public static void MakeChromatogramInfo(SignedMz precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var crawPeakFinder = Crawdads.NewCrawdadPeakFinder();
crawPeakFinder.SetChromatogram(chromGroup.Times, chromData.Intensities);
var crawdadPeak =
crawPeakFinder.GetPeak(
FindNearestIndex(chromGroup.Times, (float)chromGroup.StartTime),
FindNearestIndex(chromGroup.Times, (float)chromGroup.EndTime));
var chromPeak = new ChromPeak(crawPeakFinder, crawdadPeak, 0, chromGroup.Times, chromData.Intensities, null);
transitionChromInfo = new TransitionChromInfo(null, 0, chromPeak, new float?[0], Annotations.EMPTY,
UserSet.FALSE);
var peaks = new[] { chromPeak };
var header = new ChromGroupHeaderInfo(precursorMz,
0, // file index
1, // numTransitions
0, // startTransitionIndex
peaks.Length, // numPeaks
0, // startPeakIndex
0, // startscoreindex
0, // maxPeakIndex
chromGroup.Times.Length, // numPoints
0, // compressedSize
0, // uncompressedsize
0, //location
0, -1, -1, null, null);
chromatogramInfo = new ChromatogramInfo(header,
new Dictionary <Type, int>(), 0,
new ChromCachedFile[0],
new[] { new ChromTransition(chromData.Mz, 0, 0, 0, ChromSource.unknown), },
peaks, null,
chromGroup.Times, new[] { chromData.Intensities }, null, null);
}
public static void MakeChromatogramInfo(double precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var crawPeakFinder = new CrawdadPeakFinder();
crawPeakFinder.SetChromatogram(chromGroup.Times, chromData.Intensities);
var crawdadPeak =
crawPeakFinder.GetPeak(
FindNearestIndex(chromGroup.Times, (float)chromGroup.StartTime),
FindNearestIndex(chromGroup.Times, (float)chromGroup.EndTime));
var chromPeak = new ChromPeak(crawPeakFinder, crawdadPeak, 0, chromGroup.Times, chromData.Intensities, null);
transitionChromInfo = new TransitionChromInfo(null, 0, chromPeak, new float?[0], Annotations.EMPTY,
UserSet.FALSE);
var peaks = new[] { chromPeak };
var header = new ChromGroupHeaderInfo5(new ChromGroupHeaderInfo(
(float)precursorMz, 0, 1, 0, peaks.Length, 0, 0,
chromGroup.Times.Length, 0, 0));
chromatogramInfo = new ChromatogramInfo(header,
new Dictionary <Type, int>(), 0,
new ChromCachedFile[0],
new[] { new ChromTransition(chromData.Mz, 0, 0, 0, ChromSource.unknown), },
peaks, null,
chromGroup.Times, new[] { chromData.Intensities }, null, null);
}
public static RetentionTimeValues FromTransitionChromInfo(TransitionChromInfo transitionChromInfo)
{
if (null == transitionChromInfo || transitionChromInfo.StartRetentionTime == 0 ||
transitionChromInfo.EndRetentionTime == 0)
{
return(null);
}
double apexTime;
if (transitionChromInfo.Height == 0)
{
// TransitionChromInfo.RetentionTime cannot be trusted if the height is zero, so always
// set it to the midpoint between the start and end times.
apexTime = (transitionChromInfo.StartRetentionTime + transitionChromInfo.EndRetentionTime) / 2;
}
else
{
apexTime = transitionChromInfo.RetentionTime;
}
return(new RetentionTimeValues(apexTime,
transitionChromInfo.StartRetentionTime, transitionChromInfo.EndRetentionTime,
transitionChromInfo.Height, transitionChromInfo.Fwhm));
}
protected override FindMatch MatchTransition(TransitionChromInfo transitionChromInfo)
{
if (transitionChromInfo.IsTruncated.GetValueOrDefault(false))
{
return(new FindMatch(Resources.TruncatedPeakFinder_MatchTransition_Truncated_peak));
}
return(null);
}
protected override FindMatch MatchTransition(TransitionChromInfo transitionChromInfo)
{
if (transitionChromInfo.IsTruncated.GetValueOrDefault(false))
{
return new FindMatch(Resources.TruncatedPeakFinder_MatchTransition_Truncated_peak);
}
return null;
}
private float? GetValue(TransitionChromInfo chromInfo)
{
if (chromInfo == null)
return null;
if (_ratioIndex == RATIO_INDEX_NONE)
return chromInfo.Area;
return chromInfo.GetRatio(_ratioIndex);
}
private float?GetValue(TransitionChromInfo chromInfo)
{
if (chromInfo == null)
{
return(null);
}
return(chromInfo.MassError);
}
public static RetentionTimeValues?GetValues(TransitionChromInfo transitionChromInfo)
{
if (null == transitionChromInfo || transitionChromInfo.StartRetentionTime == 0 ||
transitionChromInfo.EndRetentionTime == 0)
{
return(null);
}
return(new RetentionTimeValues(transitionChromInfo.RetentionTime,
transitionChromInfo.StartRetentionTime, transitionChromInfo.EndRetentionTime,
transitionChromInfo.Fwhm));
}
public static RetentionTimeValues? GetValues(TransitionChromInfo transitionChromInfo)
{
if (null == transitionChromInfo || transitionChromInfo.StartRetentionTime == 0 ||
transitionChromInfo.EndRetentionTime == 0)
{
return null;
}
return new RetentionTimeValues(transitionChromInfo.RetentionTime,
transitionChromInfo.StartRetentionTime, transitionChromInfo.EndRetentionTime,
transitionChromInfo.Fwhm);
}
private float?GetValue(TransitionChromInfo chromInfo)
{
if (chromInfo == null)
{
return(null);
}
if (_ratioIndex == RATIO_INDEX_NONE)
{
return(chromInfo.Area);
}
return(chromInfo.GetRatio(_ratioIndex));
}
private TransitionChromInfo GetTransitionChromInfo(int chromIndex, int pepIndex, int transIndex)
{
TransitionChromInfo result = null;
RunUI(() =>
{
var nodePep = SkylineWindow.DocumentUI.Peptides.ElementAt(pepIndex);
var nodeGroup = nodePep.TransitionGroups.First();
var transition = nodeGroup.Transitions.ElementAt(transIndex);
result = transition.ChromInfos.ToArray()[chromIndex];
});
return(result);
}
public static void MakeChromatogramInfo(SignedMz precursorMz, LibraryChromGroup chromGroup, LibraryChromGroup.ChromData chromData, out ChromatogramInfo chromatogramInfo, out TransitionChromInfo transitionChromInfo)
{
var timeIntensities = new TimeIntensities(chromGroup.Times, chromData.Intensities, null, null);
var crawPeakFinder = Crawdads.NewCrawdadPeakFinder();
crawPeakFinder.SetChromatogram(chromGroup.Times, chromData.Intensities);
var crawdadPeak =
crawPeakFinder.GetPeak(
FindNearestIndex(chromGroup.Times, (float)chromGroup.StartTime),
FindNearestIndex(chromGroup.Times, (float)chromGroup.EndTime));
var chromPeak = new ChromPeak(crawPeakFinder, crawdadPeak, 0, timeIntensities, null);
transitionChromInfo = new TransitionChromInfo(null, 0, chromPeak,
IonMobilityFilter.EMPTY, // CONSIDER(bspratt) IMS in chromatogram libraries?
new float?[0], Annotations.EMPTY,
UserSet.FALSE);
var peaks = new[] { chromPeak };
var header = new ChromGroupHeaderInfo(precursorMz,
0, // file index
1, // numTransitions
0, // startTransitionIndex
peaks.Length, // numPeaks
0, // startPeakIndex
0, // startscoreindex
0, // maxPeakIndex
chromGroup.Times.Length, // numPoints
0, // compressedSize
0, // uncompressedsize
0, //location
0, -1, -1, null, null, null, eIonMobilityUnits.none); // CONSIDER(bspratt) IMS in chromatogram libraries?
var driftTimeFilter = IonMobilityFilter.EMPTY; // CONSIDER(bspratt) IMS in chromatogram libraries?
var groupInfo = new ChromatogramGroupInfo(header,
new Dictionary <Type, int>(),
new byte[0],
new ChromCachedFile[0],
new[] { new ChromTransition(chromData.Mz, 0, (float)(driftTimeFilter.IonMobility.Mobility ?? 0), (float)(driftTimeFilter.IonMobilityExtractionWindowWidth ?? 0), ChromSource.unknown), },
peaks,
null)
{
TimeIntensitiesGroup = TimeIntensitiesGroup.Singleton(timeIntensities)
};
chromatogramInfo = new ChromatogramInfo(groupInfo, 0);
}
protected override double GetValue(TransitionChromInfo chromInfo)
{
var retentionTimeValues = ScaleRetentionTimeValues(chromInfo.FileId, RetentionTimeValues.GetValues(chromInfo));
if (!retentionTimeValues.HasValue)
{
return(0);
}
switch (RTValue)
{
case RTPeptideValue.Retention:
return(retentionTimeValues.Value.RetentionTime);
case RTPeptideValue.FWHM:
return(retentionTimeValues.Value.Fwhm ?? 0);
case RTPeptideValue.FWB:
return(retentionTimeValues.Value.Fwb);
}
return(0);
}
private void WriteTransitionChromInfo(XmlWriter writer, TransitionChromInfo chromInfo)
{
if (chromInfo.OptimizationStep != 0)
{
writer.WriteAttribute(ATTR.step, chromInfo.OptimizationStep);
}
// Only write peak information, if it is not empty
if (!chromInfo.IsEmpty)
{
writer.WriteAttributeNullable(ATTR.mass_error_ppm, chromInfo.MassError);
writer.WriteAttribute(ATTR.retention_time, chromInfo.RetentionTime);
writer.WriteAttribute(ATTR.start_time, chromInfo.StartRetentionTime);
writer.WriteAttribute(ATTR.end_time, chromInfo.EndRetentionTime);
writer.WriteAttributeNullable(ATTR.ion_mobility, chromInfo.IonMobility.IonMobility.Mobility);
writer.WriteAttributeNullable(ATTR.ion_mobility_window, chromInfo.IonMobility.IonMobilityExtractionWindowWidth);
writer.WriteAttribute(ATTR.area, chromInfo.Area);
writer.WriteAttribute(ATTR.background, chromInfo.BackgroundArea);
writer.WriteAttribute(ATTR.height, chromInfo.Height);
writer.WriteAttribute(ATTR.fwhm, chromInfo.Fwhm);
writer.WriteAttribute(ATTR.fwhm_degenerate, chromInfo.IsFwhmDegenerate);
writer.WriteAttributeNullable(ATTR.truncated, chromInfo.IsTruncated);
writer.WriteAttribute(ATTR.identified, chromInfo.Identified.ToString().ToLowerInvariant());
writer.WriteAttribute(ATTR.rank, chromInfo.Rank);
if (SkylineVersion.SrmDocumentVersion.CompareTo(DocumentFormat.VERSION_3_61) >= 0)
{
writer.WriteAttributeNullable(ATTR.points_across, chromInfo.PointsAcrossPeak);
}
if (chromInfo.Rank != chromInfo.RankByLevel)
{
writer.WriteAttribute(ATTR.rank_by_level, chromInfo.RankByLevel);
}
}
writer.WriteAttribute(ATTR.user_set, chromInfo.UserSet);
writer.WriteAttribute(ATTR.forced_integration, chromInfo.IsForcedIntegration, false);
WriteAnnotations(writer, chromInfo.Annotations);
}
protected override double GetValue(TransitionChromInfo chromInfo)
{
return(chromInfo.Area);
}
protected override FindMatch MatchTransition(TransitionChromInfo transitionChromInfo)
{
return(transitionChromInfo.IsUserSetManual
? new FindMatch(Resources.ManuallyIntegratedPeakFinder_MatchTransition_Manually_integrated_peak)
: null);
}
protected override double GetValue(TransitionChromInfo chromInfo)
{
return(chromInfo.MassError ?? 0);
}
public void AddChromInfo(TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran, TransitionChromInfo info)
{
if (info.IsEmpty)
return;
var key = new TransitionKey(nodeGroup, nodeTran.Key(nodeGroup), nodeGroup.TransitionGroup.LabelType);
if (TranAreas.ContainsKey(key))
throw new InvalidDataException(String.Format(Resources.PeptideChromInfoCalculator_AddChromInfo_Duplicate_transition___0___found_for_peak_areas, nodeTran.Transition));
TranAreas.Add(key, info.Area);
}
private static float GetPeakCountRatio(TransitionChromInfo chromInfo, bool integrateAll)
{
return(chromInfo.IsGoodPeak(integrateAll) ? 1 : 0);
}
protected override FindMatch MatchTransition(TransitionChromInfo transitionChromInfo)
{
return transitionChromInfo.IsUserSetManual
? new FindMatch(Resources.ManuallyIntegratedPeakFinder_MatchTransition_Manually_integrated_peak)
: null;
}
protected abstract FindMatch MatchTransition(TransitionChromInfo transitionChromInfo);
public ChromGraphItem(TransitionGroupDocNode transitionGroupNode,
TransitionDocNode transition,
ChromatogramInfo chromatogram,
TransitionChromInfo tranPeakInfo,
IRegressionFunction timeRegressionFunction,
bool[] annotatePeaks,
double[] dotProducts,
double bestProduct,
bool isFullScanMs,
bool isSummary,
RawTimesInfoItem?displayRawTimes,
int step,
Color color,
float fontSize,
int width,
FullScanInfo fullScanInfo = null)
{
TransitionGroupNode = transitionGroupNode;
TransitionNode = transition;
Chromatogram = chromatogram;
TransitionChromInfo = tranPeakInfo;
TimeRegressionFunction = timeRegressionFunction;
Color = color;
FullScanInfo = fullScanInfo;
_step = step;
_fontSpec = CreateFontSpec(color, fontSize);
_width = width;
_dotProducts = dotProducts;
_bestProduct = bestProduct;
_isFullScanMs = isFullScanMs;
_isSummary = isSummary;
_displayRawTimes = displayRawTimes;
_arrayLabelIndexes = new int[annotatePeaks.Length];
if (chromatogram == null)
{
_measuredTimes = new double[0];
_displayTimes = _measuredTimes;
_intensities = new double[0];
}
else
{
// Cache values early to avoid accessing slow enumerators
// which show up under profiling.
Chromatogram.AsArrays(out _measuredTimes, out _intensities);
if (TimeRegressionFunction == null)
{
_displayTimes = _measuredTimes;
}
else
{
_displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray();
}
// Add peak times to hash set for labeling
int iLastStart = 0;
for (int i = 0; i < chromatogram.NumPeaks; i++)
{
int maxIndex = -1;
if (annotatePeaks[i])
{
ChromPeak peak = chromatogram.GetPeak(i);
maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart);
}
_arrayLabelIndexes[i] = maxIndex;
if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex))
{
_annotatedTimes.Add(maxIndex, i);
}
}
// Calculate best peak index
if (tranPeakInfo != null)
{
iLastStart = 0;
_bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart);
}
}
}
protected abstract double GetValue(TransitionChromInfo info);
private static float GetPeakCountRatio(TransitionChromInfo chromInfo)
{
return(chromInfo.Area > 0 ? 1 : 0);
}
private static void AddBestPeakTimes(TransitionChromInfo chromInfo, ref double bestStartTime,
ref double bestEndTime)
{
// Make sure all parts of the best peak are included in the
// best peak window
double end = chromInfo.EndRetentionTime;
if (end <= 0)
return;
double start = chromInfo.StartRetentionTime;
bestStartTime = Math.Min(bestStartTime, start);
bestEndTime = Math.Max(bestEndTime, end);
}
private float? GetValue(TransitionChromInfo chromInfo)
{
if (chromInfo == null)
return null;
if (_ratioIndex == RATIO_INDEX_NONE)
return chromInfo.Area;
return chromInfo.GetRatio(_ratioIndex);
}
protected override double GetValue(TransitionChromInfo chromInfo)
{
var retentionTimeValues = ScaleRetentionTimeValues(chromInfo.FileId, RetentionTimeValues.GetValues(chromInfo));
if (!retentionTimeValues.HasValue)
{
return 0;
}
switch (RTValue)
{
case RTPeptideValue.Retention:
return retentionTimeValues.Value.RetentionTime;
case RTPeptideValue.FWHM:
return retentionTimeValues.Value.Fwhm ?? 0;
case RTPeptideValue.FWB:
return retentionTimeValues.Value.Fwb;
}
return 0;
}
public ChromGraphItem(TransitionGroupDocNode transitionGroupNode,
TransitionDocNode transition,
ChromatogramInfo chromatogram,
TransitionChromInfo tranPeakInfo,
IRegressionFunction timeRegressionFunction,
bool[] annotatePeaks,
double[] dotProducts,
double bestProduct,
bool isFullScanMs,
bool isSummary,
int step,
Color color,
float fontSize,
int width,
FullScanInfo fullScanInfo = null)
{
TransitionGroupNode = transitionGroupNode;
TransitionNode = transition;
Chromatogram = chromatogram;
TransitionChromInfo = tranPeakInfo;
TimeRegressionFunction = timeRegressionFunction;
Color = color;
FullScanInfo = fullScanInfo;
_step = step;
_fontSpec = CreateFontSpec(color, fontSize);
_width = width;
_dotProducts = dotProducts;
_bestProduct = bestProduct;
_isFullScanMs = isFullScanMs;
_isSummary = isSummary;
_arrayLabelIndexes = new int[annotatePeaks.Length];
if (chromatogram == null)
{
_measuredTimes = new double[0];
_displayTimes = _measuredTimes;
_intensities = new double[0];
}
else
{
// Cache values early to avoid accessing slow enumerators
// which show up under profiling.
Chromatogram.AsArrays(out _measuredTimes, out _intensities);
if (TimeRegressionFunction == null)
{
_displayTimes = _measuredTimes;
}
else
{
_displayTimes = _measuredTimes.Select(TimeRegressionFunction.GetY).ToArray();
}
// Add peak times to hash set for labeling
int iLastStart = 0;
for (int i = 0; i < chromatogram.NumPeaks; i++)
{
int maxIndex = -1;
if (annotatePeaks[i])
{
ChromPeak peak = chromatogram.GetPeak(i);
maxIndex = GetMaxIndex(peak.StartTime, peak.EndTime, ref iLastStart);
}
_arrayLabelIndexes[i] = maxIndex;
if (maxIndex != -1 && !_annotatedTimes.ContainsKey(maxIndex))
_annotatedTimes.Add(maxIndex, i);
}
// Calculate best peak index
if (tranPeakInfo != null)
{
iLastStart = 0;
_bestPeakTimeIndex = GetMaxIndex(tranPeakInfo.StartRetentionTime, tranPeakInfo.EndRetentionTime, ref iLastStart);
}
}
}
public static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings,
TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues,
SkylineDocumentProto.Types.Transition transitionProto)
{
var stringPool = scrubber.StringPool;
IonType ionType = DataValues.FromIonType(transitionProto.FragmentType);
MeasuredIon measuredIon = null;
if (transitionProto.MeasuredIonName != null)
{
measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault(
i => i.Name.Equals(transitionProto.MeasuredIonName.Value));
if (measuredIon == null)
{
throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName));
}
ionType = IonType.custom;
}
bool isCustom = Transition.IsCustom(ionType, group);
bool isPrecursor = Transition.IsPrecursor(ionType);
CustomMolecule customIon = null;
if (isCustom)
{
if (measuredIon != null)
{
customIon = measuredIon.SettingsCustomIon;
}
else if (isPrecursor)
{
customIon = group.CustomMolecule;
}
else
{
var formula = DataValues.FromOptional(transitionProto.Formula);
var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc
var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH);
var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH);
var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH;
var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH;
customIon = new CustomMolecule(formula,
new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic),
new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average),
DataValues.FromOptional(transitionProto.CustomIonName), moleculeID);
}
}
Transition transition;
var adductString = DataValues.FromOptional(transitionProto.Adduct);
var adduct = string.IsNullOrEmpty(adductString)
? Adduct.FromChargeProtonated(transitionProto.Charge)
: Adduct.FromStringAssumeChargeOnly(adductString);
if (isCustom)
{
transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType);
}
else if (isPrecursor)
{
transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex,
group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
else
{
int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal,
group.Peptide.Length);
transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses);
var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist);
var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist);
if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null)
{
throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift);
}
TransitionLibInfo libInfo = null;
if (transitionProto.LibInfo != null)
{
libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity);
}
var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition);
var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results);
var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create(
DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy),
DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset),
DataValues.FromOptional(transitionProto.ExplicitSLens),
DataValues.FromOptional(transitionProto.ExplicitConeVoltage),
DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential));
return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results));
}
private static bool IntersectPeaks(ChromPeak peak, TransitionChromInfo chromInfo)
{
if (chromInfo == null)
return false;
// Allow start and end to share the same time, but nothing more.
return Math.Min(chromInfo.EndRetentionTime, peak.EndTime) -
Math.Max(chromInfo.StartRetentionTime, peak.StartTime) > 0;
}
public FinderChromFileKey(TransitionChromInfo transitionChromInfo)
{
ChromFileInfoId = transitionChromInfo.FileId;
OptStep = transitionChromInfo.OptimizationStep;
}
public static double?GetArea(bool treatMissingAsZero, double?qValueCutoff, bool allowTruncated, TransitionGroupDocNode transitionGroup,
TransitionDocNode transition, int replicateIndex, TransitionChromInfo chromInfo)
{
if (treatMissingAsZero && chromInfo.IsEmpty)
{
return(0);
}
if (chromInfo.IsEmpty)
{
return(null);
}
if (!allowTruncated && chromInfo.IsTruncated.GetValueOrDefault())
{
return(null);
}
if (qValueCutoff.HasValue)
{
TransitionGroupChromInfo transitionGroupChromInfo = FindTransitionGroupChromInfo(transitionGroup,
replicateIndex, chromInfo.FileId);
if (transitionGroupChromInfo != null && transitionGroupChromInfo.QValue > qValueCutoff.Value)
{
return(treatMissingAsZero ? 0 : default(double?));
}
}
return(chromInfo.Area);
}
public FinderChromFileKey(TransitionChromInfo transitionChromInfo)
{
ChromFileInfoId = transitionChromInfo.FileId;
OptStep = transitionChromInfo.OptimizationStep;
}
protected override double GetValue(TransitionChromInfo chromInfo)
{
return chromInfo.Area;
}
public void ChangeChromInfo(EditDescription editDescription, TransitionChromInfo newChromInfo)
{
var newDocNode = Transition.DocNode.ChangeResults(GetResultFile().ChangeChromInfo(Transition.DocNode.Results, newChromInfo));
Transition.ChangeDocNode(editDescription, newDocNode);
}
protected abstract double GetValue(TransitionChromInfo info);
public void Add(ChromatogramInfo chromInfo, TransitionChromInfo transitionChromInfo)
{
ChromInfos.Add(chromInfo);
if (transitionChromInfo != null)
{
float height = transitionChromInfo.Height;
TotalHeight += height;
if (height > MaxHeight || InfoPrimary == null)
{
MaxHeight = height;
InfoPrimary = chromInfo;
TransitionInfoPrimary = transitionChromInfo;
}
}
if (chromInfo != null)
{
// Sum peak heights. This may not be strictly valid, but should
// work as a good approximation for deciding which peaks to label.
int i = 0;
foreach (var peak in chromInfo.Peaks)
{
// Exclude any peaks between the boundaries of the chosen peak.
if (transitionChromInfo != null &&
transitionChromInfo.StartRetentionTime < peak.RetentionTime &&
peak.RetentionTime < transitionChromInfo.EndRetentionTime)
continue;
if (peak.IsForcedIntegration)
continue;
PeakHeights[i++] += peak.Height;
}
}
}
private void DisplayOptimizationTotals(IRegressionFunction timeRegressionFunction,
ChromatogramSet chromatograms,
float mzMatchTolerance,
ref double bestStartTime,
ref double bestEndTime)
{
// Construct and add graph items for all relevant transition groups.
float fontSize = FontSize;
int lineWidth = LineWidth;
int iColor = 0;
// Get the one and only group
var nodeGroup = _nodeGroups[0];
var chromGroupInfo = ChromGroupInfos[0];
ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo);
int numPeaks = chromGroupInfo.NumPeaks;
// Collect the chromatogram info for the transition children
// of this transition group.
var listChromInfoSets = new List<ChromatogramInfo[]>();
var listTranisitionChromInfoSets = new List<TransitionChromInfo[]>();
int totalOptCount = chromatograms.OptimizationFunction.StepCount*2 + 1;
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
var infos = chromGroupInfo.GetAllTransitionInfo((float) nodeTran.Mz, mzMatchTolerance,
chromatograms.OptimizationFunction);
if (infos.Length == 0)
continue;
// Make sure the total number of chrom info entries match the expected
// no matter what, so that chromatogram colors will match up with peak
// area charts.
if (infos.Length != totalOptCount)
infos = ResizeArrayChromInfo(infos, totalOptCount);
listChromInfoSets.Add(infos);
var transitionChromInfos = new TransitionChromInfo[totalOptCount];
int steps = infos.Length/2;
int offset = totalOptCount/2 - steps;
for (int i = 0; i < infos.Length; i++)
{
transitionChromInfos[i + offset] = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, i - steps);
}
listTranisitionChromInfoSets.Add(transitionChromInfos);
}
if (listChromInfoSets.Count == 0 || totalOptCount == 0)
throw new InvalidDataException(Resources.GraphChromatogram_DisplayOptimizationTotals_No_optimization_data_available);
// Enumerate optimization steps, grouping the data into graph data by step
var listGraphData = new List<OptimizationGraphData>();
for (int i = 0; i < listChromInfoSets.Count; i++)
{
var chromInfos = listChromInfoSets[i];
var transitionChromInfos = listTranisitionChromInfoSets[i];
for (int j = 0; j < chromInfos.Length; j++)
{
if (listGraphData.Count <= j)
listGraphData.Add(new OptimizationGraphData(numPeaks));
listGraphData[j].Add(chromInfos[j], transitionChromInfos[j]);
}
}
// Total and transform the data, and compute which optimization
// set has the most intense peak for each peak group.
int bestPeakData = -1;
TransitionChromInfo tranPeakInfo = null;
float maxPeakHeight = float.MinValue;
var maxPeakData = new int[numPeaks];
var maxPeakHeights = new float[numPeaks];
for (int i = 0; i < numPeaks; i++)
maxPeakHeights[i] = float.MinValue;
var transform = Transform;
for (int i = 0; i < listGraphData.Count; i++)
{
var graphData = listGraphData[i];
var infoPrimary = graphData.InfoPrimary;
if (infoPrimary == null)
continue;
// Sum intensities of all transitions in this
// optimization bucket
infoPrimary.SumIntensities(graphData.ChromInfos);
// Apply any transform the user has chosen
infoPrimary.Transform(transform);
for (int j = 0; j < numPeaks; j++)
{
float height = graphData.PeakHeights[j];
if (height > maxPeakHeights[j])
{
maxPeakHeights[j] = height;
maxPeakData[j] = i;
}
}
if (maxPeakHeight < graphData.TotalHeight)
{
maxPeakHeight = graphData.TotalHeight;
bestPeakData = i;
tranPeakInfo = graphData.TransitionInfoPrimary;
}
AddBestPeakTimes(graphData.TransitionInfoPrimary, ref bestStartTime, ref bestEndTime);
}
// Hide all peaks between the best peak extents
if (tranPeakInfo != null)
{
for (int j = 0; j < numPeaks; j++)
{
if (maxPeakHeights[j] == 0)
continue;
var graphData = listGraphData[maxPeakData[j]];
if (graphData.InfoPrimary == null)
continue;
ChromPeak peak = graphData.InfoPrimary.GetPeak(j);
if (peak.IsForcedIntegration)
continue;
if (IntersectPeaks(peak, tranPeakInfo))
maxPeakHeights[j] = 0;
}
}
// Create graph items
int totalSteps = totalOptCount/2;
for (int i = 0; i < listGraphData.Count; i++)
{
var graphData = listGraphData[i];
if (graphData.InfoPrimary != null)
{
int step = i - totalSteps;
int width = lineWidth;
Color color;
if (step == 0)
{
color = ChromGraphItem.ColorSelected;
width++;
}
else if (nodeGroup.HasLibInfo)
color = COLORS_LIBRARY[iColor % COLORS_LIBRARY.Length];
else
color = COLORS_LIBRARY[iColor % COLORS_LIBRARY.Length];
// color = COLORS_HEURISTIC[iColor % COLORS_HEURISTIC.Length];
TransitionChromInfo tranPeakInfoGraph = null;
if (bestPeakData == i)
tranPeakInfoGraph = tranPeakInfo;
var graphItem = new ChromGraphItem(nodeGroup,
null,
graphData.InfoPrimary,
tranPeakInfoGraph,
timeRegressionFunction,
GetAnnotationFlags(i, maxPeakData, maxPeakHeights),
null,
0,
false,
false,
step,
color,
fontSize,
width);
_graphHelper.AddChromatogram(PaneKey.PRECURSORS, graphItem);
}
iColor++;
}
}
private TransitionChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, TransitionChromInfo transitionChromInfo)
: base(measuredResults, replicateIndex, chromFileInfo, transitionChromInfo)
{
}
public void ChangeChromInfo(EditDescription editDescription, TransitionChromInfo newChromInfo)
{
var newDocNode = Transition.DocNode.ChangeResults(GetResultFile().ChangeChromInfo(Transition.DocNode.Results, newChromInfo));
Transition.ChangeDocNode(editDescription, newDocNode);
}
/// <summary>
/// Display summed transitions for multiple selected peptides.
/// </summary>
private void DisplayPeptides(IRegressionFunction timeRegressionFunction,
ChromatogramSet chromatograms,
float mzMatchTolerance,
int countLabelTypes,
IList<PeptideDocNode> peptideDocNodes,
ref double bestStartTime,
ref double bestEndTime,
out double leftPeakWidth,
out double rightPeakWidth)
{
leftPeakWidth = 0;
rightPeakWidth = 0;
// Construct and add graph items for all relevant transition groups.
float fontSize = FontSize;
int lineWidth = LineWidth;
var chromGroupInfos = ChromGroupInfos;
var lookupChromGroupInfoIndex = new Dictionary<int, int>(_nodeGroups.Length);
for (int i = 0; i < _nodeGroups.Length; i++)
lookupChromGroupInfoIndex[_nodeGroups[i].Id.GlobalIndex] = i;
// Generate a unique short identifier for each peptide.
var peptideNames = new Tuple<string,bool>[peptideDocNodes.Count];
for (int i = 0; i < peptideDocNodes.Count; i++)
peptideNames[i] = new Tuple<string,bool>(peptideDocNodes[i].RawTextId, peptideDocNodes[i].IsProteomic);
var uniqueNames = new UniquePrefixGenerator(peptideNames, 3);
var displayPeptides = new List<DisplayPeptide>();
for (int peptideIndex = 0; peptideIndex < peptideDocNodes.Count; peptideIndex++)
{
var peptideDocNode = peptideDocNodes[peptideIndex];
TransitionChromInfo bestPeakInfo = null;
ChromatogramInfo sumInfo = null;
float maxPeakHeight = float.MinValue;
foreach (var precursor in peptideDocNode.TransitionGroups)
{
int indexInfo;
if (!lookupChromGroupInfoIndex.TryGetValue(precursor.Id.GlobalIndex, out indexInfo))
continue;
var chromGroupInfo = chromGroupInfos[indexInfo];
if (chromGroupInfo == null)
continue;
ChromFileInfoId fileId = chromatograms.FindFile(chromGroupInfo);
foreach (var nodeTran in precursor.Transitions)
{
var info = chromGroupInfo.GetTransitionInfo((float)nodeTran.Mz, mzMatchTolerance);
if (info == null)
continue;
if (sumInfo == null)
sumInfo = info;
else
{
float[] sumTimes;
float[] sumIntensities;
if (!AddTransitions.Add(
info.Times, info.Intensities, sumInfo.Times, sumInfo.Intensities,
out sumTimes, out sumIntensities))
continue;
sumInfo = new ChromatogramInfo(sumTimes, sumIntensities);
}
// Keep track of which chromatogram owns the tallest member of
// the peak on the document tree.
var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, 0);
if (transitionChromInfo == null)
continue;
if (transitionChromInfo.Height > maxPeakHeight)
{
maxPeakHeight = transitionChromInfo.Height;
bestPeakInfo = transitionChromInfo;
}
}
}
if (sumInfo != null && bestPeakInfo != null)
{
displayPeptides.Add(new DisplayPeptide
{
PeptideIndex = peptideIndex,
SumInfo = sumInfo,
BestPeakInfo = bestPeakInfo
});
}
}
// Order the peptides by height of best peak.
displayPeptides = displayPeptides.OrderByDescending(e => e.BestPeakInfo.Height).ToList();
// Display only the top peptides.
int lastPeptideIndex = Math.Min(MaxPeptidesDisplayed, displayPeptides.Count);
var graphItems = new List<ChromGraphItem>();
for (int i = lastPeptideIndex-1; i >= 0; i--) // smallest peaks first for good z-ordering in graph
{
var bestPeakInfo = displayPeptides[i].BestPeakInfo;
var sumInfo = displayPeptides[i].SumInfo;
var peptideDocNode = peptideDocNodes[displayPeptides[i].PeptideIndex];
// Intersect best peak with summed transition.
if (bestPeakInfo != null && sumInfo.Times.Length > 0)
{
float startRetentionTime = Math.Max(bestPeakInfo.StartRetentionTime, sumInfo.Times[0]);
float endRetentionTime = Math.Min(bestPeakInfo.EndRetentionTime, sumInfo.Times[sumInfo.Times.Length - 1]);
if (endRetentionTime > startRetentionTime)
{
if (bestStartTime > startRetentionTime)
{
bestStartTime = startRetentionTime;
leftPeakWidth = endRetentionTime - startRetentionTime;
}
if (bestEndTime < endRetentionTime)
{
bestEndTime = endRetentionTime;
rightPeakWidth = endRetentionTime - startRetentionTime;
}
bestPeakInfo = new TransitionChromInfo(startRetentionTime, endRetentionTime);
}
}
// Get peptide graph color from SequenceTree.
var peptideGraphInfo = _stateProvider.GetPeptideGraphInfo(peptideDocNode);
Color color = peptideGraphInfo.Color;
sumInfo.Transform(Transform);
bool[] annotateAll = new bool[sumInfo.NumPeaks];
ChromGraphItem graphItem = new ChromGraphItem(null,
null,
sumInfo,
bestPeakInfo,
timeRegressionFunction,
annotateAll,
null,
0,
false,
false,
0,
color,
fontSize,
lineWidth)
{
CurveAnnotation = uniqueNames.GetUniquePrefix(peptideDocNode.RawTextId, peptideDocNode.IsProteomic),
IdPath = _groupPaths[displayPeptides[i].PeptideIndex],
GraphInfo = peptideGraphInfo
};
if (peptideGraphInfo.IsSelected)
graphItems.Insert(0, graphItem);
else
graphItems.Add(graphItem);
}
foreach (var graphItem in graphItems)
{
var curveItem = _graphHelper.AddChromatogram(new PaneKey(), graphItem);
// Make the fill color under the curve more opaque if the curve is selected.
var fillAlpha = graphItem.GraphInfo.IsSelected ? 60 : 15;
((LineItem)curveItem).Line.Fill = new Fill(Color.FromArgb(fillAlpha, graphItem.GraphInfo.Color));
}
}
protected abstract FindMatch MatchTransition(TransitionChromInfo transitionChromInfo);
private void ShadeGraph(TransitionChromInfo tranPeakInfo, ChromatogramInfo info,
IRegressionFunction timeRegressionFunction, double[] dotProducts, double bestProduct, bool isFullScanMs,
int step, float fontSize, int width, FullScanInfo fullScanInfo, PaneKey graphPaneKey)
{
if (tranPeakInfo == null)
return; // Nothing to shade
float end = tranPeakInfo.EndRetentionTime;
float start = tranPeakInfo.StartRetentionTime;
double[] allTimes;
double[] allIntensities;
info.AsArrays(out allTimes, out allIntensities);
var peakTimes = new List<float>();
var peakIntensities = new List<float>();
for (int j = 0; j < allTimes.Length; j++)
{
if (start > allTimes[j])
continue;
if (end < allTimes[j])
break;
peakTimes.Add((float) allTimes[j]);
peakIntensities.Add((float) allIntensities[j]);
}
if (peakIntensities.Count == 0)
return;
// Add peak area shading
float[] peakTimesArray = peakTimes.ToArray();
info = new ChromatogramInfo(peakTimesArray, peakIntensities.ToArray());
var peakShadeItem = new ChromGraphItem(null,
null,
info,
null,
timeRegressionFunction,
new bool[info.NumPeaks],
dotProducts,
bestProduct,
isFullScanMs,
false,
step,
ChromGraphItem.ColorSelected,
fontSize,
width,
fullScanInfo);
var peakShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, peakShadeItem);
peakShadeCurveItem.Label.IsVisible = false;
var lineItem = peakShadeCurveItem as LineItem;
if (lineItem != null)
{
const int fillAlpha = 50;
lineItem.Line.Fill = new Fill(Color.FromArgb(fillAlpha, lineItem.Color));
}
// Add peak background shading
float min = Math.Min(peakIntensities.First(), peakIntensities.Last());
info = new ChromatogramInfo(peakTimesArray,
peakIntensities.Select(intensity => Math.Min(intensity, min)).ToArray());
var backgroundShadeItem = new ChromGraphItem(null,
null,
info,
null,
timeRegressionFunction,
new bool[info.NumPeaks],
dotProducts,
bestProduct,
isFullScanMs,
false,
step,
Color.DarkGray,
fontSize,
2,
fullScanInfo);
var backgroundShadeCurveItem = _graphHelper.AddChromatogram(graphPaneKey, backgroundShadeItem);
backgroundShadeCurveItem.Label.IsVisible = false;
var lineItem2 = backgroundShadeCurveItem as LineItem;
if (lineItem2 != null)
{
const int fillAlpha = 70;
lineItem2.Line.Fill = new Fill(Color.FromArgb(fillAlpha, Color.Black));
}
}
