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Condense tandem MS data when multiple traces option is used. #2992

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Merged
eselmeister merged 1 commit into from
Jul 16, 2026
Merged

Condense tandem MS data when multiple traces option is used. #2992

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37 changes: 37 additions & 0 deletions ....chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/support/TandemDataSupport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,12 +25,15 @@
import org.eclipse.chemclipse.model.core.support.HeaderField;
import org.eclipse.chemclipse.model.support.ChromatogramSupport;
import org.eclipse.chemclipse.model.support.HeaderUtil;
import org.eclipse.chemclipse.msd.model.core.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IIon;
import org.eclipse.chemclipse.msd.model.core.IIonMSn;
import org.eclipse.chemclipse.msd.model.core.IIonTransition;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.implementation.ChromatogramMSD;
import org.eclipse.chemclipse.msd.model.implementation.IonMSn;
import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
import org.eclipse.chemclipse.msd.model.implementation.RegularMassSpectrum;
import org.eclipse.chemclipse.support.text.ValueFormat;
import org.eclipse.chemclipse.support.traces.TraceTandemMSD;
Expand Down Expand Up @@ -118,12 +121,46 @@ public static List<IChromatogramMSD> extractTandemData(IChromatogramMSD chromato
enforceFullTimeRange = true; // needed to map all traces
Map<Integer, List<IIon>> scanIonsMap = new HashMap<>();
collectTraces(new ArrayList<>(traces), scanRangesMap, retentionTimes, scanIonsMap);
condenseTraces(scanIonsMap);
createReferenceChromatogram(chromatograms, chromatogramMSD, retentionTimes, scanIonsMap, headerField, "Multiple Traces", enforceFullTimeRange);
}

return chromatograms;
}

private static void condenseTraces(Map<Integer, List<IIon>> scanIonsMap) {

for(Map.Entry<Integer, List<IIon>> entry : scanIonsMap.entrySet()) {
Map<String, IIon> ionMap = new HashMap<>();
List<IIon> ions = entry.getValue();
for(IIon ion : ions) {
if(ion instanceof IIonMSn ionMSn) {
IIonTransition ionTransition = ionMSn.getIonTransition();
double parent = ionTransition.getQ1Ion();
int daughter = AbstractIon.getIon(ionTransition.getQ3Ion());
int collisionEnergy = (int)ionTransition.getCollisionEnergy();
String tandemIdentifier = Double.toString(parent) + "_" + Integer.toString(daughter) + "_" + Integer.toString(collisionEnergy);
IIon ionMapped = ionMap.get(tandemIdentifier);
if(ionMapped == null) {
double filter1Resolution = ionTransition.getQ1Resolution();
double filter3Resolution = ionTransition.getQ3Resolution();
int transitionGroup = ionTransition.getTransitionGroup();
IIonTransition ionTransitionCopy = new IonTransition(parent, daughter, collisionEnergy, filter1Resolution, filter3Resolution, transitionGroup);
ionMapped = new IonMSn(daughter, ion.getAbundance(), ionTransitionCopy);
ionMap.put(tandemIdentifier, ionMapped);
} else {
ionMapped.setAbundance(ionMapped.getAbundance() + ion.getAbundance());
}
}
}
/*
* Clean Ions
*/
ions.clear();
ions.addAll(ionMap.values());
}
}

private static boolean matches(TraceTandemMSD trace, IIonMSn ion) {

IIonTransition ionTransition = ion.getIonTransition();
Expand Down