Fixed #683 - Add a peak filter to add a distinct classification

chemclipse/plugins/org.eclipse.chemclipse.xxd.model/META-INF/MANIFEST.MF

@@ -65,4 +65,5 @@ Service-Component: OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.Asymme
  OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.LowPassPeaksFilter.xml,
  OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.DeletePeaksByTargetFilter.xml,
  OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifierAssignFilter.xml,
- OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifierRemoveFilter.xml
+ OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifierRemoveFilter.xml,
+ OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifierAddFilter.xml

chemclipse/plugins/org.eclipse.chemclipse.xxd.model/OSGI-INF/org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifierAddFilter.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifierAddFilter">
+   <service>
+      <provide interface="org.eclipse.chemclipse.model.filter.IPeakFilter"/>
+      <provide interface="org.eclipse.chemclipse.processing.filter.Filter"/>
+      <provide interface="org.eclipse.chemclipse.processing.Processor"/>
+   </service>
+   <implementation class="org.eclipse.chemclipse.xxd.model.filter.peaks.ClassifierAddFilter"/>
+</scr:component>

chemclipse/plugins/org.eclipse.chemclipse.xxd.model/src/org/eclipse/chemclipse/xxd/model/filter/peaks/ClassifierAddFilter.java

@@ -0,0 +1,84 @@
+/*******************************************************************************
+ * Copyright (c) 2021 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.xxd.model.filter.peaks;
+
+import java.util.Collection;
+
+import org.eclipse.chemclipse.model.core.IPeak;
+import org.eclipse.chemclipse.model.core.IPeakModel;
+import org.eclipse.chemclipse.model.filter.IPeakFilter;
+import org.eclipse.chemclipse.processing.Processor;
+import org.eclipse.chemclipse.processing.core.MessageConsumer;
+import org.eclipse.chemclipse.processing.filter.CRUDListener;
+import org.eclipse.chemclipse.processing.filter.Filter;
+import org.eclipse.chemclipse.xxd.model.settings.peaks.ClassifierAddFilterSettings;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.SubMonitor;
+import org.osgi.service.component.annotations.Component;
+
+@Component(service = {IPeakFilter.class, Filter.class, Processor.class})
+public class ClassifierAddFilter implements IPeakFilter<ClassifierAddFilterSettings> {
+
+	@Override
+	public String getName() {
+
+		return "Peak Classifier (Add)";
+	}
+
+	@Override
+	public String getDescription() {
+
+		return "Adds the given classifier.";
+	}
+
+	@Override
+	public Class<ClassifierAddFilterSettings> getConfigClass() {
+
+		return ClassifierAddFilterSettings.class;
+	}
+
+	@Override
+	public boolean acceptsIPeaks(Collection<? extends IPeak> items) {
+
+		return true;
+	}
+
+	@Override
+	public <X extends IPeak> void filterIPeaks(CRUDListener<X, IPeakModel> listener, ClassifierAddFilterSettings configuration, MessageConsumer messageConsumer, IProgressMonitor monitor) throws IllegalArgumentException {
+
+		Collection<X> peaks = listener.read();
+		if(configuration == null) {
+			configuration = createConfiguration(peaks);
+		}
+		//
+		String classification = configuration.getClassification();
+		boolean skipClassifiedPeak = configuration.isSkipClassifiedPeak();
+		SubMonitor subMonitor = SubMonitor.convert(monitor, peaks.size());
+		for(X peak : peaks) {
+			/*
+			 * Peak Classifier
+			 */
+			boolean classify = true;
+			if(peak.getClassifier().size() > 0) {
+				if(skipClassifiedPeak) {
+					classify = false;
+				}
+			}
+			//
+			if(classify) {
+				peak.addClassifier(classification);
+			}
+			//
+			subMonitor.worked(1);
+		}
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.xxd.model/src/org/eclipse/chemclipse/xxd/model/settings/peaks/ClassifierAddFilterSettings.java

@@ -0,0 +1,45 @@
+/*******************************************************************************
+ * Copyright (c) 2021 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.xxd.model.settings.peaks;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyDescription;
+
+public class ClassifierAddFilterSettings {
+
+	@JsonProperty(value = "Classification", defaultValue = "")
+	@JsonPropertyDescription(value = "This is the classification that shall be set.")
+	private String classification = "";
+	@JsonProperty(value = "Skip Classified Peaks", defaultValue = "true")
+	@JsonPropertyDescription(value = "Skip peaks that have been classified already.")
+	private boolean skipClassifiedPeak = true;
+
+	public String getClassification() {
+
+		return classification;
+	}
+
+	public void setClassification(String classification) {
+
+		this.classification = classification;
+	}
+
+	public boolean isSkipClassifiedPeak() {
+
+		return skipClassifiedPeak;
+	}
+
+	public void setSkipClassifiedPeak(boolean skipClassifiedPeak) {
+
+		this.skipClassifiedPeak = skipClassifiedPeak;
+	}
+}