enable CL annotations
@@ -577,24 +577,27 @@ public class MSMSLipidTools {
minMsMsScore, mzTolRangeMSMS, ionizationType));
}
}
- }
if (chainsInLipid >= 4) {
- for (int k = 0; k < chains.size(); k++) {
- int carbonThree = chains.get(k).getNumberOfCarbons();
- int dbeThree = chains.get(k).getNumberOfDBEs();
- if (chainsInLipid == 3 && carbonOne + carbonTwo + carbonThree == totalNumberOfCAtoms
- && dbeOne + dbeTwo + dbeThree == totalNumberOfDBEs) {
+ for (int l = 0; l < chains.size(); l++) {
+ int carbonFour = chains.get(l).getNumberOfCarbons();
+ int dbeFour = chains.get(l).getNumberOfDBEs();
+ if (chainsInLipid == 4
+ && carbonOne + carbonTwo + carbonThree + carbonFour == totalNumberOfCAtoms
+ && dbeOne + dbeTwo + dbeThree + dbeFour == totalNumberOfDBEs) {
List<ILipidChain> predictedChains = new ArrayList<>();
predictedChains.add(chains.get(i));
predictedChains.add(chains.get(j));
predictedChains.add(chains.get(k));
+ predictedChains.add(chains.get(l));
if (checkChainTypesFitLipidClass(predictedChains,
lipidAnnotation.getLipidClass())) {
Set<LipidFragment> fittingFragments = extractFragmentsForFittingChains(
predictedChains, detectedFragmentsWithChainInformation);
- matchedMolecularSpeciesLevelAnnotations.add(buildNewMolecularSpeciesLevelMatch(
- fittingFragments, lipidAnnotation, accurateMz, massList, predictedChains,
- minMsMsScore, mzTolRangeMSMS, ionizationType));
+ matchedMolecularSpeciesLevelAnnotations
+ .add(buildNewMolecularSpeciesLevelMatch(fittingFragments, lipidAnnotation,
+ accurateMz, massList, predictedChains, minMsMsScore, mzTolRangeMSMS,
+ ionizationType));
+ }
}
}
}
