public PeakTransitionGroupFeatures(PeakTransitionGroupId id, IList <PeakGroupFeatures> peakGroupFeatures, bool verbose) : this()
{
Key = id.Key;
IsDecoy = id.IsDecoy;
PeakGroupFeatures = peakGroupFeatures;
if (verbose)
{
Id = id; // Avoid holding this in memory unless required for verbose output
}
}
public PeakTransitionGroupFeatures(PeakTransitionGroupId id, IList <PeakGroupFeatures> peakGroupFeatures)
{
Id = id;
PeakGroupFeatures = peakGroupFeatures;
}
private static IEnumerable <PeakTransitionGroupFeatures> GetPeakFeatures(this SrmDocument document,
PeptideGroupDocNode nodePepGroup,
PeptideDocNode nodePep,
IsotopeLabelType labelType,
IList <TransitionGroupDocNode> nodeGroups,
IList <IPeakFeatureCalculator> calcs,
IDictionary <int, int> runEnumDict,
bool verbose)
{
var chromatograms = document.Settings.MeasuredResults.Chromatograms;
float mzMatchTolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
foreach (var chromatogramSet in chromatograms)
{
ChromatogramGroupInfo[] arrayChromInfo;
if (!document.Settings.MeasuredResults.TryLoadChromatogram(chromatogramSet, nodePep, nodeGroups[0],
mzMatchTolerance, false, out arrayChromInfo))
{
continue;
}
foreach (var chromGroupInfo in arrayChromInfo)
{
var peakId = new PeakTransitionGroupId(nodePepGroup, nodePep, labelType, chromatogramSet, chromGroupInfo, runEnumDict);
var listRunFeatures = new List <PeakGroupFeatures>();
var summaryPeakData = new SummaryPeptidePeakData(document, nodePep, nodeGroups, chromatogramSet, chromGroupInfo);
var context = new PeakScoringContext(document);
while (summaryPeakData.NextPeakIndex())
{
if (!summaryPeakData.HasArea)
{
continue;
}
var features = new float[calcs.Count];
for (int i = 0; i < calcs.Count; i++)
{
features[i] = summaryPeakData.GetScore(context, calcs[i]);
}
// CONSIDER: Peak features can take up a lot of space in large scale DIA
// It may be possible to save even more by using a smaller struct
// when times are not required, which they are only for export
float retentionTime = 0, startTime = 0, endTime = 0;
if (verbose)
{
var peakTimes = summaryPeakData.RetentionTimeStatistics;
retentionTime = peakTimes.RetentionTime;
startTime = peakTimes.StartTime;
endTime = peakTimes.EndTime;
}
int peakIndex = summaryPeakData.UsedBestPeakIndex
? summaryPeakData.BestPeakIndex
: summaryPeakData.PeakIndex;
listRunFeatures.Add(new PeakGroupFeatures(peakIndex, retentionTime, startTime, endTime, features));
}
yield return(new PeakTransitionGroupFeatures(peakId, listRunFeatures.ToArray(), verbose));
}
}
}
private static IEnumerable <PeakTransitionGroupFeatures> GetPeakFeatures(this SrmDocument document,
PeptideGroupDocNode nodePepGroup,
PeptideDocNode nodePep,
IsotopeLabelType labelType,
IList <TransitionGroupDocNode> nodeGroups,
IList <IPeakFeatureCalculator> calcs,
IDictionary <int, int> runEnumDict,
bool includeMzFilters)
{
var chromatograms = document.Settings.MeasuredResults.Chromatograms;
float mzMatchTolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
foreach (var chromatogramSet in chromatograms)
{
ChromatogramGroupInfo[] arrayChromInfo;
if (!document.Settings.MeasuredResults.TryLoadChromatogram(chromatogramSet, nodePep, nodeGroups[0],
mzMatchTolerance, false, out arrayChromInfo))
{
continue;
}
foreach (var chromGroupInfo in arrayChromInfo)
{
var peakId = new PeakTransitionGroupId(nodePepGroup, nodePep, labelType, chromatogramSet, chromGroupInfo, runEnumDict);
var listRunFeatures = new List <PeakGroupFeatures>();
var summaryPeakData = new SummaryPeptidePeakData(document, nodePep, nodeGroups, chromatogramSet, chromGroupInfo);
var context = new PeakScoringContext(document);
while (summaryPeakData.NextPeakIndex())
{
if (!summaryPeakData.HasArea)
{
continue;
}
var features = new float[calcs.Count];
for (int i = 0; i < calcs.Count; i++)
{
features[i] = summaryPeakData.GetScore(context, calcs[i]);
}
MzFilterPairs[] mzFilters = null;
if (includeMzFilters)
{
mzFilters = summaryPeakData.GetMzFilters(context);
}
float retentionTime = summaryPeakData.RetentionTime;
float startTime = summaryPeakData.StartTime;
float endTime = summaryPeakData.EndTime;
bool isMaxPeakIndex = summaryPeakData.IsMaxPeakIndex;
listRunFeatures.Add(new PeakGroupFeatures(summaryPeakData.PeakIndex, retentionTime, startTime, endTime,
isMaxPeakIndex, features, mzFilters));
}
yield return(new PeakTransitionGroupFeatures(peakId, listRunFeatures.ToArray()));
}
}
}
