Fixed #2316 - Peak Target - Penalty Calculation Filter

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/identifier/AbstractIdentifierDeltaPenaltyCalculationSettings.java

@@ -27,7 +27,7 @@ public class AbstractIdentifierDeltaPenaltyCalculationSettings extends AbstractI
 	private DeltaCalculation deltaCalculation = DeltaCalculation.NONE;
 	@JsonProperty(value = "Delta Window", defaultValue = "0")
 	@JsonPropertyDescription(value = "Identify the peak if the unknown is inside of the delta window (delta -/+).")
-	@FloatSettingsProperty(minValue = IDeltaCalculationSettings.MIN_DELTA_WINDOW, maxValue = IDeltaCalculationSettings.MAX_DELTA_WINDOW)
+	@FloatSettingsProperty(minValue = MIN_DELTA_WINDOW, maxValue = MAX_DELTA_WINDOW)
 	private float deltaWindow = 0.0f;
 	/**
 	 * Penalty Calculation
@@ -37,12 +37,12 @@ public class AbstractIdentifierDeltaPenaltyCalculationSettings extends AbstractI
 	private PenaltyCalculation penaltyCalculation = PenaltyCalculation.NONE;
 	@JsonProperty(value = "Penalty Window", defaultValue = "0")
 	@JsonPropertyDescription(value = "The penalty window. The unit of the selected penalty calculation is used.")
-	@FloatSettingsProperty(minValue = IPenaltyCalculationSettings.MIN_PENALTY_WINDOW, maxValue = IPenaltyCalculationSettings.MAX_PENALTY_WINDOW)
+	@FloatSettingsProperty(minValue = MIN_PENALTY_WINDOW, maxValue = MAX_PENALTY_WINDOW)
 	private float penaltyWindow = 0.0f;
 	@JsonProperty(value = "Penalty Level Factor", defaultValue = "5.0")
 	@JsonPropertyDescription(value = "The penalty level factor.")
-	@FloatSettingsProperty(minValue = IPenaltyCalculationSettings.MIN_PENALTY_LEVEL_FACTOR, maxValue = IPenaltyCalculationSettings.MAX_PENALTY_LEVEL_FACTOR)
-	private float penaltyLevelFactor = IPenaltyCalculationSettings.DEF_PENALTY_LEVEL_FACTOR;
+	@FloatSettingsProperty(minValue = MIN_PENALTY_LEVEL_FACTOR, maxValue = MAX_PENALTY_LEVEL_FACTOR)
+	private float penaltyLevelFactor = DEF_PENALTY_LEVEL_FACTOR;
 	@JsonProperty(value = "Max Penalty", defaultValue = "20")
 	@JsonPropertyDescription(value = "The max penalty. Values between 0 (no penalty) and 100 (max penalty) are allowed.")
 	@FloatSettingsProperty(minValue = MIN_PENALTY_MATCH_FACTOR, maxValue = MAX_PENALTY_MATCH_FACTOR)
@@ -119,4 +119,4 @@ public void setMaxPenalty(float maxPenalty) {
 
 		this.maxPenalty = maxPenalty;
 	}
-}
+}

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/identifier/IIdentifierSettings.java

@@ -34,4 +34,4 @@ public interface IIdentifierSettings extends IProcessSettings {
 	 * @param limitMatchFactor
 	 */
 	void setLimitMatchFactor(float limitMatchFactor);
-}
+}

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/identifier/IPenaltyCalculationSettings.java

@@ -32,20 +32,6 @@ public interface IPenaltyCalculationSettings extends IProcessSettings {
 	float MIN_PENALTY_MATCH_FACTOR = 0.0f;
 	float MAX_PENALTY_MATCH_FACTOR = 100.0f;
 
-	/**
-	 * Limit Match Factor
-	 * 
-	 * @return float
-	 */
-	float getLimitMatchFactor();
-
-	/**
-	 * Only identify the peak if no target is available with a match factor >= the limit.
-	 * 
-	 * @param limitMatchFactor
-	 */
-	void setLimitMatchFactor(float limitMatchFactor);
-
 	/**
 	 * Retention Time / Index Penalty Calculation
 	 */
@@ -64,4 +50,4 @@ public interface IPenaltyCalculationSettings extends IProcessSettings {
 	float getMaxPenalty();
 
 	void setMaxPenalty(float maxValue);
-}
+}

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/identifier/PenaltyCalculationSupport.java

@@ -117,4 +117,4 @@ public static double calculatePenalty(double valueUnknown, double valueReference
 			return (result > maxPenalty) ? maxPenalty : result;
 		}
 	}
-}
+}

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

@@ -58,6 +58,7 @@ Service-Component: OSGI-INF/org.eclipse.chemclipse.xxd.filter.chromatogram.Inten
  OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.AreaFilter.xml,
  OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.AreaPercentFilter.xml,
  OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.AsymmetryFilter.xml,
+ OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.CalculatePenaltyFilter.xml,
  OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.ClassifiedPeaksFilter.xml,
  OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.DeleteIntegrationsFilter.xml,
  OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.DeletePeaksByModelFilter.xml,

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/OSGI-INF/org.eclipse.chemclipse.xxd.filter.peaks.CalculatePenaltyFilter.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.filter.peaks.CalculatePenaltyFilter">
+   <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.filter.peaks.CalculatePenaltyFilter"/>
+</scr:component>

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

@@ -0,0 +1,80 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Lablicate GmbH.
+ *
+ * This program and the accompanying materials are made
+ * available under the terms of the Eclipse Public License 2.0
+ * which is available at https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ * 
+ * Contributors:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.xxd.filter.peaks;
+
+import java.util.Collection;
+import java.util.Set;
+
+import org.eclipse.chemclipse.model.core.IPeak;
+import org.eclipse.chemclipse.model.core.IPeakModel;
+import org.eclipse.chemclipse.model.core.IScan;
+import org.eclipse.chemclipse.model.filter.IPeakFilter;
+import org.eclipse.chemclipse.model.identifier.IComparisonResult;
+import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
+import org.eclipse.chemclipse.model.identifier.ILibraryInformation;
+import org.eclipse.chemclipse.model.identifier.PenaltyCalculationSupport;
+import org.eclipse.chemclipse.model.selection.IChromatogramSelection;
+import org.eclipse.chemclipse.processing.Processor;
+import org.eclipse.chemclipse.processing.filter.Filter;
+import org.eclipse.chemclipse.processing.supplier.ProcessExecutionContext;
+import org.eclipse.chemclipse.xxd.filter.peaks.settings.PenaltyCalculatorFilterSettings;
+import org.eclipse.core.runtime.SubMonitor;
+import org.osgi.service.component.annotations.Component;
+
+@Component(service = {IPeakFilter.class, Filter.class, Processor.class})
+public class CalculatePenaltyFilter extends AbstractPeakFilter<PenaltyCalculatorFilterSettings> {
+
+	@Override
+	public String getName() {
+
+		return "Penalty Calculator";
+	}
+
+	@Override
+	public String getDescription() {
+
+		return "Calculate match penalties based on RT or RI deviations of unknown and library hit.";
+	}
+
+	@Override
+	public Class<PenaltyCalculatorFilterSettings> getConfigClass() {
+
+		return PenaltyCalculatorFilterSettings.class;
+	}
+
+	@Override
+	public void filterPeaks(IChromatogramSelection chromatogramSelection, PenaltyCalculatorFilterSettings configuration, ProcessExecutionContext context) throws IllegalArgumentException {
+
+		Collection<IPeak> peaks = getReadOnlyPeaks(chromatogramSelection);
+		if(configuration == null) {
+			configuration = createConfiguration(peaks);
+		}
+
+		SubMonitor subMonitor = SubMonitor.convert(context.getProgressMonitor(), peaks.size());
+		for(IPeak peak : peaks) {
+			Set<IIdentificationTarget> targets = peak.getTargets();
+			for(IIdentificationTarget identificationTarget : targets) {
+				IComparisonResult comparisonResult = identificationTarget.getComparisonResult();
+				ILibraryInformation libraryInformation = identificationTarget.getLibraryInformation();
+				IPeakModel peakModel = peak.getPeakModel();
+				IScan scan = peakModel.getPeakMaximum();
+				int retentionTimeUnknown = scan.getRetentionTime();
+				float retentionIndexUnknown = scan.getRetentionIndex();
+				int retentionTimeReference = libraryInformation.getRetentionTime();
+				float retentionIndexReference = libraryInformation.getRetentionIndex();
+				PenaltyCalculationSupport.applyPenalty(retentionTimeUnknown, retentionIndexUnknown, retentionTimeReference, retentionIndexReference, comparisonResult, configuration);
+			}
+			subMonitor.worked(1);
+		}
+	}
+}

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

@@ -20,7 +20,7 @@
 import org.eclipse.chemclipse.processing.Processor;
 import org.eclipse.chemclipse.processing.filter.Filter;
 import org.eclipse.chemclipse.processing.supplier.ProcessExecutionContext;
-import org.eclipse.chemclipse.xxd.filter.settings.DeleteTargetsFilterSettings;
+import org.eclipse.chemclipse.xxd.filter.peaks.settings.DeleteTargetsFilterSettings;
 import org.eclipse.chemclipse.xxd.filter.targets.TargetsFilter;
 import org.eclipse.core.runtime.SubMonitor;
 import org.osgi.service.component.annotations.Component;

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/settings/DeleteTargetsFilterSettings.java → chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/settings/DeleteTargetsFilterSettings.java

@@ -10,7 +10,7 @@
  * Contributors:
  * Philip Wenig - initial API and implementation
  *******************************************************************************/
-package org.eclipse.chemclipse.xxd.filter.settings;
+package org.eclipse.chemclipse.xxd.filter.peaks.settings;
 
 import org.eclipse.chemclipse.support.settings.StringSettingsProperty;
 import org.eclipse.chemclipse.xxd.filter.support.TargetsDeleteOption;

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/settings/PenaltyCalculatorFilterSettings.java

@@ -0,0 +1,113 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Lablicate GmbH.
+ *
+ * This program and the accompanying materials are made
+ * available under the terms of the Eclipse Public License 2.0
+ * which is available at https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ * 
+ * Contributors:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.xxd.filter.peaks.settings;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.eclipse.chemclipse.logging.core.Logger;
+import org.eclipse.chemclipse.model.identifier.IPenaltyCalculationSettings;
+import org.eclipse.chemclipse.model.identifier.PenaltyCalculation;
+import org.eclipse.chemclipse.support.literature.LiteratureReference;
+import org.eclipse.chemclipse.support.settings.FloatSettingsProperty;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyDescription;
+
+public class PenaltyCalculatorFilterSettings implements IPenaltyCalculationSettings {
+
+	private static final Logger logger = Logger.getLogger(PenaltyCalculatorFilterSettings.class);
+
+	@JsonProperty(value = "Penalty Calculation", defaultValue = "NONE")
+	@JsonPropertyDescription(value = "Select the strategy, how penalties are calculated.")
+	private PenaltyCalculation penaltyCalculation = PenaltyCalculation.NONE;
+	@JsonProperty(value = "Penalty Window", defaultValue = "0")
+	@JsonPropertyDescription(value = "The penalty window. The unit of the selected penalty calculation is used.")
+	@FloatSettingsProperty(minValue = IPenaltyCalculationSettings.MIN_PENALTY_WINDOW, maxValue = IPenaltyCalculationSettings.MAX_PENALTY_WINDOW)
+	private float penaltyWindow = 0.0f;
+	@JsonProperty(value = "Penalty Level Factor", defaultValue = "5.0")
+	@JsonPropertyDescription(value = "The penalty level factor.")
+	@FloatSettingsProperty(minValue = IPenaltyCalculationSettings.MIN_PENALTY_LEVEL_FACTOR, maxValue = IPenaltyCalculationSettings.MAX_PENALTY_LEVEL_FACTOR)
+	private float penaltyLevelFactor = IPenaltyCalculationSettings.DEF_PENALTY_LEVEL_FACTOR;
+	@JsonProperty(value = "Max Penalty", defaultValue = "20")
+	@JsonPropertyDescription(value = "The max penalty. Values between 0 (no penalty) and 100 (max penalty) are allowed.")
+	@FloatSettingsProperty(minValue = IPenaltyCalculationSettings.MIN_PENALTY_MATCH_FACTOR, maxValue = IPenaltyCalculationSettings.MAX_PENALTY_MATCH_FACTOR)
+	private float maxPenalty = IPenaltyCalculationSettings.DEF_PENALTY_MATCH_FACTOR;
+
+	@Override
+	public PenaltyCalculation getPenaltyCalculation() {
+
+		return penaltyCalculation;
+	}
+
+	@Override
+	public void setPenaltyCalculation(PenaltyCalculation penaltyCalculation) {
+
+		this.penaltyCalculation = penaltyCalculation;
+	}
+
+	@Override
+	public float getPenaltyWindow() {
+
+		return penaltyWindow;
+	}
+
+	@Override
+	public void setPenaltyWindow(float penaltyWindow) {
+
+		this.penaltyWindow = penaltyWindow;
+	}
+
+	@Override
+	public float getPenaltyLevelFactor() {
+
+		return penaltyLevelFactor;
+	}
+
+	@Override
+	public void setPenaltyLevelFactor(float penaltyLevelFactor) {
+
+		this.penaltyLevelFactor = penaltyLevelFactor;
+	}
+
+	@Override
+	public float getMaxPenalty() {
+
+		return maxPenalty;
+	}
+
+	@Override
+	public void setMaxPenalty(float maxPenalty) {
+
+		this.maxPenalty = maxPenalty;
+	}
+
+	@Override
+	public List<LiteratureReference> getLiteratureReferences() {
+
+		List<LiteratureReference> literatureReferences = new ArrayList<>();
+		literatureReferences.add(createLiteratureReference("S1044030599000471.ris", "10.1016/S1044-0305(99)00047-1"));
+		//
+		return literatureReferences;
+	}
+
+	private static LiteratureReference createLiteratureReference(String file, String doi) {
+
+		try {
+			return new LiteratureReference(new String(PenaltyCalculatorFilterSettings.class.getResourceAsStream(file).readAllBytes()));
+		} catch(Exception e) {
+			logger.warn(e);
+			return new LiteratureReference(doi);
+		}
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/peaks/settings/S1044030599000471.ris

@@ -0,0 +1,15 @@
+TY  - JOUR
+T1  - An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data
+AU  - Stein, S.E.
+JO  - Journal of the American Society for Mass Spectrometry
+VL  - 10
+IS  - 8
+SP  - 770
+EP  - 781
+PY  - 1999
+DA  - 1999/08/01/
+SN  - 1044-0305
+DO  - https://doi.org/10.1016/S1044-0305(99)00047-1
+UR  - https://www.sciencedirect.com/science/article/pii/S1044030599000471
+AB  - A method is presented for extracting individual component spectra from gas chromatography/mass spectrometry (GC/MS) data files and then using these spectra to identify target compounds by matching spectra in a reference library. It extends a published “model peak” approach which uses selected ion chromatograms as models for component shape. On the basis of this shape, individual mass spectral peak abundance profiles are extracted to produce a “purified” spectrum. In the present work, ion-counting noise is explicitly treated and a number of characteristic features of GC/MS data are taken into account. This allows spectrum extraction to be reliably performed down to very low signal levels and for overlapping components. A spectrum match factor for compound identification is developed that incorporates a number of new corrections, some of which employ information derived from chromatographic behavior. Test results suggest that the ability of this system to identify compounds is comparable to that of conventional analysis.
+ER  - 

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/scans/DeleteTargetsFilter.java

@@ -22,7 +22,7 @@
 import org.eclipse.chemclipse.processing.core.ProcessingMessage;
 import org.eclipse.chemclipse.processing.filter.Filter;
 import org.eclipse.chemclipse.processing.filter.FilterList;
-import org.eclipse.chemclipse.xxd.filter.settings.DeleteTargetsFilterSettings;
+import org.eclipse.chemclipse.xxd.filter.peaks.settings.DeleteTargetsFilterSettings;
 import org.eclipse.chemclipse.xxd.filter.targets.TargetsFilter;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.SubMonitor;

chemclipse/plugins/org.eclipse.chemclipse.xxd.filter/src/org/eclipse/chemclipse/xxd/filter/targets/TargetsFilter.java

@@ -26,7 +26,7 @@
 import org.eclipse.chemclipse.model.core.IScan;
 import org.eclipse.chemclipse.model.core.ITargetSupplier;
 import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
-import org.eclipse.chemclipse.xxd.filter.settings.DeleteTargetsFilterSettings;
+import org.eclipse.chemclipse.xxd.filter.peaks.settings.DeleteTargetsFilterSettings;
 
 public class TargetsFilter {
 

chemclipse/tests/org.eclipse.chemclipse.xxd.filter.fragment.test/src/org/eclipse/chemclipse/xxd/filter/targets/TargetsFilter_1_Test.java

@@ -21,7 +21,7 @@
 import org.eclipse.chemclipse.model.identifier.ILibraryInformation;
 import org.eclipse.chemclipse.model.identifier.LibraryInformation;
 import org.eclipse.chemclipse.model.implementation.IdentificationTarget;
-import org.eclipse.chemclipse.xxd.filter.settings.DeleteTargetsFilterSettings;
+import org.eclipse.chemclipse.xxd.filter.peaks.settings.DeleteTargetsFilterSettings;
 import org.eclipse.chemclipse.xxd.filter.support.TargetsDeleteOption;
 
 import junit.framework.TestCase;