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Merged
eselmeister merged 1 commit into from
Jul 7, 2026
Merged

Use a simpler interface to store scans #878

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5 changes: 2 additions & 3 deletions ....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/ChromatogramReader.java
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Expand Up @@ -34,7 +34,6 @@
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IChromatogramPeakMSD;
import org.eclipse.chemclipse.msd.model.core.IIon;
import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.core.support.PeakBuilderMSD;
import org.eclipse.core.runtime.IProgressMonitor;
Expand Down Expand Up @@ -199,7 +198,7 @@ private void readTotalIonCurrent(ExperimentStepType experimentStep, IVendorChrom
}

for(int i = 0; i < seriesSet.getLength(); i++) {
IRegularMassSpectrum scan = new VendorScan();
IScanMSD scan = new VendorScan();
VendorIon ion = new VendorIon(IIon.TIC_ION, signals.get(i));
scan.addIon(ion, false);
scan.setRetentionTime(retentionTimes.get(i));
Expand Down Expand Up @@ -248,7 +247,7 @@ private void readRetentionTime(SeriesType series, IVendorChromatogram chromatogr
}
}
for(int rt : retentionTimes) {
IRegularMassSpectrum scan = new VendorScan();
IScanMSD scan = new VendorScan();
scan.setRetentionTime(rt);
chromatogram.getScans().add(scan);
}
Expand Down
4 changes: 2 additions & 2 deletions ...erter.supplier.animl/src/net/openchrom/msd/converter/supplier/animl/model/VendorScan.java
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Expand Up @@ -12,10 +12,10 @@
*******************************************************************************/
package net.openchrom.msd.converter.supplier.animl.model;

import org.eclipse.chemclipse.msd.model.core.AbstractRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.AbstractScanMSD;
import org.eclipse.chemclipse.msd.model.core.IIon;

public class VendorScan extends AbstractRegularMassSpectrum {
public class VendorScan extends AbstractScanMSD {

private static final long serialVersionUID = -2505351146336950677L;

Expand Down
6 changes: 3 additions & 3 deletions ...verter.supplier.gaml/src/net/openchrom/msd/converter/supplier/gaml/model/IVendorScan.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2008, 2025 Lablicate GmbH.
* Copyright (c) 2008, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,7 +12,7 @@
*******************************************************************************/
package net.openchrom.msd.converter.supplier.gaml.model;

import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;

public interface IVendorScan extends IRegularMassSpectrum {
public interface IVendorScan extends IScanMSD {
}
6 changes: 3 additions & 3 deletions ...nverter.supplier.gaml/src/net/openchrom/msd/converter/supplier/gaml/model/VendorScan.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2008, 2025 Lablicate GmbH.
* Copyright (c) 2008, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,10 +12,10 @@
*******************************************************************************/
package net.openchrom.msd.converter.supplier.gaml.model;

import org.eclipse.chemclipse.msd.model.core.AbstractRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.AbstractScanMSD;
import org.eclipse.chemclipse.msd.model.core.IIon;

public class VendorScan extends AbstractRegularMassSpectrum implements IVendorScan {
public class VendorScan extends AbstractScanMSD implements IVendorScan {

/**
* Renew the serialVersionUID any time you have changed some fields or
Expand Down
4 changes: 2 additions & 2 deletions ...rter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/io/ChromatogramReader.java
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Expand Up @@ -24,7 +24,7 @@
import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IIon;
import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.core.runtime.IProgressMonitor;

import net.openchrom.msd.converter.supplier.mz5.internal.model.CVParam;
Expand Down Expand Up @@ -86,7 +86,7 @@ private void readTIC(IHDF5SimpleReader reader, CVReference[] cvReferences, CVPar
double[] totalIntensities = reader.readDoubleArray(Mz5.CHROMATOGRAM_INTENSITY);
int[] chromatogramIndex = reader.readIntArray(Mz5.CHROMATOGRAM_INDEX);
for(int i = 0; i < chromatogramIndex[0]; i++) {
IRegularMassSpectrum scan = new VendorScan();
IScanMSD scan = new VendorScan();
VendorIon ion = new VendorIon(IIon.TIC_ION, (float)totalIntensities[i]);
scan.addIon(ion, false);
scan.setRetentionTime((int)Math.round(retentionTimes[i] * timeMultiplicator));
Expand Down
6 changes: 3 additions & 3 deletions ...onverter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/model/IVendorScan.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2014, 2025 Lablicate GmbH.
* Copyright (c) 2014, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,7 +12,7 @@
*******************************************************************************/
package net.openchrom.msd.converter.supplier.mz5.model;

import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;

public interface IVendorScan extends IRegularMassSpectrum {
public interface IVendorScan extends IScanMSD {
}
6 changes: 3 additions & 3 deletions ...converter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/model/VendorScan.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2014, 2025 Lablicate GmbH.
* Copyright (c) 2014, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,10 +12,10 @@
*******************************************************************************/
package net.openchrom.msd.converter.supplier.mz5.model;

import org.eclipse.chemclipse.msd.model.core.AbstractRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.AbstractScanMSD;
import org.eclipse.chemclipse.msd.model.core.IIon;

public class VendorScan extends AbstractRegularMassSpectrum implements IVendorScan {
public class VendorScan extends AbstractScanMSD implements IVendorScan {

/**
* Renew the serialVersionUID any time you have changed some fields or
Expand Down
6 changes: 3 additions & 3 deletions ...rter.supplier.mzmlb/src/net/openchrom/msd/converter/supplier/mzmlb/model/IVendorScan.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2014, 2025 Lablicate GmbH.
* Copyright (c) 2014, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,7 +12,7 @@
*******************************************************************************/
package net.openchrom.msd.converter.supplier.mzmlb.model;

import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;

public interface IVendorScan extends IRegularMassSpectrum {
public interface IVendorScan extends IScanMSD {
}
6 changes: 3 additions & 3 deletions ...erter.supplier.mzmlb/src/net/openchrom/msd/converter/supplier/mzmlb/model/VendorScan.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2014, 2025 Lablicate GmbH.
* Copyright (c) 2014, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,10 +12,10 @@
*******************************************************************************/
package net.openchrom.msd.converter.supplier.mzmlb.model;

import org.eclipse.chemclipse.msd.model.core.AbstractRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.AbstractScanMSD;
import org.eclipse.chemclipse.msd.model.core.IIon;

public class VendorScan extends AbstractRegularMassSpectrum implements IVendorScan {
public class VendorScan extends AbstractScanMSD implements IVendorScan {

/**
* Renew the serialVersionUID any time you have changed some fields or
Expand Down