#316 - Combined Mass Spectrum

Further improvements are requires to enable mean and median calculations.
eclipse · Apr 14, 2020 · f616cda · f616cda
1 parent f157fca
commit f616cda
Show file tree

Hide file tree

Showing 15 changed files with 99 additions and 177 deletions.
diff --git a/...g.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/noise/Calculator.java b/...g.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/noise/Calculator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2010, 2019 Lablicate GmbH.
+ * Copyright (c) 2010, 2020 Lablicate GmbH.
  * 
  * All rights reserved. This
  * program and the accompanying materials are made available under the terms of
@@ -25,7 +25,6 @@
 import org.eclipse.chemclipse.msd.model.core.support.IMarkedIons;
 import org.eclipse.chemclipse.msd.model.exceptions.FilterException;
 import org.eclipse.chemclipse.msd.model.support.CombinedMassSpectrumCalculator;
-import org.eclipse.chemclipse.msd.model.support.ICombinedMassSpectrumCalculator;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignal;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignals;
 import org.eclipse.chemclipse.numeric.statistics.Calculations;
@@ -53,7 +52,7 @@ public Calculator() {
 	 */
 	public ICombinedMassSpectrum getNoiseMassSpectrum(List<ICombinedMassSpectrum> noiseMassSpectra, IMarkedIons ionsToPreserve, IProgressMonitor monitor) {
 
-		ICombinedMassSpectrumCalculator combinedMassSpectrumCalculator = new CombinedMassSpectrumCalculator();
+		CombinedMassSpectrumCalculator combinedMassSpectrumCalculator = new CombinedMassSpectrumCalculator();
 		/*
 		 * Iterate through all given noise mass spectra.
 		 */
@@ -126,7 +125,7 @@ private List<INoiseSegment> calculateNoiseSegments(List<IAnalysisSegment> analys
 				 * with the segment. The noise segment will be stored in the
 				 * noise segment list.
 				 */
-				ICombinedMassSpectrumCalculator combinedMassSpectrumCalculator = calculatorSupport.getCombinedMassSpectrumCalculator(analysisSegment, extractedIonSignals);
+				CombinedMassSpectrumCalculator combinedMassSpectrumCalculator = calculatorSupport.getCombinedMassSpectrumCalculator(analysisSegment, extractedIonSignals);
 				ICombinedMassSpectrum noiseMassSpectrum = calculatorSupport.getNoiseMassSpectrum(combinedMassSpectrumCalculator, ionsToPreserve, monitor);
 				INoiseSegment noiseSegment = new NoiseSegment(analysisSegment, noiseMassSpectrum);
 				noiseSegments.add(noiseSegment);

diff --git a/...se.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/noise/CalculatorSupport.java b/...se.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/noise/CalculatorSupport.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2010, 2019 Lablicate GmbH.
+ * Copyright (c) 2010, 2020 Lablicate GmbH.
  * 
  * All rights reserved. This
  * program and the accompanying materials are made available under the terms of
@@ -29,7 +29,6 @@
 import org.eclipse.chemclipse.msd.model.implementation.CombinedMassSpectrum;
 import org.eclipse.chemclipse.msd.model.implementation.Ion;
 import org.eclipse.chemclipse.msd.model.support.CombinedMassSpectrumCalculator;
-import org.eclipse.chemclipse.msd.model.support.ICombinedMassSpectrumCalculator;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignal;
 import org.eclipse.chemclipse.msd.model.xic.IExtractedIonSignals;
 import org.eclipse.core.runtime.IProgressMonitor;
@@ -61,10 +60,10 @@ public boolean acceptSegment(double[] values, double mean) {
 	 * 
 	 * @return
 	 */
-	public ICombinedMassSpectrumCalculator getCombinedMassSpectrumCalculator(IAnalysisSegment analysisSegment, IExtractedIonSignals extractedIonSignals) {
+	public CombinedMassSpectrumCalculator getCombinedMassSpectrumCalculator(IAnalysisSegment analysisSegment, IExtractedIonSignals extractedIonSignals) {
 
 		IExtractedIonSignal extractedIonSignal;
-		ICombinedMassSpectrumCalculator combinedMassSpectrumCalculator = new CombinedMassSpectrumCalculator();
+		CombinedMassSpectrumCalculator combinedMassSpectrumCalculator = new CombinedMassSpectrumCalculator();
 		for(int scan = analysisSegment.getStartScan(); scan <= analysisSegment.getStopScan(); scan++) {
 			try {
 				extractedIonSignal = extractedIonSignals.getExtractedIonSignal(scan);
@@ -83,7 +82,7 @@ public ICombinedMassSpectrumCalculator getCombinedMassSpectrumCalculator(IAnalys
 
 	public static ICombinedMassSpectrum getCombinedMassSpectrum(IExtractedIonSignals extractedIonSignals, IScanRange range) {
 
-		ICombinedMassSpectrumCalculator combinedMassSpectrumCalculator = new CombinedMassSpectrumCalculator();
+		CombinedMassSpectrumCalculator combinedMassSpectrumCalculator = new CombinedMassSpectrumCalculator();
 		for(int scan = range.getStartScan(); scan <= range.getStopScan(); scan++) {
 			try {
 				IExtractedIonSignal extractedIonSignal = extractedIonSignals.getExtractedIonSignal(scan);
@@ -100,7 +99,7 @@ public static ICombinedMassSpectrum getCombinedMassSpectrum(IExtractedIonSignals
 		float abundance;
 		ICombinedMassSpectrum noiseMassSpectrum = new CombinedMassSpectrum();
 		IIon noiseIon;
-		Map<Integer, Double> ions = combinedMassSpectrumCalculator.getValues();
+		Map<Integer, Double> ions = combinedMassSpectrumCalculator.getValuesIntensities();
 		for(Integer ion : ions.keySet()) {
 			/*
 			 * Check the abundance.
@@ -121,7 +120,7 @@ public static ICombinedMassSpectrum getCombinedMassSpectrum(IExtractedIonSignals
 	/*
 	 * Returns a combined mass spectrum.
 	 */
-	public ICombinedMassSpectrum getNoiseMassSpectrum(ICombinedMassSpectrumCalculator combinedMassSpectrumCalculator, IMarkedIons ionsToPreserve, IProgressMonitor monitor) {
+	public ICombinedMassSpectrum getNoiseMassSpectrum(CombinedMassSpectrumCalculator combinedMassSpectrumCalculator, IMarkedIons ionsToPreserve, IProgressMonitor monitor) {
 
 		/*
 		 * Remove the ions to preserve.
@@ -138,7 +137,7 @@ public ICombinedMassSpectrum getNoiseMassSpectrum(ICombinedMassSpectrumCalculato
 		float abundance;
 		ICombinedMassSpectrum noiseMassSpectrum = new CombinedMassSpectrum();
 		IIon noiseIon;
-		Map<Integer, Double> ions = combinedMassSpectrumCalculator.getValues();
+		Map<Integer, Double> ions = combinedMassSpectrumCalculator.getValuesIntensities();
 		for(Integer ion : ions.keySet()) {
 			/*
 			 * Check the abundance.

diff --git a/...sd.model/src/org/eclipse/chemclipse/msd/model/support/CombinedMassSpectrumCalculator.java b/...sd.model/src/org/eclipse/chemclipse/msd/model/support/CombinedMassSpectrumCalculator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2018 Lablicate GmbH.
+ * Copyright (c) 2008, 2020 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -11,6 +11,7 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.model.support;
 
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -20,41 +21,38 @@
 import org.eclipse.chemclipse.msd.model.core.AbstractIon;
 import org.eclipse.chemclipse.msd.model.core.IIon;
 import org.eclipse.chemclipse.msd.model.core.support.IMarkedIons;
+import org.eclipse.chemclipse.numeric.statistics.Calculations;
 
-public class CombinedMassSpectrumCalculator implements ICombinedMassSpectrumCalculator {
+public class CombinedMassSpectrumCalculator {
 
-	private Map<Integer, Double> combinedMassSpectrum;
+	private Map<Integer, List<Double>> combinedMassSpectrum = new HashMap<Integer, List<Double>>();
 
-	public CombinedMassSpectrumCalculator() {
-		combinedMassSpectrum = new HashMap<Integer, Double>();
-	}
-
-	@Override
-	public void addIon(double ion, float abundance) {
+	public void addIon(double ion, double abundance) {
 
 		/*
 		 * If the abundance is zero, do nothing and return.
 		 */
-		if(abundance == 0.0f) {
+		if(abundance == 0.0d) {
 			return;
 		}
 		int key = AbstractIon.getIon(ion);
 		/*
 		 * Add the abundance if still a ion exists, otherwise still add the ion.
 		 */
-		if(combinedMassSpectrum.containsKey(key)) {
-			combinedMassSpectrum.put(key, combinedMassSpectrum.get(key) + abundance);
-		} else {
-			combinedMassSpectrum.put(key, (double)abundance);
+		List<Double> intensities = combinedMassSpectrum.get(key);
+		if(intensities == null) {
+			intensities = new ArrayList<Double>();
+			combinedMassSpectrum.put(key, intensities);
 		}
+		intensities.add(abundance);
 	}
 
-	@Override
 	public void addIons(List<IIon> ions, IMarkedIons excludedIons) {
 
 		if(ions == null || excludedIons == null) {
 			return;
 		}
+		//
 		Set<Integer> excludedIonsNominal = excludedIons.getIonsNominal();
 		for(IIon ion : ions) {
 			if(!excludedIonsNominal.contains(ion.getIon())) {
@@ -63,39 +61,39 @@ public void addIons(List<IIon> ions, IMarkedIons excludedIons) {
 		}
 	}
 
-	@Override
 	public void removeIon(double ion) {
 
 		int key = AbstractIon.getIon(ion);
 		combinedMassSpectrum.remove(key);
 	}
 
-	@Override
 	public void removeIons(IMarkedIons excludedIons) {
 
 		for(Integer ion : excludedIons.getIonsNominal()) {
 			combinedMassSpectrum.remove(ion);
 		}
 	}
 
-	@Override
 	public double getAbundance(double ion) {
 
-		double result = 0.0d;
 		int key = AbstractIon.getIon(ion);
-		if(combinedMassSpectrum.containsKey(key)) {
-			result = combinedMassSpectrum.get(key);
-		}
-		return result;
+		return calculateSumIntensity(combinedMassSpectrum.get(key));
 	}
 
-	@Override
-	public Map<Integer, Double> getValues() {
+	public Map<Integer, List<Double>> getValues() {
 
 		return combinedMassSpectrum;
 	}
 
-	@Override
+	public Map<Integer, Double> getValuesIntensities() {
+
+		Map<Integer, Double> map = new HashMap<>();
+		for(Integer key : combinedMassSpectrum.keySet()) {
+			map.put(key, calculateSumIntensity(combinedMassSpectrum.get(key)));
+		}
+		return map;
+	}
+
 	public void normalize(float normalizationFactor) {
 
 		/*
@@ -107,15 +105,38 @@ public void normalize(float normalizationFactor) {
 		/*
 		 * If max is zero it doesn't even make sense to go further on.
 		 */
-		double max = Collections.max(combinedMassSpectrum.values());
+		double max = Collections.max(getValuesIntensities().values());
 		if(max == 0.0d) {
 			return;
 		}
+		//
 		double correlationFactor = normalizationFactor / max;
-		double value;
 		for(Integer key : combinedMassSpectrum.keySet()) {
-			value = correlationFactor * combinedMassSpectrum.get(key);
-			combinedMassSpectrum.put(key, value);
+			List<Double> adjustedIntensities = new ArrayList<>();
+			for(double intensity : combinedMassSpectrum.get(key)) {
+				adjustedIntensities.add(correlationFactor * intensity);
+			}
+			combinedMassSpectrum.put(key, adjustedIntensities);
+		}
+	}
+
+	public double calculateSumIntensity(List<Double> intensities) {
+
+		double sum = 0.0d;
+		if(intensities != null) {
+			int size = intensities.size();
+			double[] values = new double[size];
+			for(int i = 0; i < size; i++) {
+				values[i] = intensities.get(i);
+			}
+			/*
+			 * Add an option here to calculate the sum,
+			 * mean or median signal.
+			 */
+			sum = Calculations.getSum(values);
+			// sum = Calculations.getMean(values);
+			// sum = Calculations.getMedian(values);
 		}
+		return sum;
 	}
 }
diff --git a/...ipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/support/FilterSupport.java b/...ipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/support/FilterSupport.java
@@ -51,7 +51,7 @@ public static IScanMSD getCombinedMassSpectrum(IChromatogramSelectionMSD chromat
 		IChromatogramMSD chromatogram = chromatogramSelection.getChromatogram();
 		int startScan = chromatogram.getScanNumber(chromatogramSelection.getStartRetentionTime());
 		int stopScan = chromatogram.getScanNumber(chromatogramSelection.getStopRetentionTime());
-		ICombinedMassSpectrumCalculator massSpectrumCalculator = new CombinedMassSpectrumCalculator();
+		CombinedMassSpectrumCalculator massSpectrumCalculator = new CombinedMassSpectrumCalculator();
 		/*
 		 * Merge all selected scans.<br/> All scan intensities will be added.
 		 * Afterwards, they will be normalized.<br/> It would be also possible
@@ -88,7 +88,7 @@ public static IScanMSD getCombinedMassSpectrum(IScanMSD massSpectrum1, IScanMSD
 		 * If one of the mass spectra is null, take only the valid one to calculate the normalized mass spectrum.
 		 */
 		excludedIons = validateExcludedIons(excludedIons);
-		ICombinedMassSpectrumCalculator massSpectrumCalculator = new CombinedMassSpectrumCalculator();
+		CombinedMassSpectrumCalculator massSpectrumCalculator = new CombinedMassSpectrumCalculator();
 		//
 		if(massSpectrum1 == null) {
 			addIonsToCalculator(massSpectrum2, excludedIons, massSpectrumCalculator, useNormalize);
@@ -104,7 +104,7 @@ public static IScanMSD getCombinedMassSpectrum(IScanMSD massSpectrum1, IScanMSD
 		return getMassSpectrum(massSpectrumCalculator, useNormalize);
 	}
 
-	private static void addIonsToCalculator(IScanMSD massSpectrum, IMarkedIons excludedIons, ICombinedMassSpectrumCalculator massSpectrumCalculator, boolean useNormalize) {
+	private static void addIonsToCalculator(IScanMSD massSpectrum, IMarkedIons excludedIons, CombinedMassSpectrumCalculator massSpectrumCalculator, boolean useNormalize) {
 
 		IScanMSD massSpectrumCalculated = getCalculatedMassSpectrum(massSpectrum, excludedIons, useNormalize);
 		massSpectrumCalculator.addIons(massSpectrumCalculated.getIons(), excludedIons);
@@ -125,7 +125,7 @@ public static IScanMSD getCalculatedMassSpectrum(IScanMSD massSpectrum, IMarkedI
 		}
 		excludedIons = validateExcludedIons(excludedIons);
 		//
-		ICombinedMassSpectrumCalculator massSpectrumCalculator = new CombinedMassSpectrumCalculator();
+		CombinedMassSpectrumCalculator massSpectrumCalculator = new CombinedMassSpectrumCalculator();
 		massSpectrumCalculator.addIons(massSpectrum.getIons(), excludedIons);
 		return getMassSpectrum(massSpectrumCalculator, useNormalize);
 	}
@@ -153,12 +153,12 @@ private static IMarkedIons validateExcludedIons(IMarkedIons excludedIons) {
 	 * @param massSpectrumCalculator
 	 * @return IMassSpectrum
 	 */
-	private static IScanMSD getMassSpectrum(ICombinedMassSpectrumCalculator massSpectrumCalculator, boolean useNormalize) {
+	private static IScanMSD getMassSpectrum(CombinedMassSpectrumCalculator massSpectrumCalculator, boolean useNormalize) {
 
 		if(useNormalize) {
 			massSpectrumCalculator.normalize(NORMALIZATION_FACTOR);
 		}
-		Map<Integer, Double> ions = massSpectrumCalculator.getValues();
+		Map<Integer, Double> ions = massSpectrumCalculator.getValuesIntensities();
 		return getMassSpectrum(ions);
 	}
 

diff --git a/...d.model/src/org/eclipse/chemclipse/msd/model/support/ICombinedMassSpectrumCalculator.java b/...d.model/src/org/eclipse/chemclipse/msd/model/support/ICombinedMassSpectrumCalculator.java