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Add initial write support for mzXML chromatograms.
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chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml.ui/plugin.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <?eclipse version="3.4"?> | ||
| <plugin> | ||
| <extension | ||
| point="org.eclipse.ui.preferencePages"> | ||
| <page | ||
| category="org.eclipse.chemclipse.msd.converter.ui.converterPreferencePage" | ||
| class="org.eclipse.chemclipse.msd.converter.supplier.mzxml.ui.preferences.PreferencePage" | ||
| id="org.eclipse.chemclipse.msd.converter.supplier.mzxml.ui.preferences.converterPreferencePage" | ||
| name="mzXML Converter"> | ||
| </page> | ||
| </extension> | ||
| </plugin> |
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40
...rc/org/eclipse/chemclipse/msd/converter/supplier/mzxml/ui/preferences/PreferencePage.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 org.eclipse.chemclipse.msd.converter.supplier.mzxml.ui.preferences; | ||
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| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.preferences.PreferenceSupplier; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.ui.Activator; | ||
| import org.eclipse.chemclipse.support.ui.preferences.fieldeditors.SpacerFieldEditor; | ||
| import org.eclipse.jface.preference.ComboFieldEditor; | ||
| import org.eclipse.jface.preference.FieldEditorPreferencePage; | ||
| import org.eclipse.ui.IWorkbench; | ||
| import org.eclipse.ui.IWorkbenchPreferencePage; | ||
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| public class PreferencePage extends FieldEditorPreferencePage implements IWorkbenchPreferencePage { | ||
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| public PreferencePage() { | ||
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| super(GRID); | ||
| setPreferenceStore(Activator.getDefault().getPreferenceStore()); | ||
| setDescription("mzXML Converter"); | ||
| } | ||
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| public void createFieldEditors() { | ||
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| addField(new SpacerFieldEditor(getFieldEditorParent())); | ||
| addField(new ComboFieldEditor(PreferenceSupplier.P_CHROMATOGRAM_VERSION_SAVE, "Save (*.mzxml) as version:", PreferenceSupplier.getChromatogramVersions(), getFieldEditorParent())); | ||
| } | ||
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| public void init(IWorkbench workbench) { | ||
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| } | ||
| } |
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91 changes: 91 additions & 0 deletions
91
...org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramWriter32.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 org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io; | ||
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| import java.io.File; | ||
| import java.io.FileNotFoundException; | ||
| import java.io.IOException; | ||
| import java.math.BigInteger; | ||
| import java.nio.ByteBuffer; | ||
| import java.nio.ByteOrder; | ||
| import java.nio.DoubleBuffer; | ||
| import java.util.List; | ||
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| import javax.xml.bind.JAXBContext; | ||
| import javax.xml.bind.JAXBException; | ||
| import javax.xml.bind.Marshaller; | ||
| import javax.xml.datatype.DatatypeConfigurationException; | ||
| import javax.xml.datatype.DatatypeFactory; | ||
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| import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException; | ||
| import org.eclipse.chemclipse.converter.io.AbstractChromatogramWriter; | ||
| import org.eclipse.chemclipse.logging.core.Logger; | ||
| import org.eclipse.chemclipse.model.core.IScan; | ||
| import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model.MsRun; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model.MzXML; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model.Peaks; | ||
| import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model.Scan; | ||
| import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD; | ||
| import org.eclipse.chemclipse.msd.model.core.IIon; | ||
| import org.eclipse.chemclipse.msd.model.core.IScanMSD; | ||
| import org.eclipse.core.runtime.IProgressMonitor; | ||
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| public class ChromatogramWriter32 extends AbstractChromatogramWriter implements IChromatogramMSDWriter { | ||
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| private static final Logger logger = Logger.getLogger(ChromatogramWriter32.class); | ||
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| @Override | ||
| public void writeChromatogram(File file, IChromatogramMSD chromatogram, IProgressMonitor monitor) throws FileNotFoundException, FileIsNotWriteableException, IOException { | ||
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| try { | ||
| JAXBContext jaxbContext = JAXBContext.newInstance(org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model.MzXML.class); | ||
| Marshaller marshaller = jaxbContext.createMarshaller(); | ||
| MsRun msRun = new MsRun(); | ||
| for(IScan sourceScan : chromatogram.getScans()) { | ||
| Scan exportScan = new Scan(); | ||
| exportScan.setTotIonCurrent(sourceScan.getTotalSignal()); | ||
| exportScan.setRetentionTime(DatatypeFactory.newInstance().newDuration(sourceScan.getRetentionTime())); | ||
| IScanMSD scanMSD = (IScanMSD)sourceScan; | ||
| List<IIon> ions = scanMSD.getIons(); | ||
| double[] values = new double[ions.size() * 2]; | ||
| int i = 0; | ||
| for(IIon ion : ions) { | ||
| values[i] = ion.getIon(); | ||
| values[i + 1] = ion.getAbundance(); | ||
| i += 2; | ||
| } | ||
| exportScan.setMsLevel(BigInteger.valueOf(1)); // TODO | ||
| Peaks peaks = new Peaks(); | ||
| DoubleBuffer doubleBuffer = DoubleBuffer.wrap(values); | ||
| ByteBuffer byteBuffer = ByteBuffer.allocate(doubleBuffer.capacity() * Double.BYTES); | ||
| peaks.setPrecision(BigInteger.valueOf(64)); | ||
| peaks.setByteOrder("network"); | ||
| byteBuffer.order(ByteOrder.BIG_ENDIAN); // TODO: preferences | ||
| // TODO: compression | ||
| byteBuffer.asDoubleBuffer().put(doubleBuffer); | ||
| peaks.setValue(byteBuffer.array()); | ||
| exportScan.getPeaks().add(peaks); | ||
| msRun.getScan().add(exportScan); | ||
| } | ||
| MzXML mzXML = new MzXML(); | ||
| mzXML.setMsRun(msRun); | ||
| marshaller.marshal(mzXML, file); | ||
| } catch(JAXBException e) { | ||
| logger.warn(e); | ||
| } catch(DatatypeConfigurationException e) { | ||
| logger.warn(e); | ||
| } catch(Exception e) { | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
| } |
29 changes: 29 additions & 0 deletions
29
...er.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/IFormat.java
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|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| /******************************************************************************* | ||
| * 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 | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.io; | ||
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| public interface IFormat { | ||
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| String CONTEXT_PATH_V_200 = "org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model"; | ||
| String CONTEXT_PATH_V_210 = "org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model"; | ||
| String CONTEXT_PATH_V_220 = "org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model"; | ||
| String CONTEXT_PATH_V_300 = "org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v30.model"; | ||
| String CONTEXT_PATH_V_310 = "org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v31.model"; | ||
| String CONTEXT_PATH_V_320 = "org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model"; | ||
| String MZXML_V_200 = "mzXML_2.0"; | ||
| String MZXML_V_210 = "mzXML_2.1"; | ||
| String MZXML_V_220 = "mzXML_2.2"; | ||
| String MZXML_V_300 = "mzXML_3.0"; | ||
| String MZXML_V_310 = "mzXML_3.1"; | ||
| String MZXML_V_320 = "mzXML_3.2"; | ||
| String CHROMATOGRAM_VERSION_LATEST = MZXML_V_320; | ||
| } |
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40 changes: 40 additions & 0 deletions
40
...xml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/v32/model/MzXML.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| /******************************************************************************* | ||
| * 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 Mailände - initial API and implementation | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v32.model; | ||
|
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| import java.io.Serializable; | ||
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| import javax.xml.bind.annotation.XmlAccessType; | ||
| import javax.xml.bind.annotation.XmlAccessorType; | ||
| import javax.xml.bind.annotation.XmlElement; | ||
| import javax.xml.bind.annotation.XmlRootElement; | ||
| import javax.xml.bind.annotation.XmlType; | ||
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| @XmlAccessorType(XmlAccessType.FIELD) | ||
| @XmlType(name = "", propOrder = {"msRun"}) | ||
| @XmlRootElement(name = "mzXML", namespace = "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2") | ||
| public class MzXML implements Serializable { | ||
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| private final static long serialVersionUID = 320L; | ||
| @XmlElement(required = true) | ||
| private MsRun msRun; | ||
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| public MsRun getMsRun() { | ||
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| return msRun; | ||
| } | ||
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| public void setMsRun(MsRun value) { | ||
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| this.msRun = value; | ||
| } | ||
| } |
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