remvoe out-commented code
@@ -401,63 +401,4 @@ public class DiaMs2CorrTask extends AbstractTask {
adapTask.cancel();
}
}
-
- /*
- private ModularFeatureList runSmoothing(MZmineProject dummyProject, ModularFeatureList ms2Flist) {
- if (smoothingParameters != null) {
- final MZmineProcessingStep<SmoothingAlgorithm> smoother = smoothingParameters.getParameter(
- SmoothingParameters.smoothingAlgorithm).getValue();
- ParameterSet fullSmoothingParams = MZmineCore.getConfiguration()
- .getModuleParameters(SmoothingModule.class).cloneParameterSet();
- fullSmoothingParams.setParameter(SmoothingParameters.smoothingAlgorithm, smoother);
- fullSmoothingParams.setParameter(SmoothingParameters.suffix, "_sm");
- fullSmoothingParams.setParameter(SmoothingParameters.handleOriginal,
- OriginalFeatureListOption.REMOVE);
-
- currentTask = new SmoothingTask(dummyProject, (ModularFeatureList) ms2Flist,
- flist.getMemoryMapStorage(), fullSmoothingParams, getModuleCallDate());
- currentTask.run();
- }
- currentTask = null;
- currentTaksIndex++;
- return (ModularFeatureList) dummyProject.getCurrentFeatureLists().get(0);
- }
-
- private ModularFeatureList runResolving(MZmineProject dummyProject, ModularFeatureList ms2Flist) {
- ParameterSet fullResolverParameters = MZmineCore.getConfiguration()
- .getModuleParameters(MinimumSearchFeatureResolverModule.class);
- fullResolverParameters.setParameter(
- MinimumSearchFeatureResolverParameters.CHROMATOGRAPHIC_THRESHOLD_LEVEL,
- resolverParameters.getValue(
- MinimumSearchFeatureResolverParameters.CHROMATOGRAPHIC_THRESHOLD_LEVEL));
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.MIN_RATIO,
- resolverParameters.getValue(MinimumSearchFeatureResolverParameters.MIN_RATIO));
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.SEARCH_RT_RANGE,
- resolverParameters.getValue(MinimumSearchFeatureResolverParameters.SEARCH_RT_RANGE));
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.MIN_ABSOLUTE_HEIGHT,
- resolverParameters.getValue(MinimumSearchFeatureResolverParameters.MIN_ABSOLUTE_HEIGHT));
- fullResolverParameters.setParameter(
- MinimumSearchFeatureResolverParameters.MIN_NUMBER_OF_DATAPOINTS,
- resolverParameters.getValue(
- MinimumSearchFeatureResolverParameters.MIN_NUMBER_OF_DATAPOINTS));
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.MIN_RELATIVE_HEIGHT,
- resolverParameters.getValue(MinimumSearchFeatureResolverParameters.MIN_RELATIVE_HEIGHT));
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.PEAK_DURATION,
- resolverParameters.getValue(MinimumSearchFeatureResolverParameters.PEAK_DURATION));
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.SUFFIX, "_res");
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.handleOriginal,
- OriginalFeatureListOption.REMOVE);
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.dimension,
- ResolvingDimension.RETENTION_TIME);
- fullResolverParameters.setParameter(MinimumSearchFeatureResolverParameters.groupMS2Parameters,
- false);
-
- currentTask = new FeatureResolverTask(dummyProject, getMemoryMapStorage(), ms2Flist,
- fullResolverParameters, FeatureDataUtils.DEFAULT_CENTER_FUNCTION, getModuleCallDate());
- currentTask.run();
- currentTask = null;
- currentTaksIndex++;
-
- return (ModularFeatureList) dummyProject.getCurrentFeatureLists().get(0);
- }*/
}
