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out matchedPeaks in GetAllXics #958

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c20e07b
matchedPeaks added
zhuoxinshi Oct 10, 2025
78d64ca
Merge branch 'master' into outMatchedPeaksXic
zhuoxinshi Oct 21, 2025
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4 changes: 2 additions & 2 deletions mzLib/MassSpectrometry/PeakIndexing/IndexingEngine.cs
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Expand Up @@ -30,7 +30,7 @@
return false;

IndexedPeaks = new List<T>[(int)Math.Ceiling(scanArray.Where(p => p != null
&& p.MassSpectrum.LastX != null).Max(p => p.MassSpectrum.LastX.Value) * BinsPerDalton) + 1];

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ScanInfoArray = new ScanInfo[scanArray.Length];

for (int scanIndex = 0; scanIndex < scanArray.Length; scanIndex++)
Expand Down Expand Up @@ -85,7 +85,7 @@
/// <param name="matchedPeaks"> the dictionary that stores all the peaks already matched to an xic </param>
/// <returns> A list of IIndexedPeak objects, ordered by retention time </returns>
public List<IIndexedPeak> GetXic(double m, double retentionTime, Tolerance ppmTolerance,
int missedScansAllowed, double maxPeakHalfWidth = double.MaxValue, int? charge = null, Dictionary<IIndexedPeak, ExtractedIonChromatogram> matchedPeaks = null)

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{
// get precursor scan to start at
int scanIndex = -1;
Expand Down Expand Up @@ -120,7 +120,7 @@
/// <param name="charge"> an optional parameter used only for IIndexedMass and massIndexingEngine; must be null for mz peak indexing </param>
/// <param name="matchedPeaks"> the dictionary that stores all the peaks already matched to an xic </param>
/// <returns> A list of IIndexedPeak objects, ordered by retention time </returns>
public List<IIndexedPeak> GetXicByScanIndex(double m, int zeroBasedStartIndex, Tolerance ppmTolerance, int missedScansAllowed, double maxPeakHalfWidth = double.MaxValue, int? charge = null, Dictionary<IIndexedPeak, ExtractedIonChromatogram> matchedPeaks = null)

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{
if (IndexedPeaks == null || ScanInfoArray == null) throw new MzLibException("Error: Attempt to retrieve XIC before peak indexing was performed");

Expand All @@ -134,7 +134,7 @@
var initialPeak = GetBestPeakFromBins(allBins, m, zeroBasedStartIndex, peakPointerArray, ppmTolerance, charge);

if (initialPeak.IsNotDefaultOrNull())
xic.Add(initialPeak);

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foreach (int direction in new List<int> { -1, 1 })
{
Expand All @@ -148,7 +148,7 @@
{
// increment the scan index we're searching for
currentZeroBasedScanIndex += direction;
if(currentZeroBasedScanIndex < 0 || currentZeroBasedScanIndex > ScanInfoArray.Length - 1 || (initialPeak.IsNotDefaultOrNull() && ScanInfoArray[currentZeroBasedScanIndex] != null && Math.Abs(ScanInfoArray[currentZeroBasedScanIndex].RetentionTime - initialPeak.RetentionTime) > maxPeakHalfWidth))

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break;

for (int i = 0; i < pointerArrayCopy.Length; i++)
Expand Down Expand Up @@ -195,11 +195,11 @@
/// A generic method performing peak tracing for all the peaks in an indexingEngine and trying to find all XICs.
/// <param name="cutPeakDiscriminationFactor"> The discrimination factor to determine if a peak should be cut if we are doing peak cutting </param>
/// <returns> A list of ExtractedIonChromatogram objects representing all XICs that can be found in an indexingEngine </returns>
public virtual List<ExtractedIonChromatogram> GetAllXics(Tolerance peakFindingTolerance, int maxMissedScanAllowed, double maxRTRange, int numPeakThreshold, double? cutPeakDiscriminationFactor = null)
public virtual List<ExtractedIonChromatogram> GetAllXics(Tolerance peakFindingTolerance, int maxMissedScanAllowed, double maxRTRange, int numPeakThreshold, out Dictionary<IIndexedPeak, ExtractedIonChromatogram> matchedPeaks, double? cutPeakDiscriminationFactor = null)

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The optional parameter cutPeakDiscriminationFactor should appear before the out parameter matchedPeaks. In C#, optional parameters must come after all required parameters, but out parameters are considered required. The current ordering violates this convention and could cause API confusion.

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{
var xics = new List<ExtractedIonChromatogram>();
var matchedPeaks = new Dictionary<IIndexedPeak, ExtractedIonChromatogram>();
matchedPeaks = new Dictionary<IIndexedPeak, ExtractedIonChromatogram>();
var sortedPeaks = IndexedPeaks.Where(v => v != null).SelectMany(peaks => peaks).OrderByDescending(p => p.Intensity).ToList();

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foreach (var peak in sortedPeaks)
{
if (!matchedPeaks.ContainsKey(peak))
Expand Down
17 changes: 9 additions & 8 deletions mzLib/Test/TestXic.cs
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Expand Up @@ -147,18 +147,19 @@ public static void TestGetAllXics()
{
//Test case using FakeScans
var indexingEngine = PeakIndexingEngine.InitializeIndexingEngine(testScans);
var xics = indexingEngine.GetAllXics(new PpmTolerance(20), 2, 2, 3);
var xics = indexingEngine.GetAllXics(new PpmTolerance(20), 2, 2, 3, out var matchedPeaks);
Assert.That(xics.Count, Is.EqualTo(20));
foreach(var xic in xics)
{
Assert.That(xic.Peaks.Count, Is.EqualTo(10));
}
Assert.That(matchedPeaks.Count, Is.EqualTo(xics.Sum(xic => xic.Peaks.Count)));

//Test with massIndexingEngine
var deconParameters = new ClassicDeconvolutionParameters(1, 20, 4, 3);
var allMasses = Deconvoluter.Deconvolute(testScans[0].MassSpectrum, deconParameters);
var massIndexingEngine = MassIndexingEngine.InitializeMassIndexingEngine(testScans, deconParameters);
var massXics = massIndexingEngine.GetAllXics(new PpmTolerance(20), 2, 2, 3);
var massXics = massIndexingEngine.GetAllXics(new PpmTolerance(20), 2, 2, 3, out matchedPeaks);
Assert.That(massXics.Count, Is.EqualTo(2));
foreach (var mass in allMasses)
{
Expand All @@ -179,12 +180,12 @@ public static void TestGetAllXics()
mzAnalyzer: MZAnalyzerType.Orbitrap, totalIonCurrent: 1, injectionTime: 1.0, noiseData: null, nativeId: "scan=" + (s + 1));
}
var indexingEngine2 = PeakIndexingEngine.InitializeIndexingEngine(fakeScans2);
var xics2 = indexingEngine2.GetAllXics(new PpmTolerance(20), 2, 2, 3);
var xics2 = indexingEngine2.GetAllXics(new PpmTolerance(20), 2, 2, 3, out matchedPeaks);
Assert.That(xics2.Count, Is.EqualTo(40)); //the first three scans and the last four scans will each contain two XICs
Assert.That(xics2.SequenceEqual(xics2.OrderByDescending(x => x.ApexPeak.Intensity)));//make sure the XICs are ordered by descending apex intensity
//Test with massIndexingEngine
var massIndexingEngine2 = MassIndexingEngine.InitializeMassIndexingEngine(fakeScans2, deconParameters);
var massXics2 = massIndexingEngine2.GetAllXics(new PpmTolerance(20), 2, 2, 3);
var massXics2 = massIndexingEngine2.GetAllXics(new PpmTolerance(20), 2, 2, 3, out matchedPeaks);
Assert.That(massXics2.Count, Is.EqualTo(4));

var fakeScans3 = (MsDataScan[])testScans.Clone();
Expand All @@ -195,15 +196,15 @@ public static void TestGetAllXics()
mzAnalyzer: MZAnalyzerType.Orbitrap, totalIonCurrent: 1, injectionTime: 1.0, noiseData: null, nativeId: "scan=" + (s + 1));
}
var indexingEngine3 = PeakIndexingEngine.InitializeIndexingEngine(fakeScans3);
var xics3 = indexingEngine3.GetAllXics(new PpmTolerance(20), 2, 2, 3);
var xics3 = indexingEngine3.GetAllXics(new PpmTolerance(20), 2, 2, 3, out matchedPeaks);
Assert.That(xics3.Count, Is.EqualTo(20)); // Because the minumum number of peaks required is set to 3, the first two scans do not contain any XICs with only two consecutive peaks.
foreach (var xic in xics3)
{
Assert.That(xic.Peaks.Count, Is.EqualTo(5));
}
//Test with massIndexingEngine
var massIndexingEngine3 = MassIndexingEngine.InitializeMassIndexingEngine(fakeScans3, deconParameters);
var massXics3 = massIndexingEngine3.GetAllXics(new PpmTolerance(20), 2, 2, 3);
var massXics3 = massIndexingEngine3.GetAllXics(new PpmTolerance(20), 2, 2, 3, out matchedPeaks);
Assert.That(massXics3.Count, Is.EqualTo(2));
foreach (var xic in massXics3)
{
Expand Down Expand Up @@ -275,14 +276,14 @@ public static void TestGetAllXicsWithCutPeak()
testScans[s] = new MsDataScan(massSpectrum: new MzSpectrum(mz, intensities, false), oneBasedScanNumber: s + 1, msnOrder: 1, isCentroid: true,polarity: Polarity.Positive, retentionTime: 1.0 + s / 10.0, scanWindowRange: new MzRange(400, 1600), scanFilter: "f",mzAnalyzer: MZAnalyzerType.Orbitrap, totalIonCurrent: intensities.Sum(), injectionTime: 1.0, noiseData: null, nativeId: "scan=" + (s + 1));
}
var indexingEngine = PeakIndexingEngine.InitializeIndexingEngine(testScans);
var xics = indexingEngine.GetAllXics(new PpmTolerance(5), 2, 3, 3);
var xics = indexingEngine.GetAllXics(new PpmTolerance(5), 2, 3, 3, out var matchedPeaks);
// 10 XICs should be found without peak cutting, each containing 10 peaks
Assert.That(xics.Count(), Is.EqualTo(10));
Assert.That(xics.All(x => x.Peaks.Count == 10), Is.True);
//The XICs should have an apex at the eighth scan
Assert.That(xics.All(x => x.ApexScanIndex == 7), Is.True);

var xicsWithCutPeak = indexingEngine.GetAllXics(new PpmTolerance(5), 2, 3, 3, 0.6);
var xicsWithCutPeak = indexingEngine.GetAllXics(new PpmTolerance(5), 2, 3, 3, out matchedPeaks, 0.6);
// since each original XIC contain two apex, cutting peaks should double the number of XICs found and each XIC should contain 5 peaks now
Assert.That(xicsWithCutPeak.Count(), Is.EqualTo(20));
Assert.That(xicsWithCutPeak.All(x => x.Peaks.Count == 5), Is.True);
Expand Down
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