private ExplicitTransitionGroupValues(double?explicitIonMobility,
eIonMobilityUnits explicitIonMobilityUnits,
double?explicitCollisionalCrossSectionSqA)
{
IonMobility = explicitIonMobility;
IonMobilityUnits = explicitIonMobilityUnits;
CollisionalCrossSectionSqA = explicitCollisionalCrossSectionSqA;
}
public ValidatingIonMobilityPrecursor(Target seq,
Adduct precursorAdduct,
double collisionalCrossSection,
double ionMobility,
double highEnergyIonMobilityOffset,
eIonMobilityUnits units)
: base(new DbPrecursorIon(seq, precursorAdduct), collisionalCrossSection, ionMobility, units, highEnergyIonMobilityOffset)
{
}
public DbPrecursorAndIonMobility(DbPrecursorIon precursor, double?collisionalCrossSection, double?ionMobility, eIonMobilityUnits units,
double?highEnergyOffset)
{
DbPrecursorIon = precursor;
CollisionalCrossSectionSqA = collisionalCrossSection ?? 0;
IonMobility = ionMobility ?? 0;
IonMobilityUnits = units;
HighEnergyIonMobilityOffset = highEnergyOffset ?? 0;
}
public ValidatingIonMobilityPrecursor(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct precursorAdduct,
double collisionalCrossSection,
double ionMobility,
double highEnergyIonMobilityOffset,
eIonMobilityUnits units)
: base(new DbPrecursorIon(new Target(smallMoleculeLibraryAttributes), precursorAdduct),
collisionalCrossSection, ionMobility, units, highEnergyIonMobilityOffset)
{
}
// Single conformer ctor
public PrecursorIonMobilities(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct precursorAdduct,
double collisionalCrossSection,
double ionMobility,
double highEnergyIonMobilityOffset,
eIonMobilityUnits units)
: this(new LibKey(new Target(smallMoleculeLibraryAttributes), precursorAdduct),
IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, units, collisionalCrossSection, highEnergyIonMobilityOffset))
{
}
// Single conformer ctor
public PrecursorIonMobilities(Target seq,
Adduct precursorAdduct,
double collisionalCrossSection,
double ionMobility,
double highEnergyIonMobilityOffset,
eIonMobilityUnits units)
: this(new LibKey(seq, precursorAdduct),
IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, units, collisionalCrossSection, highEnergyIonMobilityOffset))
{
}
public IonMobilityValue ChangeIonMobilityUnits(eIonMobilityUnits units)
{
if (Equals(units, Units))
{
return(this);
}
if (Equals(units, eIonMobilityUnits.none))
{
return(EMPTY);
}
return(ChangeProp(ImClone(this), im => im.Units = units));
}
public static ExplicitTransitionGroupValues Create(double?explicitIonMobility,
eIonMobilityUnits explicitIonMobilityUnits,
double?explicitCollisionalCrossSectionSqA)
{
if (explicitIonMobility.HasValue || explicitCollisionalCrossSectionSqA.HasValue)
{
return(new ExplicitTransitionGroupValues(explicitIonMobility, explicitIonMobilityUnits,
explicitCollisionalCrossSectionSqA));
}
return(EMPTY);
}
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)
: 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 static string GetUnitsString(eIonMobilityUnits units)
{
switch (units)
{
case eIonMobilityUnits.none:
return(@"#N/A");
case eIonMobilityUnits.drift_time_msec:
return(@"msec");
case eIonMobilityUnits.inverse_K0_Vsec_per_cm2:
return(@"Vs/cm^2");
case eIonMobilityUnits.compensation_V:
return(@"V");
}
return(@"unknown ion mobility type");
}
public ExplicitTransitionGroupValues(double?explicitCollisionEnergy,
double?explicitIonMobility,
double?explicitIonMobilityHighEnergyOffset,
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 Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, 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 = _targetResolver.ResolveTarget(seq);
if (target == null || target.IsEmpty)
{
return(null);
}
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, 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);
}
public void SetIonMobilityUnits(eIonMobilityUnits units)
{
Units = units;
}
public IonMobilityValue ChangeIonMobility(double?value, eIonMobilityUnits units)
{
return(value == Mobility && units == Units ? this : GetIonMobilityValue(value, units));
}
public Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, 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))
? 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);
}
public static IonMobilityValue GetIonMobilityValue(double?value, eIonMobilityUnits units)
{
return((units == eIonMobilityUnits.none || !value.HasValue)
? EMPTY
: new IonMobilityValue(value, units));
}
public static IonMobilityValue GetIonMobilityValue(double mobility, eIonMobilityUnits units)
{
return((units == eIonMobilityUnits.none)
? EMPTY
: new IonMobilityValue(mobility, units));
}
// Private so we can issue EMPTY in the common case of no ion mobility info
private IonMobilityValue(double?mobility, eIonMobilityUnits units)
{
Mobility = mobility;
Units = units;
}
public ExplicitTransitionGroupValues ChangeIonMobility(double?imNew, eIonMobilityUnits unitsNew)
{
var explicitTransitionGroupValues = ChangeProp(ImClone(this), (im, v) => im.IonMobility = v, imNew);
return(ChangeProp(ImClone(explicitTransitionGroupValues), (im, v) => im.IonMobilityUnits = v, unitsNew));
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
IProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
_globalChromatogramExtractor = new GlobalChromatogramExtractor(dataFile);
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
var lastPrecursor = SignedMz.ZERO;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
{
continue;
}
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
if (chromKey.Precursor.IsNegative)
{
_sourceHasNegativePolarityData = true;
}
else
{
_sourceHasPositivePolarityData = true;
}
var ki = new ChromKeyProviderIdPair(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
{
FixCEOptForShimadzu();
}
if (_chromIds.Count == 0)
{
throw new NoSrmDataException(FileInfo.FilePath);
}
// CONSIDER: TIC and BPC are not well defined for SRM and produced chromatograms with over 100,000 points in
// Agilent CE optimization data. So, keep them off for now.
// foreach (int globalIndex in _globalChromatogramExtractor.GlobalChromatogramIndexes)
// {
// _chromIndices[globalIndex] = globalIndex;
// _chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromId(_globalChromatogramExtractor.GetChromatogramId(globalIndex, out int indexId), false), globalIndex));
// }
foreach (var qcTracePair in _globalChromatogramExtractor.QcTraceByIndex)
{
_chromIndices[qcTracePair.Key] = qcTracePair.Key;
_chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromQcTrace(qcTracePair.Value), qcTracePair.Key));
}
// CONSIDER(kaipot): Some way to support mzML files converted from MIDAS wiff files
_hasMidasSpectra = (dataFile.IsABFile) && SpectraChromDataProvider.HasSpectrumData(dataFile);
_ionMobilityUnits = dataFile.IonMobilityUnits;
_hasIonMobilityCombined = dataFile.HasCombinedIonMobilitySpectra; // When true, data source provides IMS data in 3-array format, which affects spectrum ID format
SetPercentComplete(50);
}