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Merge pull request #127 from Mailaender/mz5-perf
Improved performance of the mz5 chromatogram reader
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30 changes: 30 additions & 0 deletions
30
...er.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/internal/io/ProxyReader.java
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| /******************************************************************************* | ||
| * Copyright (c) 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 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Matthias Mailänder - initial API and implementation | ||
| *******************************************************************************/ | ||
| package net.openchrom.msd.converter.supplier.mz5.internal.io; | ||
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| import java.io.IOException; | ||
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| import org.eclipse.core.runtime.IProgressMonitor; | ||
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| import net.openchrom.msd.converter.supplier.mz5.io.IReaderProxy; | ||
| import net.openchrom.msd.converter.supplier.mz5.io.ReaderProxy; | ||
| import net.openchrom.msd.converter.supplier.mz5.io.support.IScanMarker; | ||
| import net.openchrom.msd.converter.supplier.mz5.model.IVendorScanProxy; | ||
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| public class ProxyReader { | ||
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| public void readMassSpectrum(double[] mzs, float[] spectrumIntensity, IScanMarker scanMarker, IVendorScanProxy massSpectrum, IProgressMonitor monitor) throws IOException { | ||
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| IReaderProxy scanReaderProxy = new ReaderProxy(); | ||
| scanReaderProxy.readMassSpectrum(mzs, spectrumIntensity, scanMarker, massSpectrum, monitor); | ||
| } | ||
| } |
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24 changes: 24 additions & 0 deletions
24
....converter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/io/IReaderProxy.java
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| @@ -0,0 +1,24 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 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 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Matthias Mailänder - initial API and implementation | ||
| *******************************************************************************/ | ||
| package net.openchrom.msd.converter.supplier.mz5.io; | ||
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| import java.io.IOException; | ||
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| import org.eclipse.core.runtime.IProgressMonitor; | ||
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| import net.openchrom.msd.converter.supplier.mz5.io.support.IScanMarker; | ||
| import net.openchrom.msd.converter.supplier.mz5.model.IVendorScanProxy; | ||
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| public interface IReaderProxy { | ||
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| void readMassSpectrum(double[] mzs, float[] spectrumIntensity, IScanMarker scanMarker, IVendorScanProxy massSpectrum, IProgressMonitor monitor) throws IOException; | ||
| } |
51 changes: 51 additions & 0 deletions
51
...d.converter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/io/ReaderProxy.java
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| @@ -0,0 +1,51 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 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 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Matthias Mailänder - initial API and implementation | ||
| *******************************************************************************/ | ||
| package net.openchrom.msd.converter.supplier.mz5.io; | ||
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| import java.io.IOException; | ||
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| import org.eclipse.chemclipse.logging.core.Logger; | ||
| import org.eclipse.chemclipse.model.exceptions.AbundanceLimitExceededException; | ||
| import org.eclipse.chemclipse.msd.model.exceptions.IonLimitExceededException; | ||
| import org.eclipse.core.runtime.IProgressMonitor; | ||
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| import net.openchrom.msd.converter.supplier.mz5.io.support.IScanMarker; | ||
| import net.openchrom.msd.converter.supplier.mz5.model.IVendorIon; | ||
| import net.openchrom.msd.converter.supplier.mz5.model.IVendorScanProxy; | ||
| import net.openchrom.msd.converter.supplier.mz5.model.VendorIon; | ||
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| public class ReaderProxy implements IReaderProxy { | ||
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| private static final Logger logger = Logger.getLogger(ReaderProxy.class); | ||
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| @Override | ||
| public void readMassSpectrum(double[] mzs, float[] spectrumIntensity, IScanMarker scanMarker, IVendorScanProxy massSpectrum, IProgressMonitor monitor) throws IOException { | ||
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| try { | ||
| double mz = 0; | ||
| int start = scanMarker.getStart(); | ||
| int offset = scanMarker.getOffset(); | ||
| for(int o = start; o < offset; o++) { | ||
| float intensity = spectrumIntensity[o]; | ||
| mz += mzs[o]; // first m/z value and then deltas | ||
| IVendorIon ion = new VendorIon(mz, intensity); | ||
| massSpectrum.addIon(ion); | ||
| } | ||
| } catch(OutOfMemoryError e) { | ||
| logger.error(e); | ||
| } catch(AbundanceLimitExceededException e) { | ||
| logger.warn(e); | ||
| } catch(IonLimitExceededException e) { | ||
| logger.warn(e); | ||
| } | ||
| } | ||
| } |
23 changes: 23 additions & 0 deletions
23
...ter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/io/support/IScanMarker.java
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|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 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 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Matthias Mailänder - initial API and implementation | ||
| *******************************************************************************/ | ||
| package net.openchrom.msd.converter.supplier.mz5.io.support; | ||
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| public interface IScanMarker { | ||
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| int getStart(); | ||
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| void setStart(int start); | ||
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| int getOffset(); | ||
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| void setOffset(int offset); | ||
| } |
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48
...rter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/io/support/ScanMarker.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 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 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Matthias Mailänder - initial API and implementation | ||
| *******************************************************************************/ | ||
| package net.openchrom.msd.converter.supplier.mz5.io.support; | ||
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| public class ScanMarker implements IScanMarker { | ||
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| private int start; | ||
| private int offset; | ||
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| public ScanMarker(int start, int offset) { | ||
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| this.start = start; | ||
| this.offset = offset; | ||
| } | ||
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| @Override | ||
| public int getStart() { | ||
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| return start; | ||
| } | ||
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| @Override | ||
| public void setStart(int start) { | ||
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| this.start = start; | ||
| } | ||
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| @Override | ||
| public int getOffset() { | ||
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| return offset; | ||
| } | ||
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| @Override | ||
| public void setOffset(int offset) { | ||
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| this.offset = offset; | ||
| } | ||
| } |
17 changes: 17 additions & 0 deletions
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...ter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/model/IVendorScanProxy.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2017, 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 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Dr. Philip Wenig - initial API and implementation | ||
| *******************************************************************************/ | ||
| package net.openchrom.msd.converter.supplier.mz5.model; | ||
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| import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrumProxy; | ||
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| public interface IVendorScanProxy extends IVendorScan, IVendorMassSpectrumProxy { | ||
| } |
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