public TargetDecoyGenerator(SrmDocument document, IPeakScoringModel scoringModel, IFeatureScoreProvider scoreProvider, IProgressMonitor progressMonitor)
: this(scoringModel,
scoreProvider != null
? scoreProvider.GetFeatureScores(document, scoringModel, progressMonitor)
: document.GetPeakFeatures(scoringModel.PeakFeatureCalculators, progressMonitor))
{
}
public PeakTransitionGroupFeatureSet GetFeatureScores(SrmDocument document, IPeakScoringModel scoringModel,
IProgressMonitor progressMonitor)
{
if (!ReferenceEquals(document, _document) ||
!ArrayUtil.EqualsDeep(_cacheCalculators, scoringModel.PeakFeatureCalculators))
{
_document = document;
_cacheCalculators = scoringModel.PeakFeatureCalculators;
_cachedFeatureScores = document.GetPeakFeatures(_cacheCalculators, progressMonitor);
}
return(_cachedFeatureScores);
}
public TargetDecoyGenerator(SrmDocument document, IPeakScoringModel scoringModel, IProgressMonitor progressMonitor = null)
{
// Determine which calculators will be used to score peaks in this document.
FeatureCalculators = scoringModel.PeakFeatureCalculators.ToArray();
_peakTransitionGroupFeaturesList = document.GetPeakFeatures(FeatureCalculators, progressMonitor);
PopulateDictionary();
EligibleScores = new bool[FeatureCalculators.Count];
// Disable calculators that have only a single score value or any unknown scores.
for (int i = 0; i < FeatureCalculators.Count; i++)
EligibleScores[i] = IsValidCalculator(i);
}
public TargetDecoyGenerator(SrmDocument document, IPeakScoringModel scoringModel, IProgressMonitor progressMonitor = null)
{
// Determine which calculators will be used to score peaks in this document.
FeatureCalculators = scoringModel.PeakFeatureCalculators.ToArray();
_peakTransitionGroupFeaturesList = document.GetPeakFeatures(FeatureCalculators, progressMonitor);
PopulateDictionary();
EligibleScores = new bool[FeatureCalculators.Count];
// Disable calculators that have only a single score value or any unknown scores.
for (int i = 0; i < FeatureCalculators.Count; i++)
{
EligibleScores[i] = IsValidCalculator(i);
}
}
private static IEnumerable <PeakTransitionGroupFeatures> GetPeakFeatures(this SrmDocument document,
PeptideGroupDocNode nodePepGroup,
PeptideDocNode nodePep,
IList <IPeakFeatureCalculator> calcs,
IDictionary <int, int> runEnumDict,
bool verbose)
{
// Get peptide features for each set of comparable groups
foreach (var nodeGroups in ComparableGroups(nodePep))
{
var arrayGroups = nodeGroups.ToArray();
var labelType = arrayGroups[0].TransitionGroup.LabelType;
foreach (var peakFeature in document.GetPeakFeatures(nodePepGroup, nodePep, labelType, arrayGroups, calcs, runEnumDict, verbose))
{
yield return(peakFeature);
}
}
}
public static PeakTransitionGroupFeatureSet GetPeakFeatures(this SrmDocument document,
IList <IPeakFeatureCalculator> calcs,
IProgressMonitor progressMonitor = null,
bool verbose = false)
{
// Get features for each peptide
int totalPeptides = document.MoleculeCount;
int currentPeptide = 0;
IProgressStatus status = new ProgressStatus(Resources.PeakFeatureEnumerator_GetPeakFeatures_Calculating_peak_group_scores);
// Set up run ID dictionary
var runEnumDict = new Dictionary <int, int>();
var chromatograms = document.Settings.MeasuredResults.Chromatograms;
foreach (var fileInfo in chromatograms.SelectMany(c => c.MSDataFileInfos))
{
runEnumDict.Add(fileInfo.FileIndex, runEnumDict.Count + 1);
}
// Using Parallel.For is quicker, but order needs to be maintained
var moleculeGroupPairs = document.GetMoleculeGroupPairs();
var peakFeatureLists = new PeakTransitionGroupFeatures[moleculeGroupPairs.Length][];
int peakFeatureCount = 0;
ParallelEx.For(0, moleculeGroupPairs.Length, i =>
{
var pair = moleculeGroupPairs[i];
var nodePepGroup = pair.NodeMoleculeGroup;
var nodePep = pair.NodeMolecule;
if (nodePep.TransitionGroupCount == 0)
{
return;
}
// Exclude standard peptides
if (nodePep.GlobalStandardType != null)
{
return;
}
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
{
throw new OperationCanceledException();
}
int?percentComplete = ProgressStatus.ThreadsafeIncementPercent(ref currentPeptide, totalPeptides);
if (percentComplete.HasValue && percentComplete.Value < 100)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(percentComplete.Value));
}
}
var peakFeatureList = new List <PeakTransitionGroupFeatures>();
foreach (var peakFeature in document.GetPeakFeatures(nodePepGroup, nodePep, calcs, runEnumDict, verbose))
{
if (peakFeature.PeakGroupFeatures.Any())
{
peakFeatureList.Add(peakFeature);
Interlocked.Increment(ref peakFeatureCount);
}
}
peakFeatureLists[i] = peakFeatureList.ToArray();
});
var result = new PeakTransitionGroupFeatures[peakFeatureCount];
int peakFeatureCurrent = 0;
int decoyCount = 0;
foreach (var peakFeatureList in peakFeatureLists)
{
if (peakFeatureList == null)
{
continue;
}
foreach (var peakFeature in peakFeatureList)
{
result[peakFeatureCurrent++] = peakFeature;
if (peakFeature.IsDecoy)
{
decoyCount++;
}
}
}
if (progressMonitor != null)
{
progressMonitor.UpdateProgress(status.ChangePercentComplete(100));
}
return(new PeakTransitionGroupFeatureSet(decoyCount, result));
}
