Add detection for legacy peak filter IDs in process methods

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/filter/IPeakFilter.java

@@ -13,6 +13,7 @@
 package org.eclipse.chemclipse.model.filter;
 
 import java.util.Collection;
+import java.util.List;
 
 import org.eclipse.chemclipse.model.core.IPeak;
 import org.eclipse.chemclipse.model.selection.IChromatogramSelection;
@@ -67,4 +68,6 @@ default DataCategory[] getDataCategories() {
 
 		return new DataCategory[]{DataCategory.CSD, DataCategory.MSD, DataCategory.WSD, DataCategory.VSD};
 	}
+
+	List<String> getLegacyIDs();
 }

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/supplier/PeakFilterProcessTypeSupplier.java

@@ -81,5 +81,11 @@ private void doFilter(IChromatogramSelection chromatogramSelection, ConfigType p
 
 			filter.filterPeaks(chromatogramSelection, processSettings, context);
 		}
+
+		@Override
+		public boolean matchesId(String id) {
+
+			return super.matchesId(id) || filter.getLegacyIDs().contains(id);
+		}
 	}
 }

chemclipse/plugins/org.eclipse.chemclipse.support/src/org/eclipse/chemclipse/support/settings/serialization/JSONSerialization.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2019, 2024 Lablicate GmbH.
+ * Copyright (c) 2019, 2025 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -44,7 +44,7 @@ public JavaType findTypeMapping(DeserializationConfig config, JavaType type) {
 
 			Class<?> sourceClass = type.getRawClass();
 			Class<?> destinationClass = MAPPINGS.get(sourceClass);
-			//
+
 			if(destinationClass == null) {
 				return null;
 			}
@@ -78,7 +78,7 @@ public Map<InputValue, Object> fromObject(Collection<? extends InputValue> input
 				}
 			}
 		}
-		//
+
 		return resultMap;
 	}
 
@@ -88,7 +88,7 @@ private Map<String, InputValue> getInputValueMap(Collection<? extends InputValue
 		for(InputValue inputValue : inputValues) {
 			inputValueMap.put(inputValue.getName(), inputValue);
 		}
-		//
+
 		return inputValueMap;
 	}
 
@@ -107,7 +107,7 @@ public String toString(Map<InputValue, Object> values) throws IOException {
 	private ObjectMapper createMapper() {
 
 		ObjectMapper objectMapper = new ObjectMapper();
-		//
+
 		SimpleModule simpleModule = new SimpleModule("ChemClipse", Version.unknownVersion());
 		simpleModule.setAbstractTypes(RESOLVER);
 		/*
@@ -123,10 +123,10 @@ private ObjectMapper createMapper() {
 				}
 			}
 		}
-		//
+
 		objectMapper.registerModule(simpleModule);
 		objectMapper.disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES);
-		//
+
 		return objectMapper;
 	}
 
@@ -157,4 +157,4 @@ public static <T> void removeMapping(Class<T> superType, Class<? extends T> subT
 
 		MAPPINGS.remove(superType, subType);
 	}
-}
+}

chemclipse/plugins/org.eclipse.chemclipse.ux.extension.ui/src/org/eclipse/chemclipse/ux/extension/ui/internal/provider/MethodListLabelProvider.java

@@ -35,7 +35,7 @@ public class MethodListLabelProvider extends AbstractChemClipseLabelProvider {
 
 	private final IProcessSupplierContext processTypeSupport;
 	private BiFunction<IProcessEntry, IProcessSupplierContext, IProcessorPreferences<?>> preferencesSupplier;
-	//
+
 	public static final String[] TITLES = {//
 			"", //
 			ExtensionMessages.name, //
@@ -44,7 +44,7 @@ public class MethodListLabelProvider extends AbstractChemClipseLabelProvider {
 			ExtensionMessages.settings, //
 			ExtensionMessages.id //
 	};
-	//
+
 	public static final int[] BOUNDS = {//
 			50, //
 			250, //
@@ -69,7 +69,7 @@ public Image getColumnImage(Object element, int columnIndex) {
 				 * Validate
 				 */
 				IStatus status = validate(processEntry);
-				//
+
 				if(status.matches(IStatus.ERROR)) {
 					return ApplicationImageFactory.getInstance().getImage(IApplicationImage.IMAGE_STATUS_ERROR, IApplicationImageProvider.SIZE_16x16);
 				}
@@ -109,11 +109,11 @@ public String getColumnText(Object element, int columnIndex) {
 		if(columnIndex == 0) {
 			return "";
 		}
-		//
+
 		if(element instanceof IProcessEntry processEntry) {
 			IProcessSupplierContext supplierContext = IProcessEntry.getContext(processEntry, processTypeSupport);
 			IProcessSupplier<?> processSupplier = supplierContext.getSupplier(processEntry.getProcessorId());
-			//
+
 			switch(columnIndex) {
 				case 1:
 					return processEntry.getName();
@@ -159,7 +159,7 @@ public String getColumnText(Object element, int columnIndex) {
 					return "";
 			}
 		}
-		//
+
 		return "n/a";
 	}
 
@@ -177,11 +177,11 @@ private IStatus validate(IProcessEntry processEntry) {
 		if(processEntry == null) {
 			return ValidationStatus.error(ExtensionMessages.processorNotAvailable);
 		}
-		//
+
 		if(preferencesSupplier == null) {
 			return ValidationStatus.error(ExtensionMessages.preferenceSupplierNotAvailable);
 		}
-		//
+
 		if(processTypeSupport == null) {
 			return ValidationStatus.error(ExtensionMessages.processTypeSupportNotAvailable);
 		}
@@ -192,15 +192,15 @@ private IStatus validate(IProcessEntry processEntry) {
 			return ValidationStatus.info(MessageFormat.format(ExtensionMessages.processorSkipValidationOptionSet, processEntry.getName()));
 		}
 		IProcessorPreferences<?> processorPreferences = preferencesSupplier.apply(processEntry, processTypeSupport);
-		//
+
 		if(processorPreferences == null) {
 			return ValidationStatus.error(MessageFormat.format(ExtensionMessages.processorPreferencesNotAvailable, processEntry.getName()));
 		}
-		//
+
 		if(processorPreferences.getSupplier().getSettingsClass() == null) {
 			return ValidationStatus.warning(MessageFormat.format(ExtensionMessages.processorHasNoSettingsClass, processEntry.getName()));
 		}
-		//
+
 		if(processorPreferences.isUseSystemDefaults()) {
 			return ValidationStatus.info(MessageFormat.format(ExtensionMessages.processorUsesSystemDefaultSettings, processEntry.getName()));
 		}

chemclipse/plugins/org.eclipse.chemclipse.ux.extension.ui/src/org/eclipse/chemclipse/ux/extension/ui/swt/MethodTreeViewer.java

@@ -44,11 +44,11 @@
 public class MethodTreeViewer extends TreeViewer {
 
 	private final TreeViewerColumn[] columns = new TreeViewerColumn[MethodListLabelProvider.TITLES.length];
-	//
+
 	private IProcessSupplierContext processingSupport;
 	private BiFunction<IProcessEntry, IProcessSupplierContext, IProcessorPreferences<?>> preferencesSupplier;
 	private AtomicReference<ProcessMethodToolbar> toolbarButtons;
-	//
+
 	private IUpdateListener updateListener = null;
 
 	public MethodTreeViewer(Composite parent, int style) {
@@ -61,12 +61,12 @@ public void createControl(IProcessSupplierContext processingSupport, BiFunction<
 		this.processingSupport = processingSupport;
 		this.preferencesSupplier = preferencesSupplier;
 		this.toolbarButtons = toolbarButtons;
-		//
+
 		setUseHashlookup(true);
 		setExpandPreCheckFilters(true);
 		getTree().setLinesVisible(true);
 		getTree().setHeaderVisible(true);
-		//
+
 		enableTooltips(enableTooltips);
 		createTree();
 	}
@@ -112,11 +112,11 @@ public boolean hasChildren(Object element) {
 						return processEntryContainer.getNumberOfEntries() > 0;
 					}
 				}
-				//
+
 				if(element instanceof ProcessEntryContainer processEntryContainer) {
 					return processEntryContainer.getNumberOfEntries() > 0;
 				}
-				//
+
 				return false;
 			}
 

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/AbstractPeakFilter.java

@@ -12,6 +12,7 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.xxd.filter.peaks;
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
@@ -54,4 +55,10 @@ protected void resetPeakSelection(IChromatogramSelection chromatogramSelection)
 		chromatogramSelection.setSelectedPeak(null);
 		chromatogramSelection.getChromatogram().setDirty(true);
 	}
+
+	@Override
+	public List<String> getLegacyIDs() {
+
+		return new ArrayList<>();
+	}
 }

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/AreaFilter.java

@@ -142,4 +142,12 @@ private void processPeak(TreatmentOption treatmentOption, IPeak peak, AreaPredic
 				throw new IllegalArgumentException("Unsupported Peak Filter Treatment Option!");
 		}
 	}
+
+	@Override
+	public List<String> getLegacyIDs() {
+
+		List<String> legacyIDs = new ArrayList<>();
+		legacyIDs.add("PeakFilter:filter:processor:class:org.eclipse.chemclipse.xxd.model.filter.peaks.AreaFilter");
+		return legacyIDs;
+	}
 }

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/AreaPercentFilter.java

@@ -162,4 +162,12 @@ private static void processPeak(TreatmentOption treatmentOption, IPeak peak, dou
 				throw new IllegalArgumentException("Unsupported Peak Filter Treatment Option!");
 		}
 	}
+
+	@Override
+	public List<String> getLegacyIDs() {
+
+		List<String> legacyIDs = new ArrayList<>();
+		legacyIDs.add("PeakFilter:filter:processor:class:org.eclipse.chemclipse.xxd.model.filter.peaks.AreaPercentFilter");
+		return legacyIDs;
+	}
 }

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/AsymmetryFilter.java

@@ -80,11 +80,11 @@ public Class<AsymmetryFilterSettings> getConfigClass() {
 	public void filterPeaks(IChromatogramSelection chromatogramSelection, AsymmetryFilterSettings configuration, ProcessExecutionContext context) throws IllegalArgumentException {
 
 		Collection<IPeak> peaks = getReadOnlyPeaks(chromatogramSelection);
-		//
+
 		if(configuration == null) {
 			configuration = createConfiguration(peaks);
 		}
-		//
+
 		SubMonitor subMonitor = SubMonitor.convert(context.getProgressMonitor(), peaks.size());
 		FactorPredicate<?> predicate = getPredicate(configuration);
 		TreatmentOption treatmentOption = configuration.getFilterTreatmentOption();
@@ -93,7 +93,7 @@ public void filterPeaks(IChromatogramSelection chromatogramSelection, AsymmetryF
 			processPeak(treatmentOption, peak, predicate, peaksToDelete);
 			subMonitor.worked(1);
 		}
-		//
+
 		deletePeaks(peaksToDelete, chromatogramSelection);
 		resetPeakSelection(chromatogramSelection);
 	}
@@ -138,4 +138,12 @@ private void processPeak(TreatmentOption treatmentOption, IPeak peak, FactorPred
 				throw new IllegalArgumentException("Unsupported Peak Filter Treatment Option!");
 		}
 	}
+
+	@Override
+	public List<String> getLegacyIDs() {
+
+		List<String> legacyIDs = new ArrayList<>();
+		legacyIDs.add("PeakFilter:filter:processor:class:org.eclipse.chemclipse.xxd.model.filter.peaks.AsymmetryFilter");
+		return legacyIDs;
+	}
 }

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/ClassifiedPeaksFilter.java

@@ -12,7 +12,9 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.xxd.filter.peaks;
 
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 import java.util.Set;
 
 import org.eclipse.chemclipse.model.core.IPeak;
@@ -53,10 +55,10 @@ public void filterPeaks(IChromatogramSelection chromatogramSelection, Classified
 		if(configuration == null) {
 			configuration = createConfiguration(peaks);
 		}
-		//
+
 		Set<String> classifications = configuration.getClassificationSet();
 		boolean activeForAnalysis = configuration.isActiveForAnalysis();
-		//
+
 		SubMonitor subMonitor = SubMonitor.convert(context.getProgressMonitor(), peaks.size());
 		for(IPeak peak : peaks) {
 			Collection<String> classifier = peak.getClassifier();
@@ -70,4 +72,12 @@ public void filterPeaks(IChromatogramSelection chromatogramSelection, Classified
 		}
 		subMonitor.done();
 	}
+
+	@Override
+	public List<String> getLegacyIDs() {
+
+		List<String> legacyIDs = new ArrayList<>();
+		legacyIDs.add("PeakFilter:filter:processor:class:org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifiedPeaksFilter");
+		return legacyIDs;
+	}
 }

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeleteIntegrationsFilter.java

@@ -11,7 +11,9 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.xxd.filter.peaks;
 
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
 import org.eclipse.chemclipse.model.core.IPeak;
 import org.eclipse.chemclipse.model.filter.IPeakFilter;
@@ -59,4 +61,12 @@ public void filterPeaks(IChromatogramSelection chromatogramSelection, DeleteInte
 			}
 		}
 	}
+
+	@Override
+	public List<String> getLegacyIDs() {
+
+		List<String> legacyIDs = new ArrayList<>();
+		legacyIDs.add("PeakFilter:filter:processor:class:org.eclipse.chemclipse.xxd.model.filter.peaks.DeleteIntegrationsFilter");
+		return legacyIDs;
+	}
 }

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/DeletePeaksByModelFilter.java

@@ -81,4 +81,12 @@ public void filterPeaks(IChromatogramSelection chromatogramSelection, DeletePeak
 			resetPeakSelection(chromatogramSelection);
 		}
 	}
+
+	@Override
+	public List<String> getLegacyIDs() {
+
+		List<String> legacyIDs = new ArrayList<>();
+		legacyIDs.add("PeakFilter:filter:processor:class:org.eclipse.chemclipse.xxd.model.filter.peaks.DeletePeaksByModelFilter");
+		return legacyIDs;
+	}
 }