private void UpdateMeasuredDriftTimesControl(IonMobilityPredictor predictor)
{
// List any measured ion mobility values, taking care to show only those matching display units
gridMeasuredDriftTimes.Rows.Clear();
if (predictor == null)
{
return;
}
_predictor = (_predictor ?? IonMobilityPredictor.EMPTY).ChangeMeasuredIonMobilityValues(predictor.MeasuredMobilityIons);
Units = _predictor.GetIonMobilityUnits();
var units = Units;
if (predictor.MeasuredMobilityIons != null)
{
bool hasHighEnergyOffsets =
predictor.MeasuredMobilityIons.Any(p => p.Value.HighEnergyIonMobilityValueOffset != 0);
cbOffsetHighEnergySpectra.Checked = hasHighEnergyOffsets;
foreach (var p in predictor.MeasuredMobilityIons)
{
var ccs = p.Value.CollisionalCrossSectionSqA.HasValue
? string.Format("{0:F04}", p.Value.CollisionalCrossSectionSqA.Value) // Not L10N
: string.Empty;
var im = p.Value.IonMobility.Units == units ? p.Value.IonMobility.Mobility : null;
var imOffset = p.Value.IonMobility.Units == units ? p.Value.HighEnergyIonMobilityValueOffset : 0;
var chargeOrAdductString = _smallMoleculeUI
? p.Key.Adduct.AdductFormula
: p.Key.Charge.ToString(LocalizationHelper.CurrentCulture);
if (hasHighEnergyOffsets)
{
gridMeasuredDriftTimes.Rows.Add(p.Key.Target,
chargeOrAdductString,
im.HasValue ? im.Value.ToString(LocalizationHelper.CurrentCulture) : string.Empty,
ccs,
imOffset.ToString(LocalizationHelper.CurrentCulture)
);
}
else
{
gridMeasuredDriftTimes.Rows.Add(p.Key.Target,
chargeOrAdductString,
im.HasValue ? im.Value.ToString(LocalizationHelper.CurrentCulture) : string.Empty,
ccs
);
}
}
}
else
{
cbOffsetHighEnergySpectra.Checked = false;
}
}
public ExplicitTransitionGroupValues(double?explicitCollisionEnergy,
double?explicitIonMobility,
double?explicitIonMobilityHighEnergyOffset,
MsDataFileImpl.eIonMobilityUnits explicitIonMobilityUnits,
double?explicitCollisionalCrossSectionSqA,
double?explicitSLens,
double?explicitConeVoltage,
double?explicitDeclusteringPotential,
double?explicitCompensationVoltage)
{
CollisionEnergy = explicitCollisionEnergy;
IonMobility = explicitIonMobility;
IonMobilityHighEnergyOffset = explicitIonMobilityHighEnergyOffset;
IonMobilityUnits = explicitIonMobilityUnits;
CollisionalCrossSectionSqA = explicitCollisionalCrossSectionSqA;
SLens = explicitSLens;
ConeVoltage = explicitConeVoltage;
DeclusteringPotential = explicitDeclusteringPotential;
CompensationVoltage = explicitCompensationVoltage;
}
public ExplicitTransitionGroupValues ChangeIonMobility(double?imNew, MsDataFileImpl.eIonMobilityUnits unitsNew)
{
var explicitTransitionGroupValues = ChangeProp(ImClone(this), (im, v) => im.IonMobility = v, imNew);
return(ChangeProp(ImClone(explicitTransitionGroupValues), (im, v) => im.IonMobilityUnits = v, unitsNew));
}
public Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, MsDataFileImpl.eIonMobilityUnits units)
{
var e = new CancelEventArgs();
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
foreach (DataGridViewRow row in _gridMeasuredDriftTimePeptides.Rows)
{
if (row.IsNewRow)
{
continue;
}
string seq;
if (!ValidateSequence(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_SEQUENCE], out seq))
{
return(null);
}
Adduct charge;
if (!ValidateCharge(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CHARGE], out charge))
{
return(null);
}
double mobility;
if (!ValidateDriftTime(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY], out mobility))
{
return(null);
}
double?ccs;
if (!ValidateCCS(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CCS], out ccs))
{
return(null);
}
double highEnergyOffset = 0; // Set default value in case user does not provide one
if (useHighEnergyOffsets && !ValidateHighEnergyDriftTimeOffset(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET], out highEnergyOffset))
{
return(null);
}
var ionMobility = IonMobilityValue.GetIonMobilityValue(mobility, units);
try
{
dict.Add(new LibKey(seq, charge.AdductCharge), IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, ccs, highEnergyOffset));
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// just take the first seen
}
}
return(dict);
}
public void SetIonMobilityUnits(MsDataFileImpl.eIonMobilityUnits units)
{
Units = units;
}
public Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, MsDataFileImpl.eIonMobilityUnits units)
{
var e = new CancelEventArgs();
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
foreach (DataGridViewRow row in _gridMeasuredDriftTimePeptides.Rows)
{
if (row.IsNewRow)
{
continue;
}
string seq;
if (!ValidateSequence(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_SEQUENCE], out seq))
{
return(null);
}
// OK, we have a non-empty "sequence" string, but is that actually a peptide or a molecule?
// See if there's anything in the document whose text representation matches what's in the list
var target = Program.MainWindow.Document.Molecules.Select(m => m.Target).FirstOrDefault(t => seq.Equals(t.ToString()));
if (target == null || target.IsEmpty)
{
// Does seq evaluate as a peptide?
target = !seq.All(c => char.IsUpper(c) || char.IsDigit(c) || "[+-,.]()".Contains(c)) // Not L10N
? new Target(CustomMolecule.FromSerializableString(seq))
: Target.FromSerializableString(seq);
}
Adduct charge;
if (!ValidateCharge(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CHARGE], target.IsProteomic, out charge))
{
return(null);
}
double mobility;
if (!ValidateDriftTime(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY], out mobility))
{
return(null);
}
double?ccs;
if (!ValidateCCS(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CCS], out ccs))
{
return(null);
}
double highEnergyOffset = 0; // Set default value in case user does not provide one
if (useHighEnergyOffsets && !ValidateHighEnergyDriftTimeOffset(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET], out highEnergyOffset))
{
return(null);
}
var ionMobility = IonMobilityValue.GetIonMobilityValue(mobility, units);
try
{
dict.Add(new LibKey(target, charge), IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, ccs, highEnergyOffset));
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// just take the first seen
}
}
return(dict);
}
} // This is private to force use of GetTransitionGroupIonMobilityInfo (for memory efficiency, as most uses are empty)
// Serialization support
public static TransitionGroupIonMobilityInfo GetTransitionGroupIonMobilityInfo(double?ccs, double?ionMobilityMS1,
double?ionMobilityFragment, double?ionMobilityWindow, MsDataFileImpl.eIonMobilityUnits units)
{
if (ccs.HasValue || ionMobilityMS1.HasValue || ionMobilityFragment.HasValue || ionMobilityWindow.HasValue)
{
return new TransitionGroupIonMobilityInfo()
{
CollisionalCrossSection = ccs,
IonMobilityMS1 = ionMobilityMS1,
IonMobilityFragment = ionMobilityFragment,
IonMobilityWindow = ionMobilityWindow,
IonMobilityUnits = units
}
}
;
return(EMPTY);
}
