}
public IonMobilityFilter GetIonMobilityWindow()
{
if (MinIonMobilityValue.HasValue && MaxIonMobilityValue.HasValue)
{
// High energy (product ion) scans may have a faster ion mobility, as in Waters MsE, that gets applied elsewhere
var width = MaxIonMobilityValue.Value - MinIonMobilityValue.Value;
var center = MinIonMobilityValue.Value + 0.5 * width;
return(IonMobilityFilter.GetIonMobilityFilter(IonMobilityValue.GetIonMobilityValue(center, IonMobilityInfo.IonMobility.Units), width, IonMobilityInfo.CollisionalCrossSectionSqA));
}
else
{
return(IonMobilityFilter.EMPTY);
}
}
public IonMobilityFilter GetIonMobilityWindow(bool highEnergy)
{
if (MinIonMobilityValue.HasValue && MaxIonMobilityValue.HasValue)
{
// High energy (product ion) scans may have a faster ion mobility, as in Waters MsE
double offset = highEnergy ? HighEnergyIonMobilityValueOffset : 0;
var width = MaxIonMobilityValue.Value - MinIonMobilityValue.Value;
var center = offset + MinIonMobilityValue.Value + 0.5 * width;
return(IonMobilityFilter.GetIonMobilityFilter(IonMobilityValue.GetIonMobilityValue(center, IonMobilityInfo.IonMobility.Units), width, IonMobilityInfo.CollisionalCrossSectionSqA));
}
else
{
return(IonMobilityFilter.EMPTY);
}
}
public ExtractedSpectrum(Target target,
Color peptideColor,
SignedMz precursorMz,
IonMobilityFilter ionMobility,
ChromExtractor chromExtractor,
int filterIndex,
SpectrumProductFilter[] productFilters,
float[] intensities,
float[] massErrors)
{
Target = target;
PeptideColor = peptideColor;
PrecursorMz = precursorMz;
IonMobility = ionMobility;
Extractor = chromExtractor;
FilterIndex = filterIndex;
ProductFilters = productFilters;
Intensities = intensities;
MassErrors = massErrors;
}
public EditDriftTimePredictorDlg(IEnumerable <IonMobilityPredictor> existing)
{
_existing = existing;
_showRegressions = true;
InitializeComponent();
foreach (MsDataFileImpl.eIonMobilityUnits units in Enum.GetValues(typeof(MsDataFileImpl.eIonMobilityUnits)))
{
if (units != MsDataFileImpl.eIonMobilityUnits.none) // Don't present "none" as an option
{
comboBoxIonMobilityUnits.Items.Add(IonMobilityFilter.IonMobilityUnitsL10NString(units));
}
}
// TODO: ion mobility libraries are more complex than initially thought - leave these conversions to the mass spec vendors for now
labelIonMobilityLibrary.Visible = comboLibrary.Visible = false;
Icon = Resources.Skyline;
_driverIonMobilityLibraryListComboDriver = new SettingsListComboDriver <IonMobilityLibrarySpec>(comboLibrary, Settings.Default.IonMobilityLibraryList);
_driverIonMobilityLibraryListComboDriver.LoadList(null);
UpdateControls();
}
/// <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;
}
/// <summary>
/// Create an ion mobility heat map graph.
/// </summary>
private void CreateIonMobilityHeatmap()
{
GraphPane.YAxis.Title.Text = IonMobilityFilter.IonMobilityUnitsL10NString(_msDataFileScanHelper.IonMobilityUnits);
graphControl.IsEnableVZoom = graphControl.IsEnableVPan = true;
if (_heatMapData == null)
{
var points = new List <Point3D>(5000);
foreach (var scan in _msDataFileScanHelper.MsDataSpectra)
{
if (!scan.IonMobility.HasValue && scan.IonMobilities == null)
{
continue;
}
for (int j = 0; j < scan.Mzs.Length; j++)
{
double mobilityValue = scan.IonMobilities != null
? scan.IonMobilities[j]
: scan.IonMobility.Mobility.Value;
points.Add(new Point3D(scan.Mzs[j], mobilityValue, scan.Intensities[j]));
}
}
_heatMapData = new HeatMapData(points);
}
double minDrift;
double maxDrift;
_msDataFileScanHelper.GetIonMobilityRange(out minDrift, out maxDrift, _msDataFileScanHelper.Source); // There may be a different drift time filter for products in Waters
if (minDrift > 0 && maxDrift < double.MaxValue)
{
// Add gray shaded box behind heat points.
var driftTimeBox = new BoxObj(
0.0,
maxDrift,
1.0,
maxDrift - minDrift,
Color.Transparent,
Color.FromArgb(50, Color.Gray))
{
Location = { CoordinateFrame = CoordType.XChartFractionYScale },
ZOrder = ZOrder.F_BehindGrid,
IsClippedToChartRect = true,
};
GraphPane.GraphObjList.Add(driftTimeBox);
// Add outline in front of heat points, so you can tell where the limits are in a dense graph.
var driftTimeOutline = new BoxObj(
0.0,
maxDrift,
1.0,
maxDrift - minDrift,
Color.FromArgb(50, Color.DarkViolet),
Color.Transparent)
{
Location = { CoordinateFrame = CoordType.XChartFractionYScale },
ZOrder = ZOrder.C_BehindChartBorder,
IsClippedToChartRect = true,
Border = new Border(Color.FromArgb(100, Color.DarkViolet), 2)
};
GraphPane.GraphObjList.Add(driftTimeOutline);
}
if (!Settings.Default.FilterIonMobilityFullScan)
{
minDrift = 0;
maxDrift = double.MaxValue;
}
var heatMapGraphPane = (HeatMapGraphPane)GraphPane;
heatMapGraphPane.SetPoints(_heatMapData, minDrift, maxDrift);
}
private void TestReports(string msg = null)
{
// Verify reports working for CCS
var row = 10;
var documentGrid = EnableDocumentGridIonMobilityResultsColumns();
var imPrecursor = .97;
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityMS1", row, imPrecursor, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "TransitionResult.IonMobilityFragment", row, imPrecursor, msg); // Document is all precursor
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityUnits", row, IonMobilityFilter.IonMobilityUnitsL10NString(eIonMobilityUnits.inverse_K0_Vsec_per_cm2), msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityWindow", row, 0.03, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.CollisionalCrossSection", row, 392.02, msg);
EnableDocumentGridColumns(documentGrid,
Resources.ReportSpecList_GetDefaults_Peptide_RT_Results,
210);
var rts = new double?[] {
12.45, 21.48, 16.93, 22.93, 13.63, 19.12, 28.97, 14.88, 14.24, 27.25, 14.97, 14.26, 25.7, 15.06, 11.93, 26.37, 12.89, 15.88,
18.34, 11.16, 10.46, 10.98, 28, 24.01, 11.15, 18.97, 23.33, 26.56, 11.94, 19, 24.2, 23.42, 26.1, 27.86, 27.76, 20.99, 26.15,
21.16, 25.99, 14.29, 26.04, 15.04, 24.07, 28.15, 20.1, 26.03, 15.07, 19.78, 27.2, 21.26, 25.39, 25.04, 11.71, 21.1, 20.51,
14.71, 25.24, 24.9, 28.57, 21.13, 17.19, 15.39, 18.08, 16.06, 26.11, 10.26, 13.11, 9.46, 10.78, 14.42, 25.16, 26.36, 17.21,
24.79, 13.9, 20.63, 19.7, 22.5, 13.97, 19.34, 19.05, 18.45, 13.96, 6.59, 26.12, 17.76, 28.31, 24.27, 29.25, 27.56, 23.72,
12.09, 8.92, 18.39, 20.23, 26.42, 28.45, 22.17, 15.17, 24.73, 28.22, 17.16, 9.59, 13.84, 22.91, 17.14, 19.92, 24.24, 27.82,
24.67, 10.41, 12.27, 21.21, 18.69, 12.68, 21.09, 22.11, 21.43, 14.51, 17.31, 21.92, 22.43, 19.53, 25.24, 25.31, 11.61, 24.37,
10.07, 24.29, 23.28, 15.83, 14.87, 28.53, 14.85, 28.5, 22.49, 19.35, 24.81, 24.57, 24.63, 24.36, 15.46, 22.7, 19.85, 22.56,
21.91, 15.97, 20.82, 13.62, 19.52, 15.55, 23.71, 30.35, 19.57, 13.57, 29.08, 15.56, 21.73, 16.05, 13.95, 25.39, 14.3, 25.3,
15.72, 10.48, 9.88, 21.31, 9.92, 26.56, 27.89, 29.85, 22.12, 25.06, 21.53, 15.25, 21.13, 22.81, 20.44, 18.23, 11.49, 25.59,
20.13, 16.32, 13.19, 9.63, 12.11, 21.84, 10.83, 12.49, 16.99, 18.83, 11.71, 12.84, 17.31, 11.13, 12.88, 24.35, 16.83, 15.26,
22.72, 8.45, 11.17, 18.41, 18.85, 22.18, 16.56, 10.02, 10.13, 25.91, 29.07
};
for (row = 0; row < rts.Length; row++)
{
var rt = rts[row];
var recordNewValues = false;
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
CheckDocumentResultsGridFieldByName(documentGrid, "PeptideRetentionTime", row, rt, msg, recordNewValues);
}
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
private void TestReports(string msg = null)
{
// Verify reports working for CCS
var documentGrid = EnableDocumentGridIonMobilityResultsColumns();
var expectedIM = new[, ]
{
// Values recorded from master branch - imMS1, imFragment, imWindow
{ 26.47, 26.63, 1.06 },
{ 25.65, 25.65, 1.03 },
{ 28.75, 28.92, 1.15 },
{ 28.26, 28.26, 1.13 },
{ 22.87, 22.87, 0.91 },
{ 27.77, 27.77, 1.11 },
{ 24.51, 24.67, 0.98 },
{ 29.41, 29.57, 1.18 },
{ 22.22, 22.38, 0.89 },
{ 25.81, 26.14, 1.03 },
{ 22.71, 22.87, 0.91 },
{ 23.36, 23.36, 0.93 },
{ 27.77, 27.77, 1.11 },
{ 28.43, 28.59, 1.14 },
{ 29.41, 27.94, 1.18 },
{ 24.02, 24.18, 0.96 },
{ 27.77, 27.94, 1.11 },
{ 25, 24.83, 1 },
{ 30.39, 30.55, 1.22 }
};
double lastMz = -1;
var colMz = FindDocumentGridColumn(documentGrid, "Precursor.Mz");
var colFragment = FindDocumentGridColumn(documentGrid, "FragmentIon");
var precursorIndex = -1;
for (var row = 0; row < SkylineWindow.Document.MoleculeTransitions.Count(); row++)
{
if (IsRecordMode)
{
Console.Write(@"{");
}
var isFragment = false;
RunUI(() =>
{
var mz = (double)documentGrid.DataGridView.Rows[row].Cells[colMz.Index].Value;
if (mz != lastMz)
{
lastMz = mz;
precursorIndex++;
}
var fragmentName = documentGrid.DataGridView.Rows[row].Cells[colFragment.Index].Value.ToString();
isFragment = fragmentName.StartsWith("y") || fragmentName.StartsWith("b");
});
var unfilteredReplicate = row % 2 == 0;
var expectedPrecursorIM = unfilteredReplicate ? null : (double?)expectedIM[precursorIndex, 0];
var expectedFragmentIM = unfilteredReplicate ? null : (double?)expectedIM[precursorIndex, isFragment ? 1 : 0];
var expectedWindow = unfilteredReplicate ? null : (double?)expectedIM[precursorIndex, 2];
var expectedUnits = IonMobilityFilter.IonMobilityUnitsL10NString(unfilteredReplicate ? eIonMobilityUnits.none : eIonMobilityUnits.drift_time_msec);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityMS1", row, expectedPrecursorIM, msg, IsRecordMode);
CheckDocumentResultsGridFieldByName(documentGrid, "TransitionResult.IonMobilityFragment", row, expectedFragmentIM, msg, IsRecordMode);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityWindow", row, expectedWindow);
CheckDocumentResultsGridFieldByName(documentGrid, "Chromatogram.ChromatogramIonMobility", row, expectedFragmentIM);
CheckDocumentResultsGridFieldByName(documentGrid, "Chromatogram.ChromatogramIonMobilityExtractionWidth", row, expectedWindow);
CheckDocumentResultsGridFieldByName(documentGrid, "Chromatogram.ChromatogramIonMobilityUnits", row, expectedUnits);
if (IsRecordMode)
{
CheckDocumentResultsGridValuesRecordedCount = 0; // We're managing our own newlines
Console.WriteLine(@"},");
}
}
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
private void TestReports(string msg = null)
{
// Verify reports working for CCS
var row = 0;
var documentGrid = EnableDocumentGridIonMobilityResultsColumns();
var imPrecursor = 1.1732;
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityMS1", row, imPrecursor, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "TransitionResult.IonMobilityFragment", row, imPrecursor, msg); // Document is all precursors
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityUnits", row, IonMobilityFilter.IonMobilityUnitsL10NString(eIonMobilityUnits.inverse_K0_Vsec_per_cm2), msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityWindow", row, 0.12, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.CollisionalCrossSection", row, 473.2742, msg);
EnableDocumentGridColumns(documentGrid,
Resources.ReportSpecList_GetDefaults_Peptide_RT_Results,
SkylineWindow.Document.PeptideCount * SkylineWindow.Document.MeasuredResults.Chromatograms.Count);
foreach (var rt in new[] {
14.35, 14.34, 14.33, 14.33, 14.15, 14.12, 14.11, 14.11, 14.63, 14.61, 14.61, 14.61, 14.75, 14.74, 14.72, 14.73, 14.06, 14.04,
14.03, 14.03, 14.43, 14.43, 14.42, 14.43, 14.36, 14.37, 14.35, 14.35, 14.31, 14.31, 14.29, 14.28, 14.48, 14.49, 14.47, 14.48,
14.69, 14.67, 14.67, 14.67, 14.61, 14.34, 14.34, 14.35, 14.25, 14.25, 14.22, 14.23, 14.37, 14.36, 14.35, 14.35, 14.51, 14.52,
14.5, 14.5, 14.24, 14.25, 14.22, 14.23, 14.81, 14.78, 14.78, 14.78, 14.63, 14.61, 14.61, 14.61, 14.48, 14.46, 14.46, 14.47,
14.52, 14.49, 14.49, 14.49, 14.67, 14.65, 14.65, 14.65, 14.46, 14.45, 14.45, 14.45, 14.44, 14.43, 14.42, 14.43, 14.24, 14.24,
14.25, 14.25, 14.48, 14.46, 14.45, 14.44, 14.19, 14.16, 14.16, 14.17, 14.38, 14.34, 14.34, 14.36, 14.88, 14.86, 14.86, 14.85,
14.22, 14.22, 14.21, 14.21, 14.19, 14.19, 14.18, 14.18, 14.11, 14.09, 14.09, 14.1, 14.72, 14.7, 14.71, 14.71, 14.64, 14.61,
14.62, 14.61, 14.12, 14.1, 14.1, 14.1, 14.23, 14.21, 14.2, 14.2
})
{
CheckDocumentResultsGridFieldByName(documentGrid, "PeptideRetentionTime", row++, rt, msg, IsRecordMode);
}
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
var charge = 0;
if (textCharge.Visible &&
!helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge))
{
return;
}
var adduct = Adduct.NonProteomicProtonatedFromCharge(charge);
if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue)
{
helper.ShowTextBoxError(textRetentionTimeWindow,
Resources
.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
return;
}
if (Adduct.IsEmpty || Adduct.AdductCharge != adduct.AdductCharge)
{
Adduct =
adduct; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty
}
if (string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
// Can the text fields be understood as mz?
if (!_formulaBox.ValidateAverageText(helper))
{
return;
}
if (!_formulaBox.ValidateMonoText(helper))
{
return;
}
}
var monoMass = new TypedMass(_formulaBox.MonoMass ?? 0, MassType.Monoisotopic);
var averageMass = new TypedMass(_formulaBox.AverageMass ?? 0, MassType.Average);
if (monoMass < CustomMolecule.MIN_MASS || averageMass < CustomMolecule.MIN_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__,
CustomMolecule.MIN_MASS));
return;
}
if (monoMass > CustomMolecule.MAX_MASS || averageMass > CustomMolecule.MAX_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__,
CustomMolecule.MAX_MASS));
return;
}
if ((_transitionSettings != null) &&
(!_transitionSettings.IsMeasurablePrecursor(
adduct.MzFromNeutralMass(monoMass, MassType.Monoisotopic)) ||
!_transitionSettings.IsMeasurablePrecursor(adduct.MzFromNeutralMass(averageMass, MassType.Average))))
{
_formulaBox.ShowTextBoxErrorFormula(helper,
Resources
.SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_);
return;
}
// Ion mobility value must have ion mobility units
if (textIonMobility.Visible && IonMobility.HasValue)
{
if (IonMobilityUnits == eIonMobilityUnits.none)
{
helper.ShowTextBoxError(textIonMobility, Resources.EditCustomMoleculeDlg_OkDialog_Please_specify_the_ion_mobility_units_);
comboBoxIonMobilityUnits.Focus();
return;
}
if (IonMobility.Value == 0 ||
(IonMobility.Value < 0 && !IonMobilityFilter.AcceptNegativeMobilityValues(IonMobilityUnits)))
{
helper.ShowTextBoxError(textIonMobility,
string.Format(Resources.SmallMoleculeTransitionListReader_ReadPrecursorOrProductColumns_Invalid_ion_mobility_value__0_, IonMobility));
textIonMobility.Focus();
return;
}
}
if (_usageMode == UsageMode.precursor)
{
// Only the adduct should be changing
SetResult(_resultCustomMolecule, Adduct);
}
else if (!string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
try
{
var name = textName.Text;
if (string.IsNullOrEmpty(name))
{
name = _formulaBox.NeutralFormula; // Clip off any adduct description
}
SetResult(new CustomMolecule(_formulaBox.NeutralFormula, name), Adduct);
}
catch (InvalidDataException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else
{
SetResult(new CustomMolecule(monoMass, averageMass, textName.Text), Adduct);
}
// Did user change the list of heavy labels?
if (_driverLabelType != null)
{
// This is the only thing the user may have altered
var newHeavyMods = _driverLabelType.GetHeavyModifications().ToArray();
if (!ArrayUtil.EqualsDeep(newHeavyMods, _peptideSettings.Modifications.HeavyModifications))
{
var labelTypes = _peptideSettings.Modifications.InternalStandardTypes.Where(t =>
newHeavyMods.Any(m => Equals(m.LabelType, t))).ToArray();
if (labelTypes.Length == 0)
{
labelTypes = new[] { newHeavyMods.First().LabelType }
}
;
PeptideModifications modifications = new PeptideModifications(
_peptideSettings.Modifications.StaticModifications,
_peptideSettings.Modifications.MaxVariableMods,
_peptideSettings.Modifications.MaxNeutralLosses,
newHeavyMods,
labelTypes);
var settings = _peptideSettings.ChangeModifications(modifications);
SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings);
if (!_parent.ChangeSettings(newSettings, true))
{
// Not expected, since we checked for a change before calling
// Otherwise, this is very confusing. The form just refuses to go away
// We would prefer to get an unhandled exception and fix this
Assume.Fail();
return;
}
_peptideSettings = newSettings.PeptideSettings;
}
}
// See if this combination of charge and label would conflict with any existing transition groups
if (_existingIds != null && _existingIds.Any(t =>
{
var transitionGroup = t as TransitionGroup;
return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) &&
Equals(transitionGroup.PrecursorAdduct.AsFormula(),
Adduct
.AsFormula()) && // Compare AsFormula so proteomic and non-proteomic protonation are seen as same thing
!ReferenceEquals(t, _initialId));
}))
{
helper.ShowTextBoxError(textName,
Resources
.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_adduct_and_label_type_already_exists_,
textName.Text);
return;
}
// See if this would conflict with any existing transitions
if (_existingIds != null && (_existingIds.Any(t =>
{
var transition = t as Transition;
return(transition != null && (Equals(transition.Adduct.AsFormula(), Adduct.AsFormula()) &&
Equals(transition.CustomIon, ResultCustomMolecule)) &&
!ReferenceEquals(t, _initialId));
})))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text);
return;
}
DialogResult = DialogResult.OK;
}
private void TestReports(int row, double expectedDtWindow, string msg = null)
{
// Verify reports working for CCS
var documentGrid = EnableDocumentGridIonMobilityResultsColumns();
var imPrecursor = _testCase == 1 ? 18.43 : 23.50;
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityMS1", row, imPrecursor, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "TransitionResult.IonMobilityFragment", row, imPrecursor, msg); // Document is all precursor
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityUnits", row, IonMobilityFilter.IonMobilityUnitsL10NString(eIonMobilityUnits.drift_time_msec), msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityWindow", row, expectedDtWindow, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.CollisionalCrossSection", row, _testCase == 1 ? 292.4 : 333.34, msg);
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
private void TestReports(string msg = null)
{
// Verify reports working for CCS
var row = 0;
var documentGrid = EnableDocumentGridIonMobilityResultsColumns();
var imPrecursor = 0.832;
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityMS1", row, imPrecursor, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "TransitionResult.IonMobilityFragment", row, imPrecursor, msg); // Document is all precursor
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityUnits", row, IonMobilityFilter.IonMobilityUnitsL10NString(eIonMobilityUnits.inverse_K0_Vsec_per_cm2), msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.IonMobilityWindow", row, 0.04, msg);
CheckDocumentResultsGridFieldByName(documentGrid, "PrecursorResult.CollisionalCrossSection", row, 337.4821, msg);
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
private static TransitionChromInfo CreateChromInfo(ChromFileInfoId fileId, int step, ChromPeak peak, IonMobilityFilter ionMobility, int ratioCount, UserSet userSet)
{
return(new TransitionChromInfo(fileId, step, peak, ionMobility, new float?[ratioCount], Annotations.EMPTY, userSet));
}
public DocNode ChangePeak(int indexSet, ChromFileInfoId fileId, int step, ChromPeak peak, IonMobilityFilter ionMobility, int ratioCount, UserSet userSet)
{
if (Results == null)
{
return(this);
}
var listChromInfo = Results[indexSet];
var listChromInfoNew = new List <TransitionChromInfo>();
if (listChromInfo.IsEmpty)
{
listChromInfoNew.Add(CreateChromInfo(fileId, step, peak, ionMobility, ratioCount, userSet));
}
else
{
bool peakAdded = false;
foreach (var chromInfo in listChromInfo)
{
// Replace an existing entry with same index values
if (ReferenceEquals(chromInfo.FileId, fileId) && chromInfo.OptimizationStep == step)
{
// Something is wrong, if the value has already been added (duplicate peak? out of order?)
if (peakAdded)
{
throw new InvalidDataException(string.Format(Resources.TransitionDocNode_ChangePeak_Duplicate_or_out_of_order_peak_in_transition__0_,
FragmentIonName));
}
// If the target peak is exactly the same as the proposed change and userSet is not overriding,
// simply return the original node unchanged
if (chromInfo.EquivalentTolerant(fileId, step, peak) && !chromInfo.UserSet.IsOverride(userSet))
{
return(this);
}
listChromInfoNew.Add(chromInfo.ChangePeak(peak, userSet));
peakAdded = true;
}
else
{
// Entries should be ordered, so if the new entry has not been added
// when an entry past it is seen, then add the new entry.
if (!peakAdded &&
chromInfo.FileIndex >= fileId.GlobalIndex &&
chromInfo.OptimizationStep > step)
{
listChromInfoNew.Add(CreateChromInfo(fileId, step, peak, ionMobility, ratioCount, userSet));
peakAdded = true;
}
listChromInfoNew.Add(chromInfo);
}
}
// Finally, make sure the peak is added
if (!peakAdded)
{
listChromInfoNew.Add(CreateChromInfo(fileId, step, peak, ionMobility, ratioCount, userSet));
}
}
return(ChangeResults(Results.ChangeAt(indexSet, new ChromInfoList <TransitionChromInfo>(listChromInfoNew))));
}
