Replace window size enum with validated integer.

eclipse · Sep 14, 2021 · 13bb6f3 · 13bb6f3
1 parent 514316a
commit 13bb6f3
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Showing 43 changed files with 376 additions and 290 deletions.
diff --git a/...chemclipse/chromatogram/msd/filter/supplier/backfolding/detector/PeakDetectorSupport.java b/...chemclipse/chromatogram/msd/filter/supplier/backfolding/detector/PeakDetectorSupport.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2011, 2018 Lablicate GmbH.
+ * Copyright (c) 2011, 2021 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -30,20 +30,20 @@
 import org.eclipse.chemclipse.numeric.core.IPoint;
 import org.eclipse.chemclipse.numeric.core.Point;
 import org.eclipse.chemclipse.numeric.miscellaneous.Evaluation;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 
 // TODO JUnit
 public class PeakDetectorSupport {
 
 	private static float NORMALIZATION_BASE = 100000.0f;
 	private static int CONSECUTIVE_SCAN_STEPS = 3;
-	private static WindowSize MOVING_AVERAGE_WINDOW = WindowSize.WIDTH_5;
+	private static int MOVING_AVERAGE_WINDOW = 5;
 	private static double threshold = 0.005d;
 
 	/**
 	 * This class has only static methods.
 	 */
 	private PeakDetectorSupport() {
+
 	}
 
 	/**

diff --git a/...g/eclipse/chemclipse/chromatogram/msd/filter/supplier/coda/calculator/CodaCalculator.java b/...g/eclipse/chemclipse/chromatogram/msd/filter/supplier/coda/calculator/CodaCalculator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2011, 2018 Lablicate GmbH.
+ * Copyright (c) 2011, 2021 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -11,12 +11,11 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.calculator;
 
+import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.msd.model.exceptions.NoExtractedIonSignalStoredException;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignal;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignals;
-import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.numeric.statistics.Calculations;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 
 // TODO JUnit
 /**
@@ -32,6 +31,7 @@ public class CodaCalculator {
 	 * Use it a singleton.
 	 */
 	private CodaCalculator() {
+
 	}
 
 	/**
@@ -43,7 +43,7 @@ private CodaCalculator() {
 	 * @param ion
 	 * @return float
 	 */
-	public static float getMCQValue(IExtractedIonSignals extractedIonSignals, WindowSize windowSize, int ion) {
+	public static float getMCQValue(IExtractedIonSignals extractedIonSignals, int windowSize, int ion) {
 
 		IExtractedIonSignal extractedIonSignal;
 		int startScan = extractedIonSignals.getStartScan();
@@ -91,11 +91,10 @@ public static float getMCQValue(IExtractedIonSignals extractedIonSignals, Window
 	 * @param windowSize
 	 * @return float
 	 */
-	private static float calculateMCQValue(double[] euclidianLengthValues, double[] standardizedSmoothedValues, WindowSize windowSize) {
+	private static float calculateMCQValue(double[] euclidianLengthValues, double[] standardizedSmoothedValues, int windowSize) {
 
-		assert (windowSize != null) : "The window size must not be null.";
 		float mcq = 0.0f;
-		int lastScan = Calculations.getWindowReducedLength(euclidianLengthValues, windowSize.getSize());
+		int lastScan = Calculations.getWindowReducedLength(euclidianLengthValues, windowSize);
 		int scans = euclidianLengthValues.length;
 		double sumSignals = 0.0f;
 		/*
@@ -107,7 +106,7 @@ private static float calculateMCQValue(double[] euclidianLengthValues, double[]
 		for(int i = 0; i < lastScan; i++) {
 			sumSignals += euclidianLengthValues[i] * standardizedSmoothedValues[i];
 		}
-		mcq = (float)((1.0d / Math.sqrt((scans - windowSize.getSize()))) * sumSignals);
+		mcq = (float)((1.0d / Math.sqrt((scans - windowSize))) * sumSignals);
 		/*
 		 * Give a warning if something tries to run out of order.
 		 */

diff --git a/...hromatogram/msd/filter/supplier/coda/calculator/MassChromatographicQualityCalculator.java b/...hromatogram/msd/filter/supplier/coda/calculator/MassChromatographicQualityCalculator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2011, 2018 Lablicate GmbH.
+ * Copyright (c) 2011, 2021 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -13,7 +13,6 @@
 
 import org.eclipse.chemclipse.chromatogram.msd.filter.supplier.coda.exceptions.CodaCalculatorException;
 import org.eclipse.chemclipse.msd.model.core.selection.IChromatogramSelectionMSD;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 
 /**
  * @author eselmeister
@@ -24,6 +23,7 @@ public class MassChromatographicQualityCalculator {
 	 * Use only static methods.
 	 */
 	private MassChromatographicQualityCalculator() {
+
 	}
 
 	/**
@@ -36,7 +36,7 @@ private MassChromatographicQualityCalculator() {
 	 * @return {@link IMassChromatographicQualityResult}
 	 * @throws CodaCalculatorException
 	 */
-	public static IMassChromatographicQualityResult calculate(IChromatogramSelectionMSD chromatogramSelection, float codaThreshold, WindowSize windowSize) throws CodaCalculatorException {
+	public static IMassChromatographicQualityResult calculate(IChromatogramSelectionMSD chromatogramSelection, float codaThreshold, int windowSize) throws CodaCalculatorException {
 
 		IMassChromatographicQualityResult result = new MassChromatographicQualityResult(chromatogramSelection, codaThreshold, windowSize);
 		return result;

diff --git a/...se/chromatogram/msd/filter/supplier/coda/calculator/MassChromatographicQualityResult.java b/...se/chromatogram/msd/filter/supplier/coda/calculator/MassChromatographicQualityResult.java
@@ -25,7 +25,6 @@
 import org.eclipse.chemclipse.msd.model.xic.ExtractedIonSignalExtractor;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignalExtractor;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignals;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 
 public class MassChromatographicQualityResult implements IMassChromatographicQualityResult {
 
@@ -41,10 +40,9 @@ public class MassChromatographicQualityResult implements IMassChromatographicQua
 	 * @param windowSize
 	 * @throws CodaCalculatorException
 	 */
-	public MassChromatographicQualityResult(IChromatogramSelectionMSD chromatogramSelection, float codaThreshold, WindowSize windowSize) throws CodaCalculatorException {
+	public MassChromatographicQualityResult(IChromatogramSelectionMSD chromatogramSelection, float codaThreshold, int windowSize) throws CodaCalculatorException {
 
 		validateChromatogramSelection(chromatogramSelection);
-		validateWindowSize(windowSize);
 		/*
 		 * Create a new excluded ions object.
 		 */
@@ -71,11 +69,10 @@ public float getDataReductionValue() {
 	 * DataReductionValue<br/>
 	 * ExcludedIons
 	 */
-	private void calculateMassChromatographicQuality(IChromatogramSelectionMSD chromatogramSelection, float codaThreshold, WindowSize windowSize, IMarkedIons excludedIons) {
+	private void calculateMassChromatographicQuality(IChromatogramSelectionMSD chromatogramSelection, float codaThreshold, int windowSize, IMarkedIons excludedIons) {
 
 		assert (chromatogramSelection != null) : "The chromatogram selection must not be null.";
 		assert (chromatogramSelection.getChromatogram() != null) : "The chromatogram must not be null.";
-		assert (windowSize != null) : "The window size must not be null.";
 		assert (excludedIons != null) : "The excluded ions must not be null.";
 		List<Float> mcqs = new ArrayList<Float>();
 		float mcq;
@@ -127,19 +124,6 @@ private float calculateDataReductionValue(List<Float> mcqs, float codaThreshold)
 		return selected / mcqs.size();
 	}
 
-	/**
-	 * Validates the window size.
-	 * 
-	 * @param windowSize
-	 * @throws CodaCalculatorException
-	 */
-	private void validateWindowSize(WindowSize windowSize) throws CodaCalculatorException {
-
-		if(windowSize == null) {
-			throw new CodaCalculatorException("The window size must not be null.");
-		}
-	}
-
 	/**
 	 * Validates the chromatogram selection.
 	 * 

diff --git a/...org/eclipse/chemclipse/chromatogram/msd/filter/supplier/coda/core/ChromatogramFilter.java b/...org/eclipse/chemclipse/chromatogram/msd/filter/supplier/coda/core/ChromatogramFilter.java
@@ -25,14 +25,13 @@
 import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;
 import org.eclipse.chemclipse.msd.model.core.selection.IChromatogramSelectionMSD;
 import org.eclipse.chemclipse.msd.model.core.support.IMarkedIons;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.chemclipse.processing.core.ProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 public class ChromatogramFilter extends AbstractChromatogramFilterMSD {
 
-	private static WindowSize MOVING_AVERAGE_WINDOW = WindowSize.WIDTH_5;
+	private static int MOVING_AVERAGE_WINDOW = 5;
 
 	@Override
 	public IProcessingInfo<?> applyFilter(IChromatogramSelectionMSD chromatogramSelection, IChromatogramFilterSettings chromatogramFilterSettings, IProgressMonitor monitor) {

diff --git a/...etector/src/org/eclipse/chemclipse/chromatogram/peak/detector/support/DetectorSlopes.java b/...etector/src/org/eclipse/chemclipse/chromatogram/peak/detector/support/DetectorSlopes.java
@@ -19,10 +19,9 @@
 import org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.savitzkygolay.processor.SavitzkyGolayFilter;
 import org.eclipse.chemclipse.model.signals.ITotalScanSignals;
 import org.eclipse.chemclipse.numeric.statistics.Calculations;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 
 /**
- * @author eselmeister
+ * @author Philip Wenig
  */
 public class DetectorSlopes implements IDetectorSlopes {
 
@@ -65,28 +64,28 @@ public void add(IDetectorSlope detectorSlope) {
 	}
 
 	@Override
-	public void calculateMovingAverage(WindowSize windowSize) {
+	public void calculateMovingAverage(int windowSize) {
 
 		/*
-		 * Return if the windowSize is null or NONE.
+		 * Return if the windowSize is NONE.
 		 */
-		if(windowSize == null || WindowSize.NONE.equals(windowSize)) {
+		if(windowSize == 0) {
 			return;
 		}
 		/*
 		 * Return if the available number of slopes are lower than the window
 		 * size.
 		 */
-		if(slopes.size() < windowSize.getSize()) {
+		if(slopes.size() < windowSize) {
 			return;
 		}
-		int diff = windowSize.getSize() / 2;
-		int windowStop = windowSize.getSize() - diff;
+		int diff = windowSize / 2;
+		int windowStop = windowSize - diff;
 		/*
 		 * Moving average calculation.
 		 */
 		int size = slopes.size() - diff;
-		double[] values = new double[windowSize.getSize()];
+		double[] values = new double[windowSize];
 		for(int i = diff; i < size; i++) {
 			for(int j = -diff, k = 0; j < windowStop; j++, k++) {
 				values[k] = slopes.get(i + j).getSlope();
@@ -98,11 +97,11 @@ public void calculateMovingAverage(WindowSize windowSize) {
 		}
 	}
 
-	public void calculateSavitzkyGolaySmooth(WindowSize windowSize) {
+	public void calculateSavitzkyGolaySmooth(int windowSize) {
 
 		int SAVITZKYGOLAY_DERIVATIVE = 0;
 		int SAVITZKYGOLAY_ORDER = 3;
-		int filterWidth = windowSize.getSize();
+		int filterWidth = windowSize;
 		double[] initialSlopes = new double[slopes.size()];
 		double[] smoothedSlopes = new double[slopes.size()];
 		for(int i = 0; i < slopes.size(); i++)

diff --git a/...tector/src/org/eclipse/chemclipse/chromatogram/peak/detector/support/IDetectorSlopes.java b/...tector/src/org/eclipse/chemclipse/chromatogram/peak/detector/support/IDetectorSlopes.java
@@ -12,10 +12,8 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.peak.detector.support;
 
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
-
 /**
- * @author eselmeister
+ * @author Philip Wenig
  */
 public interface IDetectorSlopes {
 
@@ -38,17 +36,17 @@ public interface IDetectorSlopes {
 	 * Calculates for each stored slope value a smoothed moving average value.<br/>
 	 * The window size declares the width of the moving window.
 	 * 
-	 * @param windowSize
+	 * @param int
 	 */
-	void calculateMovingAverage(WindowSize windowSize);
+	void calculateMovingAverage(int windowSize);
 
 	/**
 	 * Calculates for each stored slope value a Savitzky-Golay smooothed value.<br/>
 	 * The window size declares the filter width of the Savitzky-Golay filter.
 	 * 
-	 * @param windowSize
+	 * @param int
 	 */
-	void calculateSavitzkyGolaySmooth(WindowSize windowSize);
+	void calculateSavitzkyGolaySmooth(int windowSize);
 
 	/**
 	 * Returns the size of the slope list.

diff --git a/...clipse/chromatogram/xxd/calculator/supplier/amdiscalri/impl/AlkanePatternDetectorCSD.java b/...clipse/chromatogram/xxd/calculator/supplier/amdiscalri/impl/AlkanePatternDetectorCSD.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2020 Lablicate GmbH.
+ * Copyright (c) 2016, 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
@@ -30,7 +30,6 @@
 import org.eclipse.chemclipse.csd.model.core.selection.ChromatogramSelectionCSD;
 import org.eclipse.chemclipse.csd.model.core.selection.IChromatogramSelectionCSD;
 import org.eclipse.chemclipse.logging.core.Logger;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
 
@@ -61,7 +60,7 @@ public IChromatogramCSD parseChromatogram(String chromatogramPath, String pathRe
 				peakDetectorSettings.setThreshold(Threshold.LOW);
 				peakDetectorSettings.setIncludeBackground(false);
 				peakDetectorSettings.setMinimumSignalToNoiseRatio(50.0f);
-				peakDetectorSettings.setMovingAverageWindowSize(WindowSize.WIDTH_5);
+				peakDetectorSettings.setMovingAverageWindowSize(5);
 				peakDetectorCSD.detect(chromatogramSelectionCSD, peakDetectorSettings, monitor);
 				/*
 				 * Peak integrator

diff --git a/...clipse/chromatogram/xxd/calculator/supplier/amdiscalri/impl/AlkanePatternDetectorMSD.java b/...clipse/chromatogram/xxd/calculator/supplier/amdiscalri/impl/AlkanePatternDetectorMSD.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2020 Lablicate GmbH.
+ * Copyright (c) 2016, 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
@@ -33,7 +33,6 @@
 import org.eclipse.chemclipse.msd.model.core.IChromatogramPeakMSD;
 import org.eclipse.chemclipse.msd.model.core.selection.ChromatogramSelectionMSD;
 import org.eclipse.chemclipse.msd.model.core.selection.IChromatogramSelectionMSD;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
 
@@ -71,7 +70,7 @@ public IChromatogramMSD parseChromatogram(String chromatogramPath, String pathRe
 				peakDetectorSettings.setThreshold(Threshold.LOW);
 				peakDetectorSettings.setIncludeBackground(false);
 				peakDetectorSettings.setMinimumSignalToNoiseRatio(50.0f);
-				peakDetectorSettings.setMovingAverageWindowSize(WindowSize.WIDTH_5);
+				peakDetectorSettings.setMovingAverageWindowSize(5);
 				peakDetectorMSD.detect(chromatogramSelectionMSD, peakDetectorSettings, monitor);
 				/*
 				 * Peak integrator

diff --git a/...eclipse/chemclipse/chromatogram/xxd/edit/supplier/snip/ui/preferences/PreferencePage.java b/...eclipse/chemclipse/chromatogram/xxd/edit/supplier/snip/ui/preferences/PreferencePage.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2020 Lablicate GmbH.
+ * Copyright (c) 2013, 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
@@ -13,11 +13,10 @@
 
 import org.eclipse.chemclipse.chromatogram.xxd.edit.supplier.snip.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.chromatogram.xxd.edit.supplier.snip.ui.Activator;
-import org.eclipse.chemclipse.numeric.statistics.WindowSize;
+import org.eclipse.chemclipse.support.settings.IntSettingsProperty.Validation;
 import org.eclipse.chemclipse.support.ui.preferences.fieldeditors.DoubleFieldEditor;
-import org.eclipse.jface.preference.ComboFieldEditor;
+import org.eclipse.chemclipse.support.ui.preferences.fieldeditors.IntegerFieldEditor;
 import org.eclipse.jface.preference.FieldEditorPreferencePage;
-import org.eclipse.jface.preference.IntegerFieldEditor;
 import org.eclipse.ui.IWorkbench;
 import org.eclipse.ui.IWorkbenchPreferencePage;
 
@@ -36,12 +35,13 @@ public PreferencePage() {
 	 * GUI blocks needed to manipulate various types of preferences. Each field
 	 * editor knows how to save and restore itself.
 	 */
+	@Override
 	public void createFieldEditors() {
 
 		IntegerFieldEditor iterationsFieldEditor = new IntegerFieldEditor(PreferenceSupplier.P_ITERATIONS, "Iterations", getFieldEditorParent());
 		iterationsFieldEditor.setValidRange(PreferenceSupplier.MIN_ITERATIONS, PreferenceSupplier.MAX_ITERATIONS);
 		addField(iterationsFieldEditor);
-		addField(new ComboFieldEditor(PreferenceSupplier.P_WINDOW_SIZE, "Window size (Detector)", WindowSize.getElements(), getFieldEditorParent()));
+		addField(new IntegerFieldEditor(PreferenceSupplier.P_WINDOW_SIZE, "Window Size  (Detector)", PreferenceSupplier.MIN_WINDOW_SIZE, PreferenceSupplier.MAX_WINDOW_SIZE, Validation.ODD_NUMBER, getFieldEditorParent()));
 		addField(new DoubleFieldEditor(PreferenceSupplier.P_MAGNIFICATION_FACTOR, "Magnification factor (Filter)", PreferenceSupplier.MIN_MAGNIFICATION_FACTOR, PreferenceSupplier.MAX_MAGNIFICATION_FACTOR, getFieldEditorParent()));
 		IntegerFieldEditor transitionsFieldEditor = new IntegerFieldEditor(PreferenceSupplier.P_TRANSITIONS, "Transitions (Filter)", getFieldEditorParent());
 		transitionsFieldEditor.setValidRange(PreferenceSupplier.MIN_TRANSITIONS, PreferenceSupplier.MAX_TRANSITIONS);
@@ -53,6 +53,7 @@ public void createFieldEditors() {
 	 * @see
 	 * org.eclipse.ui.IWorkbenchPreferencePage#init(org.eclipse.ui.IWorkbench)
 	 */
+	@Override
 	public void init(IWorkbench workbench) {
 
 	}