Change defaults for library matching
@@ -927,7 +927,7 @@ public class BatchWizardController {
param.setParameter(SpectralLibrarySearchParameters.noiseLevel, 0d);
param.setParameter(SpectralLibrarySearchParameters.needsIsotopePattern, false);
param.setParameter(SpectralLibrarySearchParameters.rtTolerance, false);
- param.setParameter(SpectralLibrarySearchParameters.minMatch, 5);
+ param.setParameter(SpectralLibrarySearchParameters.minMatch, 4);
// similarity
ModuleComboParameter<SpectralSimilarityFunction> simFunction = param.getParameter(
SpectralLibrarySearchParameters.similarityFunction);
@@ -938,7 +938,7 @@ public class BatchWizardController {
Weights.MASSBANK);
weightedCosineParam.setParameter(WeightedCosineSpectralSimilarityParameters.weight,
Weights.MASSBANK);
- weightedCosineParam.setParameter(WeightedCosineSpectralSimilarityParameters.minCosine, 0.7);
+ weightedCosineParam.setParameter(WeightedCosineSpectralSimilarityParameters.minCosine, 0.65);
weightedCosineParam.setParameter(WeightedCosineSpectralSimilarityParameters.handleUnmatched,
HandleUnmatchedSignalOptions.KEEP_ALL_AND_MATCH_TO_ZERO);
@@ -948,9 +948,9 @@ public class BatchWizardController {
// finally set the libmatch module plus parameters as step
simFunction.setValue(libMatchStep);
// IMS
- param.setParameter(SpectralLibrarySearchParameters.ccsTolerance, cbIonMobility.isSelected());
+ param.setParameter(SpectralLibrarySearchParameters.ccsTolerance, false);
param.getParameter(SpectralLibrarySearchParameters.ccsTolerance).getEmbeddedParameter()
- .setValue(0.5);
+ .setValue(0.05);
return new MZmineProcessingStepImpl<>(
MZmineCore.getModuleInstance(SpectralLibrarySearchModule.class), param);
