Skip to content

Commit d2faac3

Browse files
MailaenderMailaender
authored
Revert "Type the peak model interfaces"
1 parent 5db4933 commit d2faac3

File tree

35 files changed

+117
-173
lines changed

35 files changed

+117
-173
lines changed

‎chemclipse/plugins/org.eclipse.chemclipse.chromatogram.csd.identifier/src/org/eclipse/chemclipse/chromatogram/csd/identifier/support/TargetBuilderCSD.java‎

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,7 @@
1515
import org.eclipse.chemclipse.csd.model.core.IPeakCSD;
1616
import org.eclipse.chemclipse.csd.model.core.IScanCSD;
1717
import org.eclipse.chemclipse.logging.core.Logger;
18+
import org.eclipse.chemclipse.model.core.IScan;
1819
import org.eclipse.chemclipse.model.exceptions.ReferenceMustNotBeNullException;
1920
import org.eclipse.chemclipse.model.identifier.IComparisonResult;
2021
import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
@@ -31,12 +32,14 @@ public IIdentificationTarget setPeakTargetUnknown(IPeakCSD peakCSD, String ident
3132

3233
IIdentificationTarget identificationTarget = null;
3334
try {
34-
IScanCSD scan = peakCSD.getPeakModel().getPeakMaximum();
35-
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(scan, targetUnknownSettings, "");
36-
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
37-
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
38-
identificationTarget.setIdentifier(identifier);
39-
peakCSD.getTargets().add(identificationTarget);
35+
IScan scan = peakCSD.getPeakModel().getPeakMaximum();
36+
if(scan instanceof IScanCSD unknown) {
37+
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(unknown, targetUnknownSettings, "");
38+
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
39+
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
40+
identificationTarget.setIdentifier(identifier);
41+
peakCSD.getTargets().add(identificationTarget);
42+
}
4043
} catch(ReferenceMustNotBeNullException e) {
4144
logger.warn(e);
4245
}

‎chemclipse/plugins/org.eclipse.chemclipse.chromatogram.wsd.identifier/src/org/eclipse/chemclipse/chromatogram/wsd/identifier/support/TargetBuilderWSD.java‎

Lines changed: 10 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,7 @@
1818
import java.util.List;
1919

2020
import org.eclipse.chemclipse.logging.core.Logger;
21+
import org.eclipse.chemclipse.model.core.IScan;
2122
import org.eclipse.chemclipse.model.exceptions.ReferenceMustNotBeNullException;
2223
import org.eclipse.chemclipse.model.identifier.IComparisonResult;
2324
import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
@@ -38,13 +39,15 @@ public IIdentificationTarget setPeakTargetUnknown(IPeakWSD peakWSD, String ident
3839

3940
IIdentificationTarget identificationTarget = null;
4041
try {
41-
IScanWSD scan = peakWSD.getPeakModel().getPeakMaximum();
42-
String traces = extractTraces(scan, targetUnknownSettings);
43-
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(scan, targetUnknownSettings, traces);
44-
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
45-
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
46-
identificationTarget.setIdentifier(identifier);
47-
peakWSD.getTargets().add(identificationTarget);
42+
IScan scan = peakWSD.getPeakModel().getPeakMaximum();
43+
if(scan instanceof IScanWSD unknown) {
44+
String traces = extractTraces(unknown, targetUnknownSettings);
45+
ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(unknown, targetUnknownSettings, traces);
46+
IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality());
47+
identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult);
48+
identificationTarget.setIdentifier(identifier);
49+
peakWSD.getTargets().add(identificationTarget);
50+
}
4851
} catch(ReferenceMustNotBeNullException e) {
4952
logger.warn(e);
5053
}

‎chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.integrator.supplier.trapezoid/src/org/eclipse/chemclipse/chromatogram/xxd/integrator/supplier/trapezoid/processor/PeakIntegrator.java‎

Lines changed: 18 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2008, 2026 Lablicate GmbH.
2+
* Copyright (c) 2008, 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -36,6 +36,7 @@
3636
import org.eclipse.chemclipse.model.core.IMarkedTraces;
3737
import org.eclipse.chemclipse.model.core.IPeak;
3838
import org.eclipse.chemclipse.model.core.IPeakModel;
39+
import org.eclipse.chemclipse.model.core.IScan;
3940
import org.eclipse.chemclipse.model.core.ISignal;
4041
import org.eclipse.chemclipse.model.implementation.IntegrationEntry;
4142
import org.eclipse.chemclipse.model.support.IntegrationConstraint;
@@ -271,23 +272,25 @@ private List<IIntegrationEntry> calculateIntegratedArea(IPeak peak, PeakIntegrat
271272
IPeakModelWSD peakModel = peakWSD.getPeakModel();
272273
double integratedAreaTIC = calculateTICPeakArea(peak, baselineSupport, includeBackground, useAreaConstraint);
273274

274-
IScanWSD scan = peakModel.getPeakMaximum();
275+
IScan scan = peakModel.getPeakMaximum();
275276
IIntegrationEntry integrationEntry;
276-
if(!markedTraces.isEmpty() && !markedTraces.getTraces().contains(IMarkedTrace.TOTAL_SIGNAL_AS_INT)) {
277-
Set<Integer> wavelengths = markedTraces.getTraces();
278-
WavelengthPercentages wavelengthPercentages = new WavelengthPercentages(scan);
279-
/*
280-
* Calculate the percentage integrated area for each selected ion.
281-
*/
282-
for(Integer wavelength : wavelengths) {
283-
float correctionFactor = wavelengthPercentages.getPercentage(wavelength) / WavelengthPercentages.MAX_PERCENTAGE;
284-
double integratedArea = integratedAreaTIC * correctionFactor;
285-
integrationEntry = new IntegrationEntry(wavelength, integratedArea * scaleFactor);
277+
if(scan instanceof IScanWSD scanWSD) {
278+
if(!markedTraces.isEmpty() && !markedTraces.getTraces().contains(IMarkedTrace.TOTAL_SIGNAL_AS_INT)) {
279+
Set<Integer> wavelengths = markedTraces.getTraces();
280+
WavelengthPercentages wavelengthPercentages = new WavelengthPercentages(scanWSD);
281+
/*
282+
* Calculate the percentage integrated area for each selected ion.
283+
*/
284+
for(Integer wavelength : wavelengths) {
285+
float correctionFactor = wavelengthPercentages.getPercentage(wavelength) / WavelengthPercentages.MAX_PERCENTAGE;
286+
double integratedArea = integratedAreaTIC * correctionFactor;
287+
integrationEntry = new IntegrationEntry(wavelength, integratedArea * scaleFactor);
288+
integrationEntries.add(integrationEntry);
289+
}
290+
} else {
291+
integrationEntry = new IntegrationEntry(ISignal.TOTAL_INTENSITY, integratedAreaTIC * scaleFactor);
286292
integrationEntries.add(integrationEntry);
287293
}
288-
} else {
289-
integrationEntry = new IntegrationEntry(ISignal.TOTAL_INTENSITY, integratedAreaTIC * scaleFactor);
290-
integrationEntries.add(integrationEntry);
291294
}
292295
}
293296

‎chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/AbstractPeakModelCSD.java‎

Lines changed: 1 addition & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2014, 2026 Lablicate GmbH.
2+
* Copyright (c) 2014, 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -25,16 +25,4 @@ protected AbstractPeakModelCSD(IScan peakMaximum, IPeakIntensityValues peakInten
2525

2626
super(peakMaximum, peakIntensityValues, startBackgroundAbundance, stopBackgroundAbundance);
2727
}
28-
29-
@Override
30-
public IScanCSD getPeakMaximum() {
31-
32-
return (IScanCSD)super.getPeakMaximum();
33-
}
34-
35-
@Override
36-
public IScanCSD getPeakScan(int retentionTime) {
37-
38-
return (IScanCSD)super.getPeakScan(retentionTime);
39-
}
4028
}

‎chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/IPeakModelCSD.java‎

Lines changed: 1 addition & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2014, 2026 Lablicate GmbH.
2+
* Copyright (c) 2014, 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -15,10 +15,4 @@
1515
import org.eclipse.chemclipse.model.core.IPeakModel;
1616

1717
public interface IPeakModelCSD extends IPeakModel {
18-
19-
@Override
20-
IScanCSD getPeakMaximum();
21-
22-
@Override
23-
IScanCSD getPeakScan(int retentionTime);
2418
}

‎chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/IPeakModelFSD.java‎

Lines changed: 1 addition & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2025, 2026 Lablicate GmbH.
2+
* Copyright (c) 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -15,10 +15,4 @@
1515
import org.eclipse.chemclipse.model.core.IPeakModel;
1616

1717
public interface IPeakModelFSD extends IPeakModel {
18-
19-
@Override
20-
IScanFSD getPeakMaximum();
21-
22-
@Override
23-
IScanFSD getPeakScan(int retentionTime);
2418
}

‎chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/implementation/AbstractPeakModelFSD.java‎

Lines changed: 1 addition & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2025, 2026 Lablicate GmbH.
2+
* Copyright (c) 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -13,7 +13,6 @@
1313
package org.eclipse.chemclipse.fsd.model.core.implementation;
1414

1515
import org.eclipse.chemclipse.fsd.model.core.IPeakModelFSD;
16-
import org.eclipse.chemclipse.fsd.model.core.IScanFSD;
1716
import org.eclipse.chemclipse.model.core.IPeakIntensityValues;
1817
import org.eclipse.chemclipse.model.core.IScan;
1918
import org.eclipse.chemclipse.model.exceptions.PeakException;
@@ -27,16 +26,4 @@ protected AbstractPeakModelFSD(IScan peakMaximum, IPeakIntensityValues peakInten
2726

2827
super(peakMaximum, peakIntensityValues, startBackgroundIntensity, stopBackgroundIntensity);
2928
}
30-
31-
@Override
32-
public IScanFSD getPeakMaximum() {
33-
34-
return (IScanFSD)super.getPeakMaximum();
35-
}
36-
37-
@Override
38-
public IScanFSD getPeakScan(int retentionTime) {
39-
40-
return (IScanFSD)super.getPeakScan(retentionTime);
41-
}
4229
}

‎chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractPeakModelMSD.java‎

Lines changed: 1 addition & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2008, 2026 Lablicate GmbH.
2+
* Copyright (c) 2008, 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -54,16 +54,4 @@ public IPeakMassSpectrum getPeakMassSpectrum(int retentionTime) {
5454
}
5555
return null;
5656
}
57-
58-
@Override
59-
public IScanMSD getPeakMaximum() {
60-
61-
return (IScanMSD)super.getPeakMaximum();
62-
}
63-
64-
@Override
65-
public IScanMSD getPeakScan(int retentionTime) {
66-
67-
return (IScanMSD)super.getPeakScan(retentionTime);
68-
}
6957
}

‎chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IPeakModelMSD.java‎

Lines changed: 1 addition & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2008, 2026 Lablicate GmbH.
2+
* Copyright (c) 2008, 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -60,10 +60,4 @@ public interface IPeakModelMSD extends IPeakModel {
6060
* @return IMassSpectrum
6161
*/
6262
IPeakMassSpectrum getPeakMassSpectrum(int retentionTime);
63-
64-
@Override
65-
IScanMSD getPeakMaximum();
66-
67-
@Override
68-
IScanMSD getPeakScan(int retentionTime);
6963
}

‎chemclipse/plugins/org.eclipse.chemclipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/ExtendedPeakTracesUI.java‎

Lines changed: 12 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
/*******************************************************************************
2-
* Copyright (c) 2020, 2026 Lablicate GmbH.
2+
* Copyright (c) 2020, 2025 Lablicate GmbH.
33
*
44
* This program and the accompanying materials are made
55
* available under the terms of the Eclipse Public License 2.0
@@ -23,6 +23,7 @@
2323
import org.eclipse.chemclipse.logging.core.Logger;
2424
import org.eclipse.chemclipse.model.core.IChromatogramPeak;
2525
import org.eclipse.chemclipse.model.core.IPeak;
26+
import org.eclipse.chemclipse.model.core.IScan;
2627
import org.eclipse.chemclipse.msd.model.core.IPeakMSD;
2728
import org.eclipse.chemclipse.msd.model.core.IPeakModelMSD;
2829
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
@@ -441,14 +442,16 @@ private void deleteTraces(Display display, Set<Integer> traces) {
441442
}
442443
} else if(peak instanceof IPeakWSD peakWSD) {
443444
IPeakModelWSD peakModelWSD = peakWSD.getPeakModel();
444-
IScanWSD scanWSD = peakModelWSD.getPeakMaximum();
445-
int maxDeleteTraces = scanWSD.getNumberOfScanSignals() - 1;
446-
if(traces.size() >= maxDeleteTraces) {
447-
MessageDialog.openInformation(display.getActiveShell(), CATEGORY, "It's not possible to delete all wavelengths.");
448-
} else {
449-
scanWSD.removeScanSignals(traces);
450-
updatePeak();
451-
UpdateNotifierUI.update(display, peak);
445+
IScan scan = peakModelWSD.getPeakMaximum();
446+
if(scan instanceof IScanWSD scanWSD) {
447+
int maxDeleteTraces = scanWSD.getNumberOfScanSignals() - 1;
448+
if(traces.size() >= maxDeleteTraces) {
449+
MessageDialog.openInformation(display.getActiveShell(), CATEGORY, "It's not possible to delete all wavelengths.");
450+
} else {
451+
scanWSD.removeScanSignals(traces);
452+
updatePeak();
453+
UpdateNotifierUI.update(display, peak);
454+
}
452455
}
453456
}
454457
if(peak instanceof IChromatogramPeak chromatogramPeak) {

0 commit comments

Comments
 (0)