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Merged
eselmeister merged 1 commit into from
Feb 26, 2026
Merged

Revert "Type the peak model interfaces" #2746

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15 changes: 9 additions & 6 deletions ...fier/src/org/eclipse/chemclipse/chromatogram/csd/identifier/support/TargetBuilderCSD.java
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Expand Up @@ -15,6 +15,7 @@
import org.eclipse.chemclipse.csd.model.core.IPeakCSD;
import org.eclipse.chemclipse.csd.model.core.IScanCSD;
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.exceptions.ReferenceMustNotBeNullException;
import org.eclipse.chemclipse.model.identifier.IComparisonResult;
import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
Expand All @@ -31,12 +32,14 @@ public IIdentificationTarget setPeakTargetUnknown(IPeakCSD peakCSD, String ident

IIdentificationTarget identificationTarget = null;
try {
IScanCSD scan = peakCSD.getPeakModel().getPeakMaximum();
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(scan, targetUnknownSettings, "");
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
identificationTarget.setIdentifier(identifier);
peakCSD.getTargets().add(identificationTarget);
IScan scan = peakCSD.getPeakModel().getPeakMaximum();
if(scan instanceof IScanCSD unknown) {
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(unknown, targetUnknownSettings, "");
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
identificationTarget.setIdentifier(identifier);
peakCSD.getTargets().add(identificationTarget);
}
} catch(ReferenceMustNotBeNullException e) {
logger.warn(e);
}
Expand Down
17 changes: 10 additions & 7 deletions ...fier/src/org/eclipse/chemclipse/chromatogram/wsd/identifier/support/TargetBuilderWSD.java
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Expand Up @@ -18,6 +18,7 @@
import java.util.List;

import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.exceptions.ReferenceMustNotBeNullException;
import org.eclipse.chemclipse.model.identifier.IComparisonResult;
import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
Expand All @@ -38,13 +39,15 @@ public IIdentificationTarget setPeakTargetUnknown(IPeakWSD peakWSD, String ident

IIdentificationTarget identificationTarget = null;
try {
IScanWSD scan = peakWSD.getPeakModel().getPeakMaximum();
String traces = extractTraces(scan, targetUnknownSettings);
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(scan, targetUnknownSettings, traces);
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
identificationTarget.setIdentifier(identifier);
peakWSD.getTargets().add(identificationTarget);
IScan scan = peakWSD.getPeakModel().getPeakMaximum();
if(scan instanceof IScanWSD unknown) {
String traces = extractTraces(unknown, targetUnknownSettings);
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(unknown, targetUnknownSettings, traces);
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
identificationTarget.setIdentifier(identifier);
peakWSD.getTargets().add(identificationTarget);
}
} catch(ReferenceMustNotBeNullException e) {
logger.warn(e);
}
Expand Down
31 changes: 17 additions & 14 deletions ...e/chemclipse/chromatogram/xxd/integrator/supplier/trapezoid/processor/PeakIntegrator.java
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Expand Up @@ -36,6 +36,7 @@
import org.eclipse.chemclipse.model.core.IMarkedTraces;
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.core.ISignal;
import org.eclipse.chemclipse.model.implementation.IntegrationEntry;
import org.eclipse.chemclipse.model.support.IntegrationConstraint;
Expand Down Expand Up @@ -271,23 +272,25 @@ private List<IIntegrationEntry> calculateIntegratedArea(IPeak peak, PeakIntegrat
IPeakModelWSD peakModel = peakWSD.getPeakModel();
double integratedAreaTIC = calculateTICPeakArea(peak, baselineSupport, includeBackground, useAreaConstraint);

IScanWSD scan = peakModel.getPeakMaximum();
IScan scan = peakModel.getPeakMaximum();
IIntegrationEntry integrationEntry;
if(!markedTraces.isEmpty() && !markedTraces.getTraces().contains(IMarkedTrace.TOTAL_SIGNAL_AS_INT)) {
Set<Integer> wavelengths = markedTraces.getTraces();
WavelengthPercentages wavelengthPercentages = new WavelengthPercentages(scan);
/*
* Calculate the percentage integrated area for each selected ion.
*/
for(Integer wavelength : wavelengths) {
float correctionFactor = wavelengthPercentages.getPercentage(wavelength) / WavelengthPercentages.MAX_PERCENTAGE;
double integratedArea = integratedAreaTIC * correctionFactor;
integrationEntry = new IntegrationEntry(wavelength, integratedArea * scaleFactor);
if(scan instanceof IScanWSD scanWSD) {
if(!markedTraces.isEmpty() && !markedTraces.getTraces().contains(IMarkedTrace.TOTAL_SIGNAL_AS_INT)) {
Set<Integer> wavelengths = markedTraces.getTraces();
WavelengthPercentages wavelengthPercentages = new WavelengthPercentages(scanWSD);
/*
* Calculate the percentage integrated area for each selected ion.
*/
for(Integer wavelength : wavelengths) {
float correctionFactor = wavelengthPercentages.getPercentage(wavelength) / WavelengthPercentages.MAX_PERCENTAGE;
double integratedArea = integratedAreaTIC * correctionFactor;
integrationEntry = new IntegrationEntry(wavelength, integratedArea * scaleFactor);
integrationEntries.add(integrationEntry);
}
} else {
integrationEntry = new IntegrationEntry(ISignal.TOTAL_INTENSITY, integratedAreaTIC * scaleFactor);
integrationEntries.add(integrationEntry);
}
} else {
integrationEntry = new IntegrationEntry(ISignal.TOTAL_INTENSITY, integratedAreaTIC * scaleFactor);
integrationEntries.add(integrationEntry);
}
}

Expand Down
12 changes: 0 additions & 12 deletions ....chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/AbstractPeakModelCSD.java
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Expand Up @@ -25,16 +25,4 @@ protected AbstractPeakModelCSD(IScan peakMaximum, IPeakIntensityValues peakInten

super(peakMaximum, peakIntensityValues, startBackgroundAbundance, stopBackgroundAbundance);
}

@Override
public IScanCSD getPeakMaximum() {

return (IScanCSD)super.getPeakMaximum();
}

@Override
public IScanCSD getPeakScan(int retentionTime) {

return (IScanCSD)super.getPeakScan(retentionTime);
}
}
6 changes: 0 additions & 6 deletions ...eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/IPeakModelCSD.java
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Expand Up @@ -15,10 +15,4 @@
import org.eclipse.chemclipse.model.core.IPeakModel;

public interface IPeakModelCSD extends IPeakModel {

@Override
IScanCSD getPeakMaximum();

@Override
IScanCSD getPeakScan(int retentionTime);
}
6 changes: 0 additions & 6 deletions ...eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/IPeakModelFSD.java
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Expand Up @@ -15,10 +15,4 @@
import org.eclipse.chemclipse.model.core.IPeakModel;

public interface IPeakModelFSD extends IPeakModel {

@Override
IScanFSD getPeakMaximum();

@Override
IScanFSD getPeakScan(int retentionTime);
}
13 changes: 0 additions & 13 deletions ....model/src/org/eclipse/chemclipse/fsd/model/core/implementation/AbstractPeakModelFSD.java
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Expand Up @@ -13,7 +13,6 @@
package org.eclipse.chemclipse.fsd.model.core.implementation;

import org.eclipse.chemclipse.fsd.model.core.IPeakModelFSD;
import org.eclipse.chemclipse.fsd.model.core.IScanFSD;
import org.eclipse.chemclipse.model.core.IPeakIntensityValues;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.exceptions.PeakException;
Expand All @@ -27,16 +26,4 @@ protected AbstractPeakModelFSD(IScan peakMaximum, IPeakIntensityValues peakInten

super(peakMaximum, peakIntensityValues, startBackgroundIntensity, stopBackgroundIntensity);
}

@Override
public IScanFSD getPeakMaximum() {

return (IScanFSD)super.getPeakMaximum();
}

@Override
public IScanFSD getPeakScan(int retentionTime) {

return (IScanFSD)super.getPeakScan(retentionTime);
}
}
12 changes: 0 additions & 12 deletions ....chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractPeakModelMSD.java
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Expand Up @@ -54,16 +54,4 @@ public IPeakMassSpectrum getPeakMassSpectrum(int retentionTime) {
}
return null;
}

@Override
public IScanMSD getPeakMaximum() {

return (IScanMSD)super.getPeakMaximum();
}

@Override
public IScanMSD getPeakScan(int retentionTime) {

return (IScanMSD)super.getPeakScan(retentionTime);
}
}
6 changes: 0 additions & 6 deletions ...eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IPeakModelMSD.java
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Expand Up @@ -60,10 +60,4 @@ public interface IPeakModelMSD extends IPeakModel {
* @return IMassSpectrum
*/
IPeakMassSpectrum getPeakMassSpectrum(int retentionTime);

@Override
IScanMSD getPeakMaximum();

@Override
IScanMSD getPeakScan(int retentionTime);
}
19 changes: 11 additions & 8 deletions ...nsion.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/ExtendedPeakTracesUI.java
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Expand Up @@ -23,6 +23,7 @@
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IChromatogramPeak;
import org.eclipse.chemclipse.model.core.IPeak;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.msd.model.core.IPeakMSD;
import org.eclipse.chemclipse.msd.model.core.IPeakModelMSD;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
Expand Down Expand Up @@ -441,14 +442,16 @@ private void deleteTraces(Display display, Set<Integer> traces) {
}
} else if(peak instanceof IPeakWSD peakWSD) {
IPeakModelWSD peakModelWSD = peakWSD.getPeakModel();
IScanWSD scanWSD = peakModelWSD.getPeakMaximum();
int maxDeleteTraces = scanWSD.getNumberOfScanSignals() - 1;
if(traces.size() >= maxDeleteTraces) {
MessageDialog.openInformation(display.getActiveShell(), CATEGORY, "It's not possible to delete all wavelengths.");
} else {
scanWSD.removeScanSignals(traces);
updatePeak();
UpdateNotifierUI.update(display, peak);
IScan scan = peakModelWSD.getPeakMaximum();
if(scan instanceof IScanWSD scanWSD) {
int maxDeleteTraces = scanWSD.getNumberOfScanSignals() - 1;
if(traces.size() >= maxDeleteTraces) {
MessageDialog.openInformation(display.getActiveShell(), CATEGORY, "It's not possible to delete all wavelengths.");
} else {
scanWSD.removeScanSignals(traces);
updatePeak();
UpdateNotifierUI.update(display, peak);
}
}
}
if(peak instanceof IChromatogramPeak chromatogramPeak) {
Expand Down
12 changes: 0 additions & 12 deletions ...e.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/AbtractPeakModelVSD.java
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Expand Up @@ -25,16 +25,4 @@ public AbtractPeakModelVSD(IScan peakMaximum, IPeakIntensityValues peakIntensity

super(peakMaximum, peakIntensityValues, startBackgroundAbundance, stopBackgroundAbundance);
}

@Override
public IScanVSD getPeakMaximum() {

return (IScanVSD)super.getPeakMaximum();
}

@Override
public IScanVSD getPeakScan(int retentionTime) {

return (IScanVSD)super.getPeakScan(retentionTime);
}
}
6 changes: 0 additions & 6 deletions ...eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/IPeakModelVSD.java
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Expand Up @@ -15,10 +15,4 @@
import org.eclipse.chemclipse.model.core.IPeakModel;

public interface IPeakModelVSD extends IPeakModel {

@Override
IScanVSD getPeakMaximum();

@Override
IScanVSD getPeakScan(int retentionTime);
}
15 changes: 9 additions & 6 deletions ...ipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractChromatogramPeakWSD.java
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Expand Up @@ -13,6 +13,7 @@
package org.eclipse.chemclipse.wsd.model.core;

import org.eclipse.chemclipse.model.core.IChromatogram;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.exceptions.PeakException;

public abstract class AbstractChromatogramPeakWSD extends AbstractPeakWSD implements IChromatogramPeakWSD {
Expand Down Expand Up @@ -79,12 +80,14 @@ public float getPurity() {
/*
* Extracted is the unknown and genuine the reference scan.
*/
IScanWSD peakScan = getPeakModel().getPeakMaximum();
IScanWSD genuineScanWSD = chromatogram.getScan(getScanMax());
if(genuineScanWSD != null) {
int numberOfSignals = genuineScanWSD.getNumberOfScanSignals();
if(numberOfSignals != 0) {
purity = peakScan.getNumberOfScanSignals() / (float)numberOfSignals;
IScan peakScan = getPeakModel().getPeakMaximum();
if(peakScan instanceof IScanWSD peakScanWSD) {
IScanWSD genuineScanWSD = chromatogram.getScan(getScanMax());
if(genuineScanWSD != null) {
int numberOfSignals = genuineScanWSD.getNumberOfScanSignals();
if(numberOfSignals != 0) {
purity = peakScanWSD.getNumberOfScanSignals() / (float)numberOfSignals;
}
}
}
return purity;
Expand Down
12 changes: 0 additions & 12 deletions ....chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractPeakModelWSD.java
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Expand Up @@ -25,16 +25,4 @@ public AbstractPeakModelWSD(IScan peakMaximum, IPeakIntensityValues peakIntensit

super(peakMaximum, peakIntensityValues, startBackgroundAbundance, stopBackgroundAbundance);
}

@Override
public IScanWSD getPeakMaximum() {

return (IScanWSD)super.getPeakMaximum();
}

@Override
public IScanWSD getPeakScan(int retentionTime) {

return (IScanWSD)super.getPeakScan(retentionTime);
}
}
6 changes: 0 additions & 6 deletions ...eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/IPeakModelWSD.java
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Expand Up @@ -15,10 +15,4 @@
import org.eclipse.chemclipse.model.core.IPeakModel;

public interface IPeakModelWSD extends IPeakModel {

@Override
IScanWSD getPeakMaximum();

@Override
IScanWSD getPeakScan(int retentionTime);
}
3 changes: 2 additions & 1 deletion ...rg/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1001.java
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Expand Up @@ -31,6 +31,7 @@
import org.eclipse.chemclipse.csd.model.core.IScanCSD;
import org.eclipse.chemclipse.model.baseline.IBaselineModel;
import org.eclipse.chemclipse.model.core.IIntegrationEntry;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format;
import org.eclipse.core.runtime.IProgressMonitor;
Expand Down Expand Up @@ -210,7 +211,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance

IScanCSD scan = peakModel.getPeakMaximum();
IScan scan = peakModel.getPeakMaximum();
dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time
dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index
dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal
Expand Down
3 changes: 2 additions & 1 deletion ...rg/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1002.java
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Expand Up @@ -31,6 +31,7 @@
import org.eclipse.chemclipse.csd.model.core.IScanCSD;
import org.eclipse.chemclipse.model.baseline.IBaselineModel;
import org.eclipse.chemclipse.model.core.IIntegrationEntry;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format;
import org.eclipse.core.runtime.IProgressMonitor;
Expand Down Expand Up @@ -209,7 +210,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance

IScanCSD scan = peakModel.getPeakMaximum();
IScan scan = peakModel.getPeakMaximum();
dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time
dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index
dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal
Expand Down
3 changes: 2 additions & 1 deletion ...rg/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1003.java
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Expand Up @@ -31,6 +31,7 @@
import org.eclipse.chemclipse.csd.model.core.IScanCSD;
import org.eclipse.chemclipse.model.baseline.IBaselineModel;
import org.eclipse.chemclipse.model.core.IIntegrationEntry;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format;
import org.eclipse.core.runtime.IProgressMonitor;
Expand Down Expand Up @@ -211,7 +212,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance

IScanCSD scan = peakModel.getPeakMaximum();
IScan scan = peakModel.getPeakMaximum();
dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time
dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index
dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal
Expand Down
3 changes: 2 additions & 1 deletion ...rg/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1004.java
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Expand Up @@ -31,6 +31,7 @@
import org.eclipse.chemclipse.csd.model.core.IScanCSD;
import org.eclipse.chemclipse.model.baseline.IBaselineModel;
import org.eclipse.chemclipse.model.core.IIntegrationEntry;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format;
import org.eclipse.core.runtime.IProgressMonitor;
Expand Down Expand Up @@ -213,7 +214,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance
dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance

IScanCSD scan = peakModel.getPeakMaximum();
IScan scan = peakModel.getPeakMaximum();
dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time
dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index
dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal
Expand Down
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