diff --git a/chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mzml.feature/feature.xml b/chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mzml.feature/feature.xml index b67ddc07a1..ffaaa3f8d3 100644 --- a/chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mzml.feature/feature.xml +++ b/chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mzml.feature/feature.xml @@ -26,16 +26,22 @@ + version="0.0.0"/> + version="0.0.0"/> + + + + + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF index a6cb5f56de..13aea6d314 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF @@ -1,7 +1,7 @@ Manifest-Version: 1.0 Automatic-Module-Name: org.eclipse.chemclipse.msd.converter.supplier.mzml.ui Bundle-ManifestVersion: 2 -Bundle-Name: mzML UI +Bundle-Name: mzML MSD UI Bundle-SymbolicName: org.eclipse.chemclipse.msd.converter.supplier.mzml.ui;singleton:=true Bundle-Version: 0.9.0.qualifier Bundle-Activator: org.eclipse.chemclipse.msd.converter.supplier.mzml.ui.Activator diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/ui/preferences/PreferencePage.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/ui/preferences/PreferencePage.java index ef4f76183d..ad71a1659d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/ui/preferences/PreferencePage.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/ui/preferences/PreferencePage.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2021 Lablicate GmbH. + * Copyright (c) 2021, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -29,6 +29,7 @@ public PreferencePage() { setDescription("mzML Converter"); } + @Override public void createFieldEditors() { addField(new SpacerFieldEditor(getFieldEditorParent())); @@ -36,6 +37,7 @@ public void createFieldEditors() { addField(new BooleanFieldEditor(PreferenceSupplier.P_CHROMATOGRAM_SAVE_COMPRESSION, "Compress values", getFieldEditorParent())); } + @Override public void init(IWorkbench workbench) { } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/META-INF/MANIFEST.MF index d64c4d1502..4e1b29b8eb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/META-INF/MANIFEST.MF +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/META-INF/MANIFEST.MF @@ -15,14 +15,16 @@ Require-Bundle: org.eclipse.core.runtime, org.eclipse.chemclipse.converter;bundle-version="0.8.0", org.eclipse.chemclipse.model;bundle-version="0.8.0", org.eclipse.chemclipse.support;bundle-version="0.8.0", - org.apache.commons.commons-codec;bundle-version="1.15.0", - org.eclipse.chemclipse.xxd.converter.supplier.mzml, - org.apache.commons.lang3;bundle-version="3.13.0" + org.eclipse.chemclipse.xxd.converter.supplier.mzml;bundle-version="0.9.0", + org.apache.commons.lang3 Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-ActivationPolicy: lazy Import-Package: jakarta.xml.bind, jakarta.xml.bind.annotation, jakarta.xml.bind.annotation.adapters -Export-Package: org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io, - org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter, - org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model +Export-Package: org.eclipse.chemclipse.msd.converter.supplier.mzml, + org.eclipse.chemclipse.msd.converter.supplier.mzml.converter, + org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io, + org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model, + org.eclipse.chemclipse.msd.converter.supplier.mzml.io, + org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/plugin.xml b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/plugin.xml index bee9954c5f..e9867f266b 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/plugin.xml +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/plugin.xml @@ -7,11 +7,11 @@ description="Reads mzML Chromatograms" exportConverter="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.ChromatogramExportConverter" fileExtension=".mzML" - filterName="mzML Chromatogram (*.mzML)" + filterName="MSD Chromatogram (*.mzML)" id="org.eclipse.chemclipse.msd.converter.supplier.mzml" importContentMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.ChromatogramFileContentMatcher" importConverter="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.ChromatogramImportConverter" - importMagicNumberMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MagicNumberMatcher" + importMagicNumberMatcher="org.eclipse.chemclipse.xxd.converter.supplier.mzml.converter.MagicNumberMatcher" isExportable="true" isImportable="true"> @@ -26,7 +26,7 @@ id="org.eclipse.chemclipse.msd.converter.supplier.mzml.ms" importContentMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MassSpectrumFileContentMatcher" importConverter="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MassSpectrumImportConverter" - importMagicNumberMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MagicNumberMatcher" + importMagicNumberMatcher="org.eclipse.chemclipse.xxd.converter.supplier.mzml.converter.MagicNumberMatcher" isExportable="false" isImportable="true"> diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/PathResolver.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/PathResolver.java index 6f8a74b052..39289ec19a 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/PathResolver.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/PathResolver.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2013, 2018 Lablicate GmbH. + * Copyright (c) 2013, 2024 Lablicate GmbH. * * All rights reserved. * This program and the accompanying materials are made available under the @@ -25,7 +25,7 @@ public class PathResolver { /** * Returns a absolute path of the specified Folder. For example * TESTDATA_IMPORT_EMPTY as an absolute Path: - * $PluginPath$/testData/files/EMPTY.D/DATA.MS + * $PluginPath$/testData/files/data.mzML * * @param string * @return String absolutePath @@ -36,7 +36,7 @@ public static String getAbsolutePath(String string) { IPath path = new Path(string); URL url = FileLocator.find(bundle, path, null); try { - return FileLocator.resolve(url).getPath().toString(); + return FileLocator.resolve(url).getPath(); } catch(IOException e) { e.printStackTrace(); } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramExportConverter.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramExportConverter.java index bb806505a7..e2ded4ce6b 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramExportConverter.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramExportConverter.java @@ -23,7 +23,6 @@ import org.eclipse.chemclipse.model.core.IPeak; import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io.ChromatogramWriter; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.SpecificationValidator; import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD; import org.eclipse.chemclipse.processing.core.IProcessingInfo; import org.eclipse.core.runtime.IProgressMonitor; @@ -38,7 +37,6 @@ public class ChromatogramExportConverter extends AbstractChromatogramExportConve @Override public IProcessingInfo convert(File file, IChromatogram chromatogram, IProgressMonitor monitor) { - file = SpecificationValidator.validateSpecification(file); IProcessingInfo processingInfo = super.validate(file); if(!processingInfo.hasErrorMessages() && chromatogram instanceof IChromatogramMSD chromatogramMSD) { monitor.subTask(EXPORT_CHROMATOGRAM); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramFileContentMatcher.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramFileContentMatcher.java index 8d4fd3b2a7..b2a772b487 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramFileContentMatcher.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramFileContentMatcher.java @@ -36,6 +36,7 @@ public boolean checkFileFormat(File file) { XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(new FileInputStream(file)); boolean hasChromatogramList = false; boolean hasRootElement = false; + boolean hasMS = false; while(xmlStreamReader.hasNext()) { int eventType = xmlStreamReader.next(); if(eventType == XMLStreamConstants.START_ELEMENT) { @@ -44,8 +45,24 @@ public boolean checkFileFormat(File file) { hasRootElement = true; } else if(elementName.equals("chromatogramList")) { hasChromatogramList = true; + } else if(elementName.equals("fileContent")) { + while(xmlStreamReader.hasNext()) { + int innerEventType = xmlStreamReader.next(); + if(innerEventType == XMLStreamConstants.START_ELEMENT && xmlStreamReader.getLocalName().equals("cvParam")) { + String accession = xmlStreamReader.getAttributeValue(null, "accession"); + String paramName = xmlStreamReader.getAttributeValue(null, "name"); + if(accession.equals("MS:1000579") && paramName.equals("MS1 spectrum") || // + accession.equals("MS:1000580") && paramName.equals("MSn spectrum")) { + hasMS = true; + break; + } + } + if(innerEventType == XMLStreamConstants.END_ELEMENT && xmlStreamReader.getLocalName().equals("fileContent")) { + break; + } + } } - if(hasRootElement && hasChromatogramList) { + if(hasRootElement && hasChromatogramList && hasMS) { isValidFormat = true; break; } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverter.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverter.java index 6561f9104f..c69a7c4665 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverter.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverter.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2013, 2023 Lablicate GmbH. + * Copyright (c) 2013, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -20,7 +20,6 @@ import org.eclipse.chemclipse.model.core.IChromatogramOverview; import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io.ChromatogramReader; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.SpecificationValidator; import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD; import org.eclipse.chemclipse.processing.core.IProcessingInfo; import org.eclipse.core.runtime.IProgressMonitor; @@ -41,7 +40,6 @@ public IProcessingInfo convert(File file, IProgressMonitor mon /* * Read the chromatogram. */ - file = SpecificationValidator.validateSpecification(file); IChromatogramMSDReader reader = new ChromatogramReader(); monitor.subTask(IMPORT_CHROMATOGRAM); try { @@ -64,7 +62,6 @@ public IProcessingInfo convertOverview(File file, IProgre IProcessingInfo processingInfo = super.validate(file); if(!processingInfo.hasErrorMessages()) { - file = SpecificationValidator.validateSpecification(file); IChromatogramMSDReader reader = new ChromatogramReader(); monitor.subTask(IMPORT_CHROMATOGRAM_OVERVIEW); try { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/MassSpectrumImportConverter.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/MassSpectrumImportConverter.java index ee573d9a9a..96bf91cf4b 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/MassSpectrumImportConverter.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/MassSpectrumImportConverter.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2021, 2022 Lablicate GmbH. + * Copyright (c) 2021, 2024 Lablicate GmbH. * * All rights reserved. * This program and the accompanying materials are made available under the @@ -17,14 +17,15 @@ import org.eclipse.chemclipse.converter.exceptions.FileIsEmptyException; import org.eclipse.chemclipse.converter.exceptions.FileIsNotReadableException; +import org.eclipse.chemclipse.converter.l10n.ConverterMessages; import org.eclipse.chemclipse.logging.core.Logger; import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader; import org.eclipse.chemclipse.msd.converter.massspectrum.AbstractMassSpectrumImportConverter; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io.MassSpectrumReader; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.SpecificationValidator; import org.eclipse.chemclipse.msd.model.core.IMassSpectra; import org.eclipse.chemclipse.processing.core.IProcessingInfo; import org.eclipse.core.runtime.IProgressMonitor; +import org.eclipse.osgi.util.NLS; public class MassSpectrumImportConverter extends AbstractMassSpectrumImportConverter { @@ -37,26 +38,25 @@ public IProcessingInfo convert(File file, IProgressMonitor monitor IProcessingInfo processingInfo = super.validate(file); if(!processingInfo.hasErrorMessages()) { try { - file = SpecificationValidator.validateSpecification(file); IMassSpectraReader massSpectraReader = new MassSpectrumReader(); IMassSpectra massSpectra = massSpectraReader.read(file, monitor); if(massSpectra != null && !massSpectra.isEmpty()) { processingInfo.setProcessingResult(massSpectra); } else { - processingInfo.addErrorMessage(DESCRIPTION, "No mass spectra are stored." + file.getAbsolutePath()); + processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.noMassSpectraStored, file.getAbsolutePath())); } } catch(FileNotFoundException e) { logger.warn(e); - processingInfo.addErrorMessage(DESCRIPTION, "The file couldn't be found: " + file.getAbsolutePath()); + processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotFound, file.getAbsolutePath())); } catch(FileIsNotReadableException e) { logger.warn(e); - processingInfo.addErrorMessage(DESCRIPTION, "The file is not readable: " + file.getAbsolutePath()); + processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotReadable, file.getAbsolutePath())); } catch(FileIsEmptyException e) { logger.warn(e); - processingInfo.addErrorMessage(DESCRIPTION, "The file is empty: " + file.getAbsolutePath()); + processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.emptyFile, file.getAbsolutePath())); } catch(IOException e) { logger.warn(e); - processingInfo.addErrorMessage(DESCRIPTION, "Something has gone completely wrong: " + file.getAbsolutePath()); + processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath())); } } return processingInfo; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramReader.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramReader.java index 8dece0164c..d4ca46620b 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramReader.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramReader.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2014, 2023 Lablicate GmbH. + * Copyright (c) 2014, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -16,15 +16,15 @@ import java.io.FileReader; import java.io.IOException; +import org.eclipse.chemclipse.converter.exceptions.UnknownVersionException; import org.eclipse.chemclipse.model.core.IChromatogramOverview; import org.eclipse.chemclipse.msd.converter.io.AbstractChromatogramMSDReader; import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader10; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.ChromatogramReaderVersion10; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.ChromatogramReaderVersion110; +import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.ChromatogramReaderVersion10; +import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.ChromatogramReaderVersion110; import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD; -import org.eclipse.chemclipse.xxd.converter.supplier.io.exception.UnknownVersionException; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader10; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; import org.eclipse.core.runtime.IProgressMonitor; public class ChromatogramReader extends AbstractChromatogramMSDReader implements IChromatogramMSDReader { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramWriter.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramWriter.java index 0720e5438d..f3f3f4dc40 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramWriter.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramWriter.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2014, 2023 Lablicate GmbH. + * Copyright (c) 2014, 2024 Lablicate GmbH. * * All rights reserved. * This program and the accompanying materials are made available under the @@ -18,10 +18,10 @@ import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException; import org.eclipse.chemclipse.converter.io.AbstractChromatogramWriter; import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.ChromatogramWriterVersion110; +import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.ChromatogramWriterVersion110; import org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences.PreferenceSupplier; import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; import org.eclipse.core.runtime.IProgressMonitor; public class ChromatogramWriter extends AbstractChromatogramWriter implements IChromatogramMSDWriter { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/MassSpectrumReader.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/MassSpectrumReader.java index f11ccf3943..e3ca1b91c8 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/MassSpectrumReader.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/MassSpectrumReader.java @@ -1,6 +1,6 @@ /******************************************************************************* - * Copyright (c) 2013, 2023 Lablicate GmbH. - * + * Copyright (c) 2013, 2024 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, @@ -15,12 +15,12 @@ import java.io.FileReader; import java.io.IOException; +import org.eclipse.chemclipse.converter.exceptions.UnknownVersionException; import org.eclipse.chemclipse.msd.converter.io.AbstractMassSpectraReader; import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.MassSpectrumReaderVersion110; +import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.MassSpectrumReaderVersion110; import org.eclipse.chemclipse.msd.model.core.IMassSpectra; -import org.eclipse.chemclipse.xxd.converter.supplier.io.exception.UnknownVersionException; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; import org.eclipse.core.runtime.IProgressMonitor; public class MassSpectrumReader extends AbstractMassSpectraReader implements IMassSpectraReader { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryWriter.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryWriter.java deleted file mode 100644 index 615ce9327a..0000000000 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryWriter.java +++ /dev/null @@ -1,96 +0,0 @@ -/******************************************************************************* - * Copyright (c) 2021, 2023 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.mzml.internal.converter; - -import java.io.ByteArrayOutputStream; -import java.math.BigInteger; -import java.nio.ByteBuffer; -import java.nio.ByteOrder; -import java.nio.DoubleBuffer; -import java.nio.FloatBuffer; -import java.util.zip.Deflater; - -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.ChromatogramWriterVersion110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.BinaryDataArrayType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVParamType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences.PreferenceSupplier; - -import jakarta.xml.bind.DatatypeConverter; - -public class BinaryWriter { - - private BinaryWriter() { - - } - - public static BinaryDataArrayType createBinaryData(float[] values) { - - FloatBuffer floatBuffer = FloatBuffer.wrap(values); - ByteBuffer byteBuffer = ByteBuffer.allocate(floatBuffer.capacity() * Float.BYTES); - byteBuffer.order(ByteOrder.LITTLE_ENDIAN); - byteBuffer.asFloatBuffer().put(floatBuffer); - BinaryDataArrayType binaryDataArrayType = createBinaryDataArray(byteBuffer); - CVParamType cvParamData = new CVParamType(); - cvParamData.setCvRef(ChromatogramWriterVersion110.MS); - cvParamData.setAccession("MS:1000521"); - cvParamData.setName("32-bit float"); - binaryDataArrayType.getCvParam().add(cvParamData); - return binaryDataArrayType; - } - - public static BinaryDataArrayType createBinaryData(double[] values) { - - DoubleBuffer doubleBuffer = DoubleBuffer.wrap(values); - ByteBuffer byteBuffer = ByteBuffer.allocate(doubleBuffer.capacity() * Double.BYTES); - byteBuffer.order(ByteOrder.LITTLE_ENDIAN); - byteBuffer.asDoubleBuffer().put(doubleBuffer); - BinaryDataArrayType binaryDataArrayType = createBinaryDataArray(byteBuffer); - CVParamType cvParamData = new CVParamType(); - cvParamData.setCvRef(ChromatogramWriterVersion110.MS); - cvParamData.setAccession("MS:1000523"); - cvParamData.setName("64-bit float"); - binaryDataArrayType.getCvParam().add(cvParamData); - return binaryDataArrayType; - } - - private static BinaryDataArrayType createBinaryDataArray(ByteBuffer byteBuffer) { - - BinaryDataArrayType binaryDataArrayType = new BinaryDataArrayType(); - boolean compression = PreferenceSupplier.getChromatogramSaveCompression(); - if(compression) { - CVParamType cvParamCompression = new CVParamType(); - cvParamCompression.setCvRef(ChromatogramWriterVersion110.MS); - cvParamCompression.setAccession("MS:1000574"); - cvParamCompression.setName("zlib compression"); - binaryDataArrayType.getCvParam().add(cvParamCompression); - Deflater compresser = new Deflater(); - compresser.setInput(byteBuffer.array()); - compresser.finish(); - ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); - byte[] readBuffer = new byte[1024]; - while(!compresser.finished()) { - int compressCount = compresser.deflate(readBuffer); - if(compressCount > 0) { - outputStream.write(readBuffer, 0, compressCount); - } - } - byte[] outputByteArray = outputStream.toByteArray(); - String characters = DatatypeConverter.printBase64Binary(outputByteArray); - binaryDataArrayType.setEncodedLength(BigInteger.valueOf(characters.length())); - binaryDataArrayType.setBinary(outputByteArray); - compresser.end(); - } else { - binaryDataArrayType.setBinary(byteBuffer.array()); - } - return binaryDataArrayType; - } -} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/SpecificationValidator.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/SpecificationValidator.java deleted file mode 100644 index c2c2285856..0000000000 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/SpecificationValidator.java +++ /dev/null @@ -1,55 +0,0 @@ -/******************************************************************************* - * Copyright (c) 2013, 2018 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 org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter; - -import java.io.File; - -public class SpecificationValidator { - - /** - * Use only static methods. - */ - private SpecificationValidator() { - } - - /** - * Validates the given chromatogram file.
- * If the file is denoted only by a directory path, /CHROMATOGRAM.mzML will - * be added. E.g.: /home/user/chrom will be validated to - * /home/user/chrom/CHROMATOGRAM.mzML - * - * @param file - */ - public static File validateSpecification(File file) { - - if(file == null) { - return null; - } - /* - * Validate - */ - File validFile; - String path = file.getAbsolutePath().toLowerCase(); - if(file.isDirectory()) { - validFile = new File(file.getAbsolutePath() + File.separator + "CHROMATOGRAM.mzML"); - } else { - if(path.endsWith(".")) { - validFile = new File(file.getAbsolutePath() + "mzML"); - } else if(!path.endsWith(".mzml")) { - validFile = new File(file.getAbsolutePath() + ".mzML"); - } else { - validFile = file; - } - } - return validFile; - } -} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramWriterVersion110.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramWriterVersion110.java deleted file mode 100644 index 51417c5531..0000000000 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramWriterVersion110.java +++ /dev/null @@ -1,585 +0,0 @@ -/******************************************************************************* - * Copyright (c) 2021, 2024 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.mzml.internal.io; - -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.math.BigInteger; -import java.util.Date; -import java.util.GregorianCalendar; -import java.util.List; - -import javax.xml.datatype.DatatypeConfigurationException; -import javax.xml.datatype.DatatypeFactory; - -import org.apache.commons.codec.digest.DigestUtils; -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.IChromatogram; -import org.eclipse.chemclipse.model.core.IChromatogramOverview; -import org.eclipse.chemclipse.model.core.IScan; -import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.Activator; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.BinaryWriter; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.BinaryDataArrayListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.BinaryDataArrayType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVParamType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ChromatogramListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ChromatogramType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.DataProcessingListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.DataProcessingType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.FileDescriptionType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.InstrumentConfigurationListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.InstrumentConfigurationType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.MzMLType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ObjectFactory; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ParamGroupType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ProcessingMethodType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.RunType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ScanListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ScanType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SoftwareListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SoftwareRefType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SoftwareType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SourceFileListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SourceFileType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SpectrumListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SpectrumType; -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.chemclipse.msd.model.core.IRegularMassSpectrum; -import org.eclipse.core.runtime.IProduct; -import org.eclipse.core.runtime.IProgressMonitor; -import org.eclipse.core.runtime.Platform; -import org.osgi.framework.Version; - -import jakarta.xml.bind.JAXBContext; -import jakarta.xml.bind.JAXBException; -import jakarta.xml.bind.Marshaller; - -public class ChromatogramWriterVersion110 extends AbstractChromatogramWriter implements IChromatogramMSDWriter { - - private static final Logger logger = Logger.getLogger(ChromatogramWriterVersion110.class); - // - public static final CVType MS = createMS(); - public static final CVType UO = createUO(); - - @Override - public void writeChromatogram(File file, IChromatogramMSD chromatogram, IProgressMonitor monitor) throws FileIsNotWriteableException, IOException { - - try { - JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class); - Marshaller marshaller = jaxbContext.createMarshaller(); - // - RunType run = new RunType(); - SoftwareListType softwareList = createSoftwareList(); - InstrumentConfigurationListType instrumentConfigurationList = createInstrumentConfigurationList(softwareList.getSoftware().get(0)); - run.setDefaultInstrumentConfigurationRef(instrumentConfigurationList.getInstrumentConfiguration().get(0)); - SourceFileListType sourceFileList = createSourceFileList(chromatogram); - run.setDefaultSourceFileRef(sourceFileList.getSourceFile().get(0)); - run.setId(chromatogram.getName()); - // - DataProcessingListType dataProcessingList = createDataProcessingList(softwareList.getSoftware().get(0)); - SpectrumListType spectrumList = new SpectrumListType(); - spectrumList.setDefaultDataProcessingRef(dataProcessingList.getDataProcessing().get(0)); - ChromatogramListType chromatogramList = new ChromatogramListType(); - chromatogramList.setDefaultDataProcessingRef(dataProcessingList.getDataProcessing().get(0)); - chromatogramList.setCount(BigInteger.valueOf(1)); // TODO export referenced chromatograms - // - int scans = chromatogram.getNumberOfScans(); - spectrumList.setCount(BigInteger.valueOf(scans)); - float[] totalSignals = new float[scans]; - float[] retentionTimes = new float[scans]; - int i = 0; - for(IScan scan : chromatogram.getScans()) { - SpectrumType spectrum = new SpectrumType(); - spectrum.setId("scan=" + scan.getScanNumber()); - spectrum.setIndex(BigInteger.valueOf((scan.getScanNumber() - 1))); - // TIC - totalSignals[i] = scan.getTotalSignal(); - retentionTimes[i] = (float)(scan.getRetentionTime() / IChromatogramOverview.SECOND_CORRELATION_FACTOR); - i++; - // - // full spectra - IScanMSD scanMSD = (IScanMSD)scan; - // - CVParamType cvParamTotalIonCurrent = new CVParamType(); - cvParamTotalIonCurrent.setCvRef(MS); - cvParamTotalIonCurrent.setAccession("MS:1000285"); - cvParamTotalIonCurrent.setName("total ion current"); - cvParamTotalIonCurrent.setValue(String.valueOf(scanMSD.getTotalSignal())); - spectrum.getCvParam().add(cvParamTotalIonCurrent); - // - CVParamType cvParamBasePeak = new CVParamType(); - cvParamBasePeak.setCvRef(MS); - cvParamBasePeak.setAccession("MS:1000504"); - cvParamBasePeak.setName("base peak m/z"); - cvParamBasePeak.setUnitCvRef(MS); - cvParamBasePeak.setUnitAccession("MS:1000040"); - cvParamBasePeak.setUnitName("m/z"); - cvParamBasePeak.setValue(String.valueOf(scanMSD.getBasePeak())); - spectrum.getCvParam().add(cvParamBasePeak); - // - CVParamType cvParamBasePeakIntensity = new CVParamType(); - cvParamBasePeakIntensity.setCvRef(MS); - cvParamBasePeakIntensity.setAccession("MS:1000505"); - cvParamBasePeakIntensity.setName("base peak intensity"); - cvParamBasePeakIntensity.setUnitCvRef(MS); - cvParamBasePeakIntensity.setUnitAccession("MS:1000131"); - cvParamBasePeakIntensity.setUnitName("number of detector counts"); - cvParamBasePeakIntensity.setValue(String.valueOf(scanMSD.getBasePeakAbundance())); - spectrum.getCvParam().add(cvParamBasePeakIntensity); - // - List ionList = scanMSD.getIons(); - double[] ions = new double[ionList.size()]; - float[] abundances = new float[ionList.size()]; - int j = 0; - for(IIon ion : ionList) { - ions[j] = ion.getIon(); - abundances[j] = ion.getAbundance(); - j++; - } - BinaryDataArrayListType binaryDataArrayList = new BinaryDataArrayListType(); - binaryDataArrayList.setCount(BigInteger.valueOf(2)); - // - BinaryDataArrayType ionsBinaryDataArrayType = BinaryWriter.createBinaryData(ions); - CVParamType cvParamIons = new CVParamType(); - cvParamIons.setCvRef(MS); - cvParamIons.setAccession("MS:1000514"); - cvParamIons.setName("m/z array"); - cvParamIons.setUnitCvRef(MS); - cvParamIons.setUnitAccession("MS:1000040"); - cvParamIons.setUnitName("m/z"); - ionsBinaryDataArrayType.getCvParam().add(cvParamIons); - binaryDataArrayList.getBinaryDataArray().add(ionsBinaryDataArrayType); - // - BinaryDataArrayType abundancesBinaryDataArrayType = BinaryWriter.createBinaryData(abundances); - CVParamType cvParamAbundances = new CVParamType(); - cvParamAbundances.setCvRef(MS); - cvParamAbundances.setAccession("MS:1000515"); - cvParamAbundances.setName("intensity array"); - cvParamAbundances.setUnitCvRef(MS); - cvParamAbundances.setUnitAccession("MS:1000131"); - cvParamAbundances.setUnitName("number of counts"); - abundancesBinaryDataArrayType.getCvParam().add(cvParamAbundances); - binaryDataArrayList.getBinaryDataArray().add(abundancesBinaryDataArrayType); - // - CVParamType cvParamRetentionTime = new CVParamType(); - cvParamRetentionTime.setCvRef(MS); - cvParamRetentionTime.setAccession("MS:1000016"); - cvParamRetentionTime.setName("scan start time"); - cvParamRetentionTime.setUnitCvRef(UO); - cvParamRetentionTime.setUnitAccession("UO:0000031"); - cvParamRetentionTime.setUnitName("minute"); - cvParamRetentionTime.setValue(String.valueOf(scanMSD.getRetentionTime() / IChromatogramOverview.MINUTE_CORRELATION_FACTOR)); - ScanType scanType = new ScanType(); - scanType.getCvParam().add(cvParamRetentionTime); - // - ScanListType scanList = new ScanListType(); - CVParamType cvParamCombination = new CVParamType(); - cvParamCombination.setCvRef(MS); - cvParamCombination.setAccession("MS:1000795"); - cvParamCombination.setName("no combination"); - scanList.getCvParam().add(cvParamCombination); - scanList.setCount(BigInteger.valueOf(1)); - scanList.getScan().add(scanType); - // - spectrum.setScanList(scanList); - spectrum.setBinaryDataArrayList(binaryDataArrayList); - IRegularMassSpectrum massSpectrum = (IRegularMassSpectrum)scanMSD; - CVParamType cvParamType = new CVParamType(); - if(massSpectrum.getMassSpectrometer() == 1) { - cvParamType.setCvRef(MS); - cvParamType.setAccession("MS:1000579"); - cvParamType.setName("MS1 spectrum"); - } else { - cvParamType.setCvRef(MS); - cvParamType.setAccession("MS:1000580"); - cvParamType.setName("MSn spectrum"); - } - spectrum.getCvParam().add(cvParamType); - CVParamType cvParamLevel = new CVParamType(); - cvParamLevel.setCvRef(MS); - cvParamLevel.setAccession("MS:1000511"); - cvParamLevel.setName("ms level"); - cvParamLevel.setValue(String.valueOf(massSpectrum.getMassSpectrometer())); - spectrum.getCvParam().add(cvParamLevel); - if(massSpectrum.getMassSpectrumType() == 0) { - CVParamType cvSpectrumType = new CVParamType(); - cvSpectrumType.setCvRef(MS); - cvSpectrumType.setAccession("MS:1000127"); - cvSpectrumType.setName("centroid spectrum"); - spectrum.getCvParam().add(cvSpectrumType); - } else if(massSpectrum.getMassSpectrumType() == 1) { - CVParamType cvSpectrumType = new CVParamType(); - cvSpectrumType.setCvRef(MS); - cvSpectrumType.setAccession("MS:1000128"); - cvSpectrumType.setName("profile spectrum"); - spectrum.getCvParam().add(cvSpectrumType); - } - spectrum.setDefaultArrayLength(ions.length); - spectrumList.getSpectrum().add(spectrum); - } - run.setSpectrumList(spectrumList); - // - BinaryDataArrayListType binaryDataArrayList = new BinaryDataArrayListType(); - binaryDataArrayList.setCount(BigInteger.valueOf(2)); - // - BinaryDataArrayType totalSignalsBinaryDataArrayType = BinaryWriter.createBinaryData(totalSignals); - CVParamType cvParamTotalSignals = new CVParamType(); - cvParamTotalSignals.setCvRef(MS); - cvParamTotalSignals.setAccession("MS:1000515"); - cvParamTotalSignals.setName("intensity array"); - cvParamTotalSignals.setUnitCvRef(MS); - cvParamTotalSignals.setUnitAccession("MS:1000131"); - cvParamTotalSignals.setUnitName("number of counts"); - totalSignalsBinaryDataArrayType.getCvParam().add(cvParamTotalSignals); - binaryDataArrayList.getBinaryDataArray().add(totalSignalsBinaryDataArrayType); - // - BinaryDataArrayType retentionTimesBinaryDataArrayType = BinaryWriter.createBinaryData(retentionTimes); - CVParamType cvParamRetentionTime = new CVParamType(); - cvParamRetentionTime.setCvRef(MS); - cvParamRetentionTime.setAccession("MS:1000595"); - cvParamRetentionTime.setName("time array"); - cvParamRetentionTime.setUnitAccession("UO:0000010"); - cvParamRetentionTime.setUnitName("second"); - retentionTimesBinaryDataArrayType.getCvParam().add(cvParamRetentionTime); - binaryDataArrayList.getBinaryDataArray().add(retentionTimesBinaryDataArrayType); - // - ChromatogramType tic = new ChromatogramType(); - tic.setId("tic"); - tic.setIndex(BigInteger.valueOf(0)); - CVParamType cvParam = new CVParamType(); - cvParam.setCvRef(MS); - cvParam.setAccession("MS:1000235"); - cvParam.setName("total ion current chromatogram"); - cvParam.setValue(""); - tic.getCvParam().add(cvParam); - tic.setDefaultArrayLength(totalSignals.length); - tic.setBinaryDataArrayList(binaryDataArrayList); - chromatogramList.getChromatogram().add(tic); - run.setChromatogramList(chromatogramList); - // - Date date = chromatogram.getDate(); - if(date != null) { - GregorianCalendar calendar = new GregorianCalendar(); - calendar.setTime(date); - run.setStartTimeStamp(DatatypeFactory.newInstance().newXMLGregorianCalendar(calendar)); - } - MzMLType mzML = new MzMLType(); - mzML.setId(chromatogram.getFile().getName()); - // - CVListType cvList = new CVListType(); - cvList.setCount(BigInteger.valueOf(2)); - cvList.getCv().add(MS); - cvList.getCv().add(UO); - mzML.setCvList(cvList); - // - mzML.setFileDescription(createFileDescription(chromatogram, sourceFileList)); - mzML.setInstrumentConfigurationList(instrumentConfigurationList); - mzML.setSoftwareList(softwareList); - mzML.setDataProcessingList(dataProcessingList); - mzML.setVersion(XmlReader110.VERSION); - mzML.setRun(run); - marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, "http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd"); - marshaller.marshal(mzML, file); - } catch(JAXBException e) { - logger.warn(e); - } catch(DatatypeConfigurationException e) { - logger.warn(e); - } - } - - private SourceFileListType createSourceFileList(IChromatogram chromatogram) { - - SourceFileListType sourceFileListType = new SourceFileListType(); - sourceFileListType.setCount(BigInteger.valueOf(1)); - File file = chromatogram.getFile(); - SourceFileType sourceFile = new SourceFileType(); - sourceFile.setLocation(file.getAbsolutePath()); - sourceFile.setId(file.getName()); - sourceFile.setName(file.getName()); - // - CVParamType cvParamSHA1 = new CVParamType(); - cvParamSHA1.setCvRef(MS); - cvParamSHA1.setAccession("MS:1000569"); - cvParamSHA1.setName("SHA-1"); - cvParamSHA1.setValue(calculateSHA1(file)); - sourceFile.getCvParam().add(cvParamSHA1); - // - if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.xxd.converter.supplier.chemclipse")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1003374"); - cvParamFileFormat.setName("Open Chromatography Binary OCB format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.mz5")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000560"); - cvParamFileFormat.setName("mz5 format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.cdf")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1002443"); - cvParamFileFormat.setName("Andi-CHROM format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.mzmlb")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000560"); - cvParamFileFormat.setName("mzMLb format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.shimadzu.lcd")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1003009"); - cvParamFileFormat.setName("Shimadzu Biotech LCD format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.waters.micromass")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000526"); - cvParamFileFormat.setName("Waters raw format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.absciex")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000562"); - cvParamFileFormat.setName("ABI WIFF format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.finnigan.raw")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000563"); - cvParamFileFormat.setName("Thermo RAW format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.msd.converter.supplier.mzdata")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000564"); - cvParamFileFormat.setName("PSI mzData format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.msd.converter.supplier.mzxml.chromatogram")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000566"); - cvParamFileFormat.setName("ISB mzXML format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.bruker.baf")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000815"); - cvParamFileFormat.setName("Bruker BAF format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.bruker.flex.chromatogram")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1000825"); - cvParamFileFormat.setName("Bruker FID format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.msd.converter.supplier.mgf")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1001062"); - cvParamFileFormat.setName("Mascot MGF format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.masshunter.msd")) { - CVParamType cvParamFileFormat = new CVParamType(); - cvParamFileFormat.setCvRef(MS); - cvParamFileFormat.setAccession("MS:1001509"); - cvParamFileFormat.setName("Agilent MassHunter format"); - cvParamFileFormat.setValue(""); - sourceFile.getCvParam().add(cvParamFileFormat); - sourceFileListType.setCount(BigInteger.valueOf(2)); - } - sourceFileListType.getSourceFile().add(sourceFile); - return sourceFileListType; - } - - private static String calculateSHA1(File file) { - - try (FileInputStream fis = new FileInputStream(file)) { - return DigestUtils.sha1Hex(fis); - } catch(IOException e) { - logger.warn(e); - } - return ""; - } - - private FileDescriptionType createFileDescription(IChromatogramMSD chromatogram, SourceFileListType sourceFiles) { - - FileDescriptionType fileDescriptionType = new FileDescriptionType(); - fileDescriptionType.setSourceFileList(sourceFiles); - ParamGroupType fileContent = new ParamGroupType(); - // - IScanMSD scanMSD = (IScanMSD)chromatogram.getScan(1); - IRegularMassSpectrum massSpectrum = (IRegularMassSpectrum)scanMSD; - // - CVParamType cvParamSpectrum = new CVParamType(); - if(massSpectrum.getMassSpectrometer() == 1) { - cvParamSpectrum.setCvRef(MS); - cvParamSpectrum.setAccession("MS:1000579"); - cvParamSpectrum.setName("MS1 spectrum"); - } else { - cvParamSpectrum.setCvRef(MS); - cvParamSpectrum.setAccession("MS:1000580"); - cvParamSpectrum.setName("MSn spectrum"); - } - cvParamSpectrum.setValue(""); - fileContent.getCvParam().add(cvParamSpectrum); - // - CVParamType cvParamSpectrumType = new CVParamType(); - if(massSpectrum.getMassSpectrumType() == 0) { - cvParamSpectrumType.setCvRef(MS); - cvParamSpectrumType.setAccession("MS:1000127"); - cvParamSpectrumType.setName("centroid spectrum"); - } else if(massSpectrum.getMassSpectrumType() == 1) { - cvParamSpectrumType.setCvRef(MS); - cvParamSpectrumType.setAccession("MS:1000128"); - cvParamSpectrumType.setName("profile spectrum"); - } - cvParamSpectrumType.setValue(""); - fileContent.getCvParam().add(cvParamSpectrumType); - fileDescriptionType.setFileContent(fileContent); - // - if(!chromatogram.getOperator().isEmpty()) { - ParamGroupType paramGroupType = new ParamGroupType(); - CVParamType cvParam = new CVParamType(); - cvParam.setCvRef(MS); - cvParam.setAccession("MS:1000586"); - cvParam.setName("contact name"); - cvParam.setValue(chromatogram.getOperator()); - paramGroupType.getCvParam().add(cvParam); - fileDescriptionType.getContact().add(paramGroupType); - } - return fileDescriptionType; - } - - private SoftwareListType createSoftwareList() { - - SoftwareListType softwareList = new SoftwareListType(); - softwareList.setCount(BigInteger.valueOf(1)); - SoftwareType software = new SoftwareType(); - IProduct product = Platform.getProduct(); - software.setId("Unknown"); - if(product != null) { - software.setId(product.getName()); - Version version = product.getDefiningBundle().getVersion(); - software.setVersion(version.getMajor() + "." + version.getMinor() + "." + version.getMicro()); - if(product.getName().equals("ChemClipse")) { - CVParamType cvParamSoftware = new CVParamType(); - cvParamSoftware.setCvRef(MS); - cvParamSoftware.setAccession("MS:1003376"); - cvParamSoftware.setName("ChemClipse"); - cvParamSoftware.setValue(""); - software.getCvParam().add(cvParamSoftware); - } - if(product.getName().equals("OpenChrom")) { - CVParamType cvParamSoftware = new CVParamType(); - cvParamSoftware.setCvRef(MS); - cvParamSoftware.setAccession("MS:1003377"); - cvParamSoftware.setName("OpenChrom"); - cvParamSoftware.setValue(""); - software.getCvParam().add(cvParamSoftware); - } - } - softwareList.getSoftware().add(software); - return softwareList; - } - - private InstrumentConfigurationListType createInstrumentConfigurationList(SoftwareType software) { - - InstrumentConfigurationListType instrumentConfigurationList = new InstrumentConfigurationListType(); - instrumentConfigurationList.setCount(BigInteger.valueOf(1)); - InstrumentConfigurationType instrumentConfiguration = new InstrumentConfigurationType(); - instrumentConfiguration.setId("unknown"); - SoftwareRefType softwareRef = new SoftwareRefType(); - softwareRef.setRef(software); - instrumentConfiguration.setSoftwareRef(softwareRef); - instrumentConfigurationList.getInstrumentConfiguration().add(instrumentConfiguration); - return instrumentConfigurationList; - } - - private DataProcessingListType createDataProcessingList(SoftwareType software) { - - DataProcessingListType dataProcessingList = new DataProcessingListType(); - dataProcessingList.setCount(BigInteger.valueOf(1)); - DataProcessingType dataProcessing = new DataProcessingType(); - dataProcessing.setId(Activator.getContext().getBundle().getSymbolicName()); - ProcessingMethodType processingMethod = new ProcessingMethodType(); - processingMethod.setSoftwareRef(software); - processingMethod.setOrder(BigInteger.valueOf(1)); - CVParamType exportParam = new CVParamType(); - exportParam.setCvRef(MS); - exportParam.setAccession("MS:1000544"); - exportParam.setName("Conversion to mzML"); - exportParam.setValue(""); - processingMethod.getCvParam().add(exportParam); - dataProcessing.getProcessingMethod().add(processingMethod); - dataProcessingList.getDataProcessing().add(dataProcessing); - return dataProcessingList; - } - - private static CVType createMS() { - - CVType cvTypeMS = new CVType(); - cvTypeMS.setId("MS"); - cvTypeMS.setFullName("Proteomics Standards Initiative Mass Spectrometry Ontology"); - cvTypeMS.setVersion("4.1.123"); - cvTypeMS.setURI("https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.123/psi-ms.obo"); - return cvTypeMS; - } - - private static CVType createUO() { - - CVType cvTypeUnit = new CVType(); - cvTypeUnit.setId("UO"); - cvTypeUnit.setFullName("Unit Ontology"); - cvTypeUnit.setVersion("2023:05:23"); - cvTypeUnit.setURI("https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/v2023-05-23/unit-ontology.obo"); - return cvTypeUnit; - } -} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion10.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion10.java similarity index 81% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion10.java rename to chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion10.java index c87c99e15c..d0baed31da 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion10.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion10.java @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io; +package org.eclipse.chemclipse.msd.converter.supplier.mzml.io; import java.io.File; import java.io.IOException; @@ -24,24 +24,6 @@ import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorChromatogram; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.BinaryReader10; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader10; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.BinaryDataArrayType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.CVParamType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.ChromatogramType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.DataProcessingType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.InstrumentConfigurationType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.MzMLType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.ParamGroupType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.PrecursorType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.ProcessingMethodType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.RunType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.SampleListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.SampleType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.ScanType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.SoftwareType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.SpectrumType; import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD; import org.eclipse.chemclipse.msd.model.core.IIonTransition; import org.eclipse.chemclipse.msd.model.core.IIonTransitionGroup; @@ -50,6 +32,23 @@ import org.eclipse.chemclipse.msd.model.implementation.IonTransition; import org.eclipse.chemclipse.msd.model.implementation.VendorMassSpectrum; import org.eclipse.chemclipse.support.history.EditInformation; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.BinaryReader10; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader10; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.ChromatogramType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.DataProcessingType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.InstrumentConfigurationType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.ParamGroupType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.PrecursorType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.ProcessingMethodType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.RunType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SampleListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SampleType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.ScanType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SoftwareType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SpectrumType; import org.eclipse.core.runtime.IProgressMonitor; import org.xml.sax.SAXException; @@ -84,7 +83,7 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t } } } - XmlReader.addIons(intensities, retentionTimes, chromatogram); + XmlMassSpectrumReader.addIons(intensities, retentionTimes, chromatogram); } catch(JAXBException e) { logger.warn(e); } catch(SAXException e) { @@ -201,7 +200,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep intensities = binaryData.getValue(); } } - XmlReader.addIons(intensities, mzs, massSpectrum); + XmlMassSpectrumReader.addIons(intensities, mzs, massSpectrum); chromatogram.addScan(massSpectrum); } } catch(DataFormatException e) { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion110.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java similarity index 66% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion110.java rename to chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java index b115f7367a..ba4cd6fe5c 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/ChromatogramReaderVersion110.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io; +package org.eclipse.chemclipse.msd.converter.supplier.mzml.io; import java.io.File; import java.io.IOException; @@ -24,24 +24,6 @@ import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorChromatogram; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.BinaryReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.BinaryDataArrayType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVParamType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ChromatogramType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.DataProcessingType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.InstrumentConfigurationType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.MzMLType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ParamGroupType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.PrecursorType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ProcessingMethodType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.RunType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SampleListType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SampleType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ScanType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SoftwareType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SpectrumType; import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD; import org.eclipse.chemclipse.msd.model.core.IIonTransition; import org.eclipse.chemclipse.msd.model.core.IIonTransitionGroup; @@ -49,7 +31,18 @@ import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum; import org.eclipse.chemclipse.msd.model.implementation.IonTransition; import org.eclipse.chemclipse.msd.model.implementation.VendorMassSpectrum; -import org.eclipse.chemclipse.support.history.EditInformation; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.BinaryReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.MetadataReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ChromatogramType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ParamGroupType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.PrecursorType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.RunType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ScanType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumType; import org.eclipse.core.runtime.IProgressMonitor; import org.xml.sax.SAXException; @@ -68,8 +61,9 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t // try { chromatogram = new VendorChromatogram(); - // - RunType run = XmlReader110.getMzML(file).getRun(); + MzMLType mzML = XmlReader110.getMzML(file); + MetadataReader110.readMetadata(mzML, chromatogram); + RunType run = mzML.getRun(); for(ChromatogramType chromatogramType : run.getChromatogramList().getChromatogram()) { if(chromatogramType.getId().equals("TIC")) { if(chromatogramType.getCvParam().stream().anyMatch(n -> n.getAccession().equals("MS:1000235") && n.getName().equals("total ion current chromatogram"))) { @@ -84,7 +78,7 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t } } } - XmlReader.addIons(intensities, retentionTimes, chromatogram); + XmlMassSpectrumReader.addIons(intensities, retentionTimes, chromatogram); } catch(JAXBException e) { logger.warn(e); } catch(SAXException e) { @@ -94,7 +88,6 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t } catch(DataFormatException e) { logger.warn(e); } - // return chromatogram; } @@ -110,38 +103,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep chromatogram.setFile(file); // MzMLType mzML = XmlReader110.getMzML(file); - for(ParamGroupType contact : mzML.getFileDescription().getContact()) { - for(CVParamType cvParam : contact.getCvParam()) { - if(chromatogram.getOperator().isEmpty()) { - chromatogram.setOperator(cvParam.getValue()); - } else { - chromatogram.setOperator(String.join(", ", chromatogram.getOperator(), cvParam.getValue())); - } - } - } - SampleListType sampleList = mzML.getSampleList(); - if(sampleList != null) { - for(SampleType sample : sampleList.getSample()) { - chromatogram.setSampleName(sample.getName()); - } - } - for(InstrumentConfigurationType instrument : mzML.getInstrumentConfigurationList().getInstrumentConfiguration()) { - for(CVParamType cvParam : instrument.getCvParam()) { - if(cvParam.getAccession().equals("MS:1000554")) { - chromatogram.setInstrument(cvParam.getName()); - } - } - } - for(DataProcessingType dataProcessing : mzML.getDataProcessingList().getDataProcessing()) { - for(ProcessingMethodType processingMethod : dataProcessing.getProcessingMethod()) { - SoftwareType software = (SoftwareType)processingMethod.getSoftwareRef(); - for(CVParamType cvParam : processingMethod.getCvParam()) { - String operation = cvParam.getName(); - String editor = software.getId() + " " + software.getVersion(); - chromatogram.getEditHistory().add(new EditInformation(operation, editor)); - } - } - } + MetadataReader110.readMetadata(mzML, chromatogram); RunType run = mzML.getRun(); for(SpectrumType spectrum : run.getSpectrumList().getSpectrum()) { IRegularMassSpectrum massSpectrum = new VendorMassSpectrum(); @@ -199,7 +161,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep intensities = binaryData.getValue(); } } - XmlReader.addIons(intensities, mzs, massSpectrum); + XmlMassSpectrumReader.addIons(intensities, mzs, massSpectrum); chromatogram.addScan(massSpectrum); } } catch(DataFormatException e) { @@ -211,7 +173,6 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep } catch(JAXBException e) { logger.warn(e); } - // return chromatogram; } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramWriterVersion110.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramWriterVersion110.java new file mode 100644 index 0000000000..789407bb86 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramWriterVersion110.java @@ -0,0 +1,508 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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.mzml.io; + +import java.io.File; +import java.io.IOException; +import java.math.BigInteger; +import java.util.List; + +import javax.xml.datatype.DatatypeConfigurationException; +import javax.xml.datatype.XMLGregorianCalendar; + +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.IChromatogram; +import org.eclipse.chemclipse.model.core.IChromatogramOverview; +import org.eclipse.chemclipse.model.core.IScan; +import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter; +import org.eclipse.chemclipse.msd.converter.supplier.mzml.Activator; +import org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences.PreferenceSupplier; +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.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlWriter110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ChromatogramListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ChromatogramType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.DataProcessingListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.DataProcessingType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.FileDescriptionType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.InstrumentConfigurationListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.InstrumentConfigurationType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ObjectFactory; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ParamGroupType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ProcessingMethodType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.RunType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ScanListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ScanType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareRefType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SourceFileListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SourceFileType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumType; +import org.eclipse.core.runtime.IProgressMonitor; + +import jakarta.xml.bind.JAXBContext; +import jakarta.xml.bind.JAXBException; +import jakarta.xml.bind.Marshaller; + +public class ChromatogramWriterVersion110 extends AbstractChromatogramWriter implements IChromatogramMSDWriter { + + private static final Logger logger = Logger.getLogger(ChromatogramWriterVersion110.class); + + @Override + public void writeChromatogram(File file, IChromatogramMSD chromatogram, IProgressMonitor monitor) throws FileIsNotWriteableException, IOException { + + try { + JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class); + Marshaller marshaller = jaxbContext.createMarshaller(); + // + RunType run = new RunType(); + SoftwareListType softwareList = XmlWriter110.createSoftwareList(); + InstrumentConfigurationListType instrumentConfigurationList = createInstrumentConfigurationList(softwareList.getSoftware().get(0)); + run.setDefaultInstrumentConfigurationRef(instrumentConfigurationList.getInstrumentConfiguration().get(0)); + SourceFileListType sourceFileList = createSourceFileList(chromatogram); + run.setDefaultSourceFileRef(sourceFileList.getSourceFile().get(0)); + run.setId(chromatogram.getName()); + // + DataProcessingListType dataProcessingList = createDataProcessingList(softwareList.getSoftware().get(0)); + SpectrumListType spectrumList = new SpectrumListType(); + spectrumList.setDefaultDataProcessingRef(dataProcessingList.getDataProcessing().get(0)); + ChromatogramListType chromatogramList = new ChromatogramListType(); + chromatogramList.setDefaultDataProcessingRef(dataProcessingList.getDataProcessing().get(0)); + chromatogramList.setCount(BigInteger.valueOf(1)); // TODO export referenced chromatograms + // + int scans = chromatogram.getNumberOfScans(); + spectrumList.setCount(BigInteger.valueOf(scans)); + float[] totalSignals = new float[scans]; + float[] retentionTimes = new float[scans]; + writeScans(chromatogram, totalSignals, retentionTimes, spectrumList); + run.setSpectrumList(spectrumList); + // + ChromatogramType tic = createTIC(totalSignals, retentionTimes); + chromatogramList.getChromatogram().add(tic); + run.setChromatogramList(chromatogramList); + // + XMLGregorianCalendar date = XmlWriter110.createDate(chromatogram); + if(date != null) { + run.setStartTimeStamp(date); + } + MzMLType mzML = new MzMLType(); + mzML.setId(chromatogram.getFile().getName()); + // + CVListType cvList = new CVListType(); + cvList.setCount(BigInteger.valueOf(2)); + cvList.getCv().add(XmlWriter110.MS); + cvList.getCv().add(XmlWriter110.UO); + mzML.setCvList(cvList); + // + mzML.setFileDescription(createFileDescription(chromatogram, sourceFileList)); + mzML.setInstrumentConfigurationList(instrumentConfigurationList); + mzML.setSoftwareList(softwareList); + mzML.setDataProcessingList(dataProcessingList); + mzML.setVersion(XmlReader110.VERSION); + mzML.setRun(run); + marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, "http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd"); + marshaller.marshal(mzML, file); + } catch(JAXBException e) { + logger.warn(e); + } catch(DatatypeConfigurationException e) { + logger.warn(e); + } + } + + private ChromatogramType createTIC(float[] totalSignals, float[] retentionTimes) { + + BinaryDataArrayListType binaryDataArrayList = new BinaryDataArrayListType(); + binaryDataArrayList.setCount(BigInteger.valueOf(2)); + boolean compression = PreferenceSupplier.getChromatogramSaveCompression(); + // + BinaryDataArrayType totalSignalsBinaryDataArrayType = XmlWriter110.createBinaryData(totalSignals, compression); + totalSignalsBinaryDataArrayType.getCvParam().add(XmlWriter110.createIntensityArrayType()); + binaryDataArrayList.getBinaryDataArray().add(totalSignalsBinaryDataArrayType); + // + BinaryDataArrayType retentionTimesBinaryDataArrayType = XmlWriter110.createBinaryData(retentionTimes, compression); + retentionTimesBinaryDataArrayType.getCvParam().add(XmlWriter110.createRetentionTimeType()); + binaryDataArrayList.getBinaryDataArray().add(retentionTimesBinaryDataArrayType); + // + ChromatogramType tic = new ChromatogramType(); + tic.setId("tic"); + tic.setIndex(BigInteger.valueOf(0)); + tic.getCvParam().add(createTotalIonCurrrentType()); + tic.setDefaultArrayLength(totalSignals.length); + tic.setBinaryDataArrayList(binaryDataArrayList); + return tic; + } + + private void writeScans(IChromatogramMSD chromatogram, float[] totalSignals, float[] retentionTimes, SpectrumListType spectrumList) { + + int i = 0; + for(IScan scan : chromatogram.getScans()) { + SpectrumType spectrum = new SpectrumType(); + spectrum.setId("scan=" + scan.getScanNumber()); + spectrum.setIndex(BigInteger.valueOf((scan.getScanNumber() - 1))); + // TIC + totalSignals[i] = scan.getTotalSignal(); + retentionTimes[i] = (float)(scan.getRetentionTime() / IChromatogramOverview.SECOND_CORRELATION_FACTOR); + i++; + spectrum.getCvParam().add(createTotalIonCurrentType(scan)); + IScanMSD scanMSD = (IScanMSD)scan; + // full spectra + // + spectrum.getCvParam().add(createBasePeakMassType(scanMSD)); + spectrum.getCvParam().add(createBasePeakIntensity(scanMSD)); + // + List ionList = scanMSD.getIons(); + double[] ions = new double[ionList.size()]; + float[] abundances = new float[ionList.size()]; + int j = 0; + for(IIon ion : ionList) { + ions[j] = ion.getIon(); + abundances[j] = ion.getAbundance(); + j++; + } + BinaryDataArrayListType binaryDataArrayList = new BinaryDataArrayListType(); + binaryDataArrayList.setCount(BigInteger.valueOf(2)); + // + boolean compression = PreferenceSupplier.getChromatogramSaveCompression(); + BinaryDataArrayType ionsBinaryDataArrayType = XmlWriter110.createBinaryData(ions, compression); + ionsBinaryDataArrayType.getCvParam().add(createIonType()); + binaryDataArrayList.getBinaryDataArray().add(ionsBinaryDataArrayType); + // + BinaryDataArrayType abundancesBinaryDataArrayType = XmlWriter110.createBinaryData(abundances, compression); + abundancesBinaryDataArrayType.getCvParam().add(XmlWriter110.createIntensityArrayType()); + binaryDataArrayList.getBinaryDataArray().add(abundancesBinaryDataArrayType); + // + ScanType scanType = new ScanType(); + scanType.getCvParam().add(createScanStartTimeType(scanMSD)); + // + ScanListType scanList = new ScanListType(); + scanList.getCvParam().add(createCombinationType()); + scanList.setCount(BigInteger.valueOf(1)); + scanList.getScan().add(scanType); + // + spectrum.setScanList(scanList); + spectrum.setBinaryDataArrayList(binaryDataArrayList); + IRegularMassSpectrum massSpectrum = (IRegularMassSpectrum)scanMSD; + spectrum.getCvParam().add(createSpectrumDimension(massSpectrum)); + spectrum.getCvParam().add(createSpectrumLevel(massSpectrum)); + spectrum.getCvParam().add(createSpectrumType(massSpectrum)); + spectrum.setDefaultArrayLength(ions.length); + spectrumList.getSpectrum().add(spectrum); + } + } + + private CVParamType createBasePeakIntensity(IScanMSD scanMSD) { + + CVParamType cvParamBasePeakIntensity = new CVParamType(); + cvParamBasePeakIntensity.setCvRef(XmlWriter110.MS); + cvParamBasePeakIntensity.setAccession("MS:1000505"); + cvParamBasePeakIntensity.setName("base peak intensity"); + cvParamBasePeakIntensity.setUnitCvRef(XmlWriter110.MS); + cvParamBasePeakIntensity.setUnitAccession("MS:1000131"); + cvParamBasePeakIntensity.setUnitName("number of detector counts"); + cvParamBasePeakIntensity.setValue(String.valueOf(scanMSD.getBasePeakAbundance())); + return cvParamBasePeakIntensity; + } + + private CVParamType createBasePeakMassType(IScanMSD scanMSD) { + + CVParamType cvParamBasePeak = new CVParamType(); + cvParamBasePeak.setCvRef(XmlWriter110.MS); + cvParamBasePeak.setAccession("MS:1000504"); + cvParamBasePeak.setName("base peak m/z"); + cvParamBasePeak.setUnitCvRef(XmlWriter110.MS); + cvParamBasePeak.setUnitAccession("MS:1000040"); + cvParamBasePeak.setUnitName("m/z"); + cvParamBasePeak.setValue(String.valueOf(scanMSD.getBasePeak())); + return cvParamBasePeak; + } + + private CVParamType createTotalIonCurrentType(IScan scan) { + + CVParamType cvParamTotalIonCurrent = new CVParamType(); + cvParamTotalIonCurrent.setCvRef(XmlWriter110.MS); + cvParamTotalIonCurrent.setAccession("MS:1000285"); + cvParamTotalIonCurrent.setName("total ion current"); + cvParamTotalIonCurrent.setValue(String.valueOf(scan.getTotalSignal())); + return cvParamTotalIonCurrent; + } + + private CVParamType createCombinationType() { + + CVParamType cvParamCombination = new CVParamType(); + cvParamCombination.setCvRef(XmlWriter110.MS); + cvParamCombination.setAccession("MS:1000795"); + cvParamCombination.setName("no combination"); + return cvParamCombination; + } + + private CVParamType createTotalIonCurrrentType() { + + CVParamType cvParam = new CVParamType(); + cvParam.setCvRef(XmlWriter110.MS); + cvParam.setAccession("MS:1000235"); + cvParam.setName("total ion current chromatogram"); + cvParam.setValue(""); + return cvParam; + } + + private CVParamType createScanStartTimeType(IScan scan) { + + CVParamType cvParamScanStartTime = new CVParamType(); + cvParamScanStartTime.setCvRef(XmlWriter110.MS); + cvParamScanStartTime.setAccession("MS:1000016"); + cvParamScanStartTime.setName("scan start time"); + cvParamScanStartTime.setUnitCvRef(XmlWriter110.UO); + cvParamScanStartTime.setUnitAccession("UO:0000031"); + cvParamScanStartTime.setUnitName("minute"); + cvParamScanStartTime.setValue(String.valueOf(scan.getRetentionTime() / IChromatogramOverview.MINUTE_CORRELATION_FACTOR)); + return cvParamScanStartTime; + } + + private CVParamType createIonType() { + + CVParamType cvParamIons = new CVParamType(); + cvParamIons.setCvRef(XmlWriter110.MS); + cvParamIons.setAccession("MS:1000514"); + cvParamIons.setName("m/z array"); + cvParamIons.setUnitCvRef(XmlWriter110.MS); + cvParamIons.setUnitAccession("MS:1000040"); + cvParamIons.setUnitName("m/z"); + return cvParamIons; + } + + private SourceFileListType createSourceFileList(IChromatogram chromatogram) { + + SourceFileListType sourceFileListType = new SourceFileListType(); + sourceFileListType.setCount(BigInteger.valueOf(1)); + SourceFileType sourceFile = XmlWriter110.createSourceFile(chromatogram); + // + if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.xxd.converter.supplier.chemclipse")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1003374"); + cvParamFileFormat.setName("Open Chromatography Binary OCB format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.mz5")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000560"); + cvParamFileFormat.setName("mz5 format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.cdf")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1002443"); + cvParamFileFormat.setName("Andi-CHROM format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.mzmlb")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000560"); + cvParamFileFormat.setName("mzMLb format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.shimadzu.lcd")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1003009"); + cvParamFileFormat.setName("Shimadzu Biotech LCD format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.waters.micromass")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000526"); + cvParamFileFormat.setName("Waters raw format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.absciex")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000562"); + cvParamFileFormat.setName("ABI WIFF format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.finnigan.raw")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000563"); + cvParamFileFormat.setName("Thermo RAW format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.msd.converter.supplier.mzdata")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000564"); + cvParamFileFormat.setName("PSI mzData format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.msd.converter.supplier.mzxml.chromatogram")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000566"); + cvParamFileFormat.setName("ISB mzXML format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.bruker.baf")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000815"); + cvParamFileFormat.setName("Bruker BAF format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.bruker.flex.chromatogram")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1000825"); + cvParamFileFormat.setName("Bruker FID format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.msd.converter.supplier.mgf")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1001062"); + cvParamFileFormat.setName("Mascot MGF format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } else if(chromatogram.getConverterId().equals("net.openchrom.msd.converter.supplier.masshunter.msd")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1001509"); + cvParamFileFormat.setName("Agilent MassHunter format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } + sourceFileListType.getSourceFile().add(sourceFile); + return sourceFileListType; + } + + private FileDescriptionType createFileDescription(IChromatogramMSD chromatogram, SourceFileListType sourceFiles) { + + FileDescriptionType fileDescriptionType = new FileDescriptionType(); + fileDescriptionType.setSourceFileList(sourceFiles); + ParamGroupType fileContent = new ParamGroupType(); + IScanMSD scanMSD = (IScanMSD)chromatogram.getScan(1); + IRegularMassSpectrum massSpectrum = (IRegularMassSpectrum)scanMSD; + fileContent.getCvParam().add(createSpectrumDimension(massSpectrum)); + fileContent.getCvParam().add(createSpectrumType(massSpectrum)); + fileDescriptionType.setFileContent(fileContent); + ParamGroupType paramGroupType = XmlWriter110.getOperator(chromatogram); + if(paramGroupType != null) { + fileDescriptionType.getContact().add(paramGroupType); + } + return fileDescriptionType; + } + + private CVParamType createSpectrumDimension(IRegularMassSpectrum massSpectrum) { + + CVParamType cvParamSpectrum = new CVParamType(); + if(massSpectrum.getMassSpectrometer() == 1) { + cvParamSpectrum.setCvRef(XmlWriter110.MS); + cvParamSpectrum.setAccession("MS:1000579"); + cvParamSpectrum.setName("MS1 spectrum"); + } else { + cvParamSpectrum.setCvRef(XmlWriter110.MS); + cvParamSpectrum.setAccession("MS:1000580"); + cvParamSpectrum.setName("MSn spectrum"); + } + cvParamSpectrum.setValue(""); + return cvParamSpectrum; + } + + private CVParamType createSpectrumLevel(IRegularMassSpectrum massSpectrum) { + + CVParamType cvParamLevel = new CVParamType(); + cvParamLevel.setCvRef(XmlWriter110.MS); + cvParamLevel.setAccession("MS:1000511"); + cvParamLevel.setName("ms level"); + cvParamLevel.setValue(String.valueOf(massSpectrum.getMassSpectrometer())); + return cvParamLevel; + } + + private CVParamType createSpectrumType(IRegularMassSpectrum massSpectrum) { + + CVParamType cvParamSpectrumType = new CVParamType(); + if(massSpectrum.getMassSpectrumType() == 0) { + cvParamSpectrumType.setCvRef(XmlWriter110.MS); + cvParamSpectrumType.setAccession("MS:1000127"); + cvParamSpectrumType.setName("centroid spectrum"); + } else if(massSpectrum.getMassSpectrumType() == 1) { + cvParamSpectrumType.setCvRef(XmlWriter110.MS); + cvParamSpectrumType.setAccession("MS:1000128"); + cvParamSpectrumType.setName("profile spectrum"); + } + cvParamSpectrumType.setValue(""); + return cvParamSpectrumType; + } + + private InstrumentConfigurationListType createInstrumentConfigurationList(SoftwareType software) { + + InstrumentConfigurationListType instrumentConfigurationList = new InstrumentConfigurationListType(); + instrumentConfigurationList.setCount(BigInteger.valueOf(1)); + InstrumentConfigurationType instrumentConfiguration = new InstrumentConfigurationType(); + instrumentConfiguration.setId("unknown"); + SoftwareRefType softwareRef = new SoftwareRefType(); + softwareRef.setRef(software); + instrumentConfiguration.setSoftwareRef(softwareRef); + instrumentConfigurationList.getInstrumentConfiguration().add(instrumentConfiguration); + return instrumentConfigurationList; + } + + private DataProcessingListType createDataProcessingList(SoftwareType software) { + + DataProcessingListType dataProcessingList = new DataProcessingListType(); + dataProcessingList.setCount(BigInteger.valueOf(1)); + DataProcessingType dataProcessing = new DataProcessingType(); + dataProcessing.setId(Activator.getContext().getBundle().getSymbolicName()); + ProcessingMethodType processingMethod = new ProcessingMethodType(); + processingMethod.setSoftwareRef(software); + processingMethod.setOrder(BigInteger.valueOf(1)); + CVParamType exportParam = new CVParamType(); + exportParam.setCvRef(XmlWriter110.MS); + exportParam.setAccession("MS:1000544"); + exportParam.setName("Conversion to mzML"); + exportParam.setValue(""); + processingMethod.getCvParam().add(exportParam); + dataProcessing.getProcessingMethod().add(processingMethod); + dataProcessingList.getDataProcessing().add(dataProcessing); + return dataProcessingList; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/MassSpectrumReaderVersion110.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/MassSpectrumReaderVersion110.java similarity index 78% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/MassSpectrumReaderVersion110.java rename to chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/MassSpectrumReaderVersion110.java index 247ef7559d..aadd648aec 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/io/MassSpectrumReaderVersion110.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/MassSpectrumReaderVersion110.java @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io; +package org.eclipse.chemclipse.msd.converter.supplier.mzml.io; import java.io.File; import java.io.IOException; @@ -23,19 +23,18 @@ import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorMassSpectra; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorMassSpectra; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.BinaryReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.BinaryDataArrayType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVParamType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.FileDescriptionType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.MzMLType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ParamGroupType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.RunType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.SpectrumType; import org.eclipse.chemclipse.msd.model.core.IMassSpectra; import org.eclipse.chemclipse.msd.model.core.IStandaloneMassSpectrum; import org.eclipse.chemclipse.msd.model.implementation.VendorMassSpectrum; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.BinaryReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.FileDescriptionType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ParamGroupType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.RunType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumType; import org.eclipse.core.runtime.IProgressMonitor; import org.xml.sax.SAXException; @@ -91,7 +90,7 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException } } } - XmlReader.addIons(mzs, intensities, massSpectrum); + XmlMassSpectrumReader.addIons(mzs, intensities, massSpectrum); } catch(SAXException e) { logger.warn(e); } catch(JAXBException e) { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/XmlMassSpectrumReader.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java rename to chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/XmlMassSpectrumReader.java index 855b1d2b24..a21045835d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/XmlMassSpectrumReader.java @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter; +package org.eclipse.chemclipse.msd.converter.supplier.mzml.io; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram; import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorIon; @@ -17,9 +17,9 @@ import org.eclipse.chemclipse.msd.model.core.IIon; import org.eclipse.chemclipse.msd.model.core.IScanMSD; -public class XmlReader { +public class XmlMassSpectrumReader { - private XmlReader() { + private XmlMassSpectrumReader() { } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/preferences/PreferenceSupplier.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/preferences/PreferenceSupplier.java index 9030788069..e8fc6b3032 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/preferences/PreferenceSupplier.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/preferences/PreferenceSupplier.java @@ -13,9 +13,9 @@ package org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences; import org.eclipse.chemclipse.msd.converter.supplier.mzml.Activator; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110; import org.eclipse.chemclipse.support.preferences.AbstractPreferenceSupplier; import org.eclipse.chemclipse.support.preferences.IPreferenceSupplier; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; public class PreferenceSupplier extends AbstractPreferenceSupplier implements IPreferenceSupplier { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.arw/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.arw/META-INF/MANIFEST.MF index 3a9c84f683..c505a974d0 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.arw/META-INF/MANIFEST.MF +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.arw/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Automatic-Module-Name: org.eclipse.chemclipse.wsd.converter.supplier.arw Eclipse-RegisterBuddy: org.eclipse.chemclipse.model, org.eclipse.chemclipse.wsd.model Bundle-ManifestVersion: 2 -Bundle-Name: ARW (DAD) Converter +Bundle-Name: ARW (HPLC-DAD) Converter Bundle-SymbolicName: org.eclipse.chemclipse.wsd.converter.supplier.arw;singleton:=true Bundle-Version: 0.9.0.qualifier Bundle-Activator: org.eclipse.chemclipse.wsd.converter.supplier.arw.Activator diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.classpath b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.classpath new file mode 100644 index 0000000000..81fe078c20 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.classpath @@ -0,0 +1,7 @@ + + + + + + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.gitignore b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.gitignore new file mode 100644 index 0000000000..5e56e040ec --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.gitignore @@ -0,0 +1 @@ +/bin diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.project b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.project new file mode 100644 index 0000000000..defcfe61a8 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.project @@ -0,0 +1,28 @@ + + + org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.pde.ManifestBuilder + + + + + org.eclipse.pde.SchemaBuilder + + + + + + org.eclipse.pde.PluginNature + org.eclipse.jdt.core.javanature + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.settings/org.eclipse.core.resources.prefs b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 0000000000..801fab74d0 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +encoding/=utf8 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.settings/org.eclipse.jdt.core.prefs b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000000..9154beff79 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,7 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=17 +org.eclipse.jdt.core.compiler.compliance=17 +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.source=17 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF new file mode 100644 index 0000000000..d6a8796f46 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF @@ -0,0 +1,17 @@ +Manifest-Version: 1.0 +Automatic-Module-Name: org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui +Bundle-ManifestVersion: 2 +Bundle-Name: mzML HPLC-DAD UI +Bundle-SymbolicName: org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui;singleton:=true +Bundle-Version: 0.9.0.qualifier +Bundle-Activator: org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui.Activator +Bundle-Vendor: ChemClipse +Require-Bundle: org.eclipse.ui, + org.eclipse.core.runtime, + org.eclipse.chemclipse.support.ui, + org.eclipse.chemclipse.xxd.process.ui, + org.eclipse.chemclipse.rcp.ui.icons, + org.eclipse.chemclipse.ux.extension.xxd.ui;bundle-version="0.9.0", + org.eclipse.chemclipse.wsd.converter.supplier.mzml;bundle-version="0.9.0" +Bundle-RequiredExecutionEnvironment: JavaSE-17 +Bundle-ActivationPolicy: lazy diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/OSGI-INF/l10n/bundle_en.properties b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/OSGI-INF/l10n/bundle_en.properties new file mode 100644 index 0000000000..70d792b0b8 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/OSGI-INF/l10n/bundle_en.properties @@ -0,0 +1,12 @@ +############################################################################### +# Copyright (c) 2015, 2017 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 +############################################################################### +#Properties file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/build.properties b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/build.properties new file mode 100644 index 0000000000..948f0bdf02 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/build.properties @@ -0,0 +1,6 @@ +source.. = src/ +output.. = bin/ +bin.includes = META-INF/,\ + .,\ + OSGI-INF/,\ + plugin.xml diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/plugin.xml b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/plugin.xml new file mode 100644 index 0000000000..af197c082e --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/plugin.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/Activator.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/Activator.java new file mode 100644 index 0000000000..c2c92a7580 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/Activator.java @@ -0,0 +1,63 @@ +/******************************************************************************* + * Copyright (c) 2013, 2024 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 org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui; + +import org.eclipse.ui.plugin.AbstractUIPlugin; +import org.osgi.framework.BundleContext; + +/** + * The activator class controls the plug-in life cycle + */ +public class Activator extends AbstractUIPlugin { + + // The shared instance + private static Activator plugin; + + /** + * The constructor + */ + public Activator() { + + } + + /* + * (non-Javadoc) + * @see org.eclipse.ui.plugin.AbstractUIPlugin#start(org.osgi.framework.BundleContext) + */ + @Override + public void start(BundleContext context) throws Exception { + + super.start(context); + plugin = this; + } + + /* + * (non-Javadoc) + * @see org.eclipse.ui.plugin.AbstractUIPlugin#stop(org.osgi.framework.BundleContext) + */ + @Override + public void stop(BundleContext context) throws Exception { + + plugin = null; + super.stop(context); + } + + /** + * Returns the shared instance + * + * @return the shared instance + */ + public static Activator getDefault() { + + return plugin; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/icon/MenuIcon.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/icon/MenuIcon.java new file mode 100644 index 0000000000..ab006d5dcb --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/icon/MenuIcon.java @@ -0,0 +1,27 @@ +/******************************************************************************* + * Copyright (c) 2022, 2024 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.wsd.converter.supplier.mzml.ui.icon; + +import org.eclipse.chemclipse.rcp.ui.icons.core.ApplicationImageFactory; +import org.eclipse.chemclipse.rcp.ui.icons.core.IApplicationImage; +import org.eclipse.chemclipse.rcp.ui.icons.core.IApplicationImageProvider; +import org.eclipse.chemclipse.xxd.process.ui.menu.IMenuIcon; +import org.eclipse.swt.graphics.Image; + +public class MenuIcon implements IMenuIcon { + + @Override + public Image getImage() { + + return ApplicationImageFactory.getInstance().getImage(IApplicationImage.IMAGE_XML_FILE, IApplicationImageProvider.SIZE_16x16); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/preferences/PreferencePage.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/preferences/PreferencePage.java new file mode 100644 index 0000000000..a407a1d367 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/ui/preferences/PreferencePage.java @@ -0,0 +1,44 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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.wsd.converter.supplier.mzml.ui.preferences; + +import org.eclipse.chemclipse.support.ui.preferences.fieldeditors.SpacerFieldEditor; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.preferences.PreferenceSupplier; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui.Activator; +import org.eclipse.jface.preference.BooleanFieldEditor; +import org.eclipse.jface.preference.ComboFieldEditor; +import org.eclipse.jface.preference.FieldEditorPreferencePage; +import org.eclipse.ui.IWorkbench; +import org.eclipse.ui.IWorkbenchPreferencePage; + +public class PreferencePage extends FieldEditorPreferencePage implements IWorkbenchPreferencePage { + + public PreferencePage() { + + super(GRID); + setPreferenceStore(Activator.getDefault().getPreferenceStore()); + setDescription("mzML Converter"); + } + + @Override + public void createFieldEditors() { + + addField(new SpacerFieldEditor(getFieldEditorParent())); + addField(new ComboFieldEditor(PreferenceSupplier.P_CHROMATOGRAM_VERSION_SAVE, "Save (*.mzML) as version:", PreferenceSupplier.getChromatogramVersions(), getFieldEditorParent())); + addField(new BooleanFieldEditor(PreferenceSupplier.P_CHROMATOGRAM_SAVE_COMPRESSION, "Compress values", getFieldEditorParent())); + } + + @Override + public void init(IWorkbench workbench) { + + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.classpath b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.classpath new file mode 100644 index 0000000000..81fe078c20 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.classpath @@ -0,0 +1,7 @@ + + + + + + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.gitignore b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.gitignore new file mode 100644 index 0000000000..5e56e040ec --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.gitignore @@ -0,0 +1 @@ +/bin diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.project b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.project new file mode 100644 index 0000000000..c2efe570aa --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.project @@ -0,0 +1,28 @@ + + + org.eclipse.chemclipse.wsd.converter.supplier.mzml + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.pde.ManifestBuilder + + + + + org.eclipse.pde.SchemaBuilder + + + + + + org.eclipse.pde.PluginNature + org.eclipse.jdt.core.javanature + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.core.resources.prefs b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 0000000000..801fab74d0 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +encoding/=utf8 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.jdt.core.prefs b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000000..9154beff79 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,7 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=17 +org.eclipse.jdt.core.compiler.compliance=17 +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.source=17 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.pde.core.prefs b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.pde.core.prefs new file mode 100644 index 0000000000..f29e940a00 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/.settings/org.eclipse.pde.core.prefs @@ -0,0 +1,3 @@ +eclipse.preferences.version=1 +pluginProject.extensions=false +resolve.requirebundle=false diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/META-INF/MANIFEST.MF new file mode 100644 index 0000000000..c2531b094c --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/META-INF/MANIFEST.MF @@ -0,0 +1,24 @@ +Manifest-Version: 1.0 +Automatic-Module-Name: org.eclipse.chemclipse.wsd.converter.supplier.arw +Eclipse-RegisterBuddy: org.eclipse.chemclipse.model, org.eclipse.chemclipse.wsd.model +Export-Package: org.eclipse.chemclipse.wsd.converter.supplier.mzml.preferences +Bundle-ManifestVersion: 2 +Bundle-Name: mzML (HPLC-DAD) Converter +Bundle-SymbolicName: org.eclipse.chemclipse.wsd.converter.supplier.mzml;singleton:=true +Bundle-Version: 0.9.0.qualifier +Bundle-Activator: org.eclipse.chemclipse.wsd.converter.supplier.mzml.Activator +Bundle-Vendor: Chemclipse +Require-Bundle: org.eclipse.core.runtime, + org.eclipse.chemclipse.converter;bundle-version="0.8.0", + org.eclipse.chemclipse.wsd.converter;bundle-version="0.8.0", + org.eclipse.chemclipse.model;bundle-version="0.8.0", + org.eclipse.chemclipse.wsd.model;bundle-version="0.8.0", + org.eclipse.chemclipse.logging;bundle-version="0.8.0", + org.eclipse.chemclipse.processing;bundle-version="0.8.0", + org.eclipse.chemclipse.support;bundle-version="0.8.0", + org.eclipse.chemclipse.xxd.converter.supplier.mzml, + org.apache.commons.lang3;bundle-version="3.13.0" +Bundle-RequiredExecutionEnvironment: JavaSE-17 +Import-Package: jakarta.xml.bind;version="[4.0.0,5.0.0)", + org.osgi.framework;version="1.3.0" +Bundle-ActivationPolicy: lazy diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/OSGI-INF/l10n/bundle_en.properties b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/OSGI-INF/l10n/bundle_en.properties new file mode 100644 index 0000000000..597fd0bfba --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/OSGI-INF/l10n/bundle_en.properties @@ -0,0 +1 @@ +#Properties file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/build.properties b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/build.properties new file mode 100644 index 0000000000..948f0bdf02 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/build.properties @@ -0,0 +1,6 @@ +source.. = src/ +output.. = bin/ +bin.includes = META-INF/,\ + .,\ + OSGI-INF/,\ + plugin.xml diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/plugin.xml b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/plugin.xml new file mode 100644 index 0000000000..c7bfa6ce42 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/plugin.xml @@ -0,0 +1,19 @@ + + + + + + + + \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/Activator.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/Activator.java new file mode 100644 index 0000000000..93482af1b4 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/Activator.java @@ -0,0 +1,45 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml; + +import org.osgi.framework.BundleActivator; +import org.osgi.framework.BundleContext; + +public class Activator implements BundleActivator { + + private static BundleContext context; + + public static BundleContext getContext() { + + return context; + } + + /* + * (non-Javadoc) + * @see org.osgi.framework.BundleActivator#start(org.osgi.framework.BundleContext) + */ + @Override + public void start(BundleContext bundleContext) throws Exception { + + Activator.context = bundleContext; + } + + /* + * (non-Javadoc) + * @see org.osgi.framework.BundleActivator#stop(org.osgi.framework.BundleContext) + */ + @Override + public void stop(BundleContext bundleContext) throws Exception { + + Activator.context = null; + } +} \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/PathResolver.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/PathResolver.java new file mode 100644 index 0000000000..8a45dd797a --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/PathResolver.java @@ -0,0 +1,45 @@ +/******************************************************************************* + * Copyright (c) 2013, 2024 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 org.eclipse.chemclipse.wsd.converter.supplier.mzml; + +import java.io.IOException; +import java.net.URL; + +import org.eclipse.core.runtime.FileLocator; +import org.eclipse.core.runtime.IPath; +import org.eclipse.core.runtime.Path; +import org.eclipse.core.runtime.Platform; +import org.osgi.framework.Bundle; + +public class PathResolver { + + /** + * Returns a absolute path of the specified Folder. For example + * TESTDATA_IMPORT_EMPTY as an absolute Path: + * $PluginPath$/testData/files/data.mzML + * + * @param string + * @return String absolutePath + */ + public static String getAbsolutePath(String string) { + + Bundle bundle = Platform.getBundle(Activator.getContext().getBundle().getSymbolicName()); + IPath path = new Path(string); + URL url = FileLocator.find(bundle, path, null); + try { + return FileLocator.resolve(url).getPath(); + } catch(IOException e) { + e.printStackTrace(); + } + return null; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramExportConverter.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramExportConverter.java new file mode 100644 index 0000000000..b2e8977d3b --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramExportConverter.java @@ -0,0 +1,57 @@ +/******************************************************************************* + * Copyright (c) 2024 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.wsd.converter.supplier.mzml.converter; + +import java.io.File; +import java.io.IOException; + +import org.eclipse.chemclipse.converter.chromatogram.AbstractChromatogramExportConverter; +import org.eclipse.chemclipse.converter.chromatogram.IChromatogramExportConverter; +import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException; +import org.eclipse.chemclipse.converter.l10n.ConverterMessages; +import org.eclipse.chemclipse.logging.core.Logger; +import org.eclipse.chemclipse.model.core.IChromatogram; +import org.eclipse.chemclipse.model.core.IPeak; +import org.eclipse.chemclipse.processing.core.IProcessingInfo; +import org.eclipse.chemclipse.wsd.converter.io.IChromatogramWSDWriter; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.converter.io.ChromatogramWriter; +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; +import org.eclipse.core.runtime.IProgressMonitor; +import org.eclipse.osgi.util.NLS; + +public class ChromatogramExportConverter extends AbstractChromatogramExportConverter implements IChromatogramExportConverter { + + private static final Logger logger = Logger.getLogger(ChromatogramExportConverter.class); + private static final String DESCRIPTION = "mzML Chromatogram Export Converter"; + private static final String EXPORT_CHROMATOGRAM = "Export mzML Chromatogram"; + + @Override + public IProcessingInfo convert(File file, IChromatogram chromatogram, IProgressMonitor monitor) { + + IProcessingInfo processingInfo = super.validate(file); + if(!processingInfo.hasErrorMessages() && chromatogram instanceof IChromatogramWSD chromatogramMSD) { + monitor.subTask(EXPORT_CHROMATOGRAM); + IChromatogramWSDWriter writer = new ChromatogramWriter(); + try { + writer.writeChromatogram(file, chromatogramMSD, monitor); + } catch(IOException e) { + logger.error(e); + processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToWriteFile, file.getAbsolutePath())); + } catch(FileIsNotWriteableException e) { + logger.error(e); + processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotWritable, file.getAbsolutePath())); + } + processingInfo.setProcessingResult(file); + } + return processingInfo; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramImportConverter.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramImportConverter.java new file mode 100644 index 0000000000..619dc2e30d --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramImportConverter.java @@ -0,0 +1,65 @@ +/******************************************************************************* + * Copyright (c) 2024 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.wsd.converter.supplier.mzml.converter; + +import java.io.File; +import java.io.IOException; + +import org.eclipse.chemclipse.converter.chromatogram.AbstractChromatogramImportConverter; +import org.eclipse.chemclipse.converter.l10n.ConverterMessages; +import org.eclipse.chemclipse.logging.core.Logger; +import org.eclipse.chemclipse.model.core.IChromatogramOverview; +import org.eclipse.chemclipse.processing.core.IProcessingInfo; +import org.eclipse.chemclipse.wsd.converter.io.IChromatogramWSDReader; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.converter.io.ChromatogramReader; +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; +import org.eclipse.core.runtime.IProgressMonitor; +import org.eclipse.osgi.util.NLS; + +public class ChromatogramImportConverter extends AbstractChromatogramImportConverter { + + private static final Logger logger = Logger.getLogger(ChromatogramImportConverter.class); + + @Override + public IProcessingInfo convert(File file, IProgressMonitor monitor) { + + IProcessingInfo processingInfo = super.validate(file); + if(!processingInfo.hasErrorMessages()) { + IChromatogramWSDReader chromatogramReader = new ChromatogramReader(); + try { + IChromatogramWSD chromatogram = chromatogramReader.read(file, monitor); + processingInfo.setProcessingResult(chromatogram); + } catch(IOException e) { + logger.warn(e); + processingInfo.addErrorMessage(ConverterMessages.importChromatogram, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath())); + } + } + return processingInfo; + } + + @Override + public IProcessingInfo convertOverview(File file, IProgressMonitor monitor) { + + IProcessingInfo processingInfo = super.validate(file); + if(!processingInfo.hasErrorMessages()) { + IChromatogramWSDReader chromatogramReader = new ChromatogramReader(); + try { + IChromatogramOverview chromatogramOverview = chromatogramReader.readOverview(file, monitor); + processingInfo.setProcessingResult(chromatogramOverview); + } catch(IOException e) { + logger.warn(e); + processingInfo.addErrorMessage(ConverterMessages.importChromatogram, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath())); + } + } + return processingInfo; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/FileContentMatcher.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/FileContentMatcher.java new file mode 100644 index 0000000000..4b511bb0cd --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/FileContentMatcher.java @@ -0,0 +1,72 @@ +/******************************************************************************* + * Copyright (c) 2024 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.wsd.converter.supplier.mzml.converter; + +import java.io.File; +import java.io.FileInputStream; + +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLStreamConstants; +import javax.xml.stream.XMLStreamReader; + +import org.eclipse.chemclipse.converter.core.AbstractFileContentMatcher; +import org.eclipse.chemclipse.converter.core.IFileContentMatcher; + +public class FileContentMatcher extends AbstractFileContentMatcher implements IFileContentMatcher { + + @Override + public boolean checkFileFormat(File file) { + + boolean isValidFormat = false; + try { + XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance(); + XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(new FileInputStream(file)); + boolean hasChromatogramList = false; + boolean hasRootElement = false; + boolean hasPDA = false; + while(xmlStreamReader.hasNext()) { + int eventType = xmlStreamReader.next(); + if(eventType == XMLStreamConstants.START_ELEMENT) { + String elementName = xmlStreamReader.getLocalName(); + if(elementName.equals("mzML")) { + hasRootElement = true; + } else if(elementName.equals("chromatogramList")) { + hasChromatogramList = true; + } else if(elementName.equals("fileContent")) { + while(xmlStreamReader.hasNext()) { + int innerEventType = xmlStreamReader.next(); + if(innerEventType == XMLStreamConstants.START_ELEMENT && xmlStreamReader.getLocalName().equals("cvParam")) { + String accession = xmlStreamReader.getAttributeValue(null, "accession"); + String paramName = xmlStreamReader.getAttributeValue(null, "name"); + if(accession.equals("MS:1000806") && paramName.equals("absorption spectrum")) { + hasPDA = true; + break; + } + } + if(innerEventType == XMLStreamConstants.END_ELEMENT && xmlStreamReader.getLocalName().equals("fileContent")) { + break; + } + } + } + if(hasRootElement && hasChromatogramList && hasPDA) { + isValidFormat = true; + break; + } + } + } + xmlStreamReader.close(); + } catch(Exception e) { + // fail silently + } + return isValidFormat; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/io/ChromatogramReader.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/io/ChromatogramReader.java new file mode 100644 index 0000000000..23bd397a5c --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/io/ChromatogramReader.java @@ -0,0 +1,59 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + * Lorenz Gerber - adjust failed parsing behaviour + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.converter.io; + +import java.io.File; +import java.io.FileReader; +import java.io.IOException; + +import org.eclipse.chemclipse.converter.exceptions.UnknownVersionException; +import org.eclipse.chemclipse.model.core.IChromatogramOverview; +import org.eclipse.chemclipse.wsd.converter.io.AbstractChromatogramWSDReader; +import org.eclipse.chemclipse.wsd.converter.io.IChromatogramWSDReader; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.io.ChromatogramReaderVersion110; +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; +import org.eclipse.core.runtime.IProgressMonitor; + +public class ChromatogramReader extends AbstractChromatogramWSDReader implements IChromatogramWSDReader { + + public static IChromatogramWSDReader getReader(final File file) throws IOException { + + IChromatogramWSDReader chromatogramReader = null; + try (final FileReader fileReader = new FileReader(file)) { + final char[] charBuffer = new char[500]; + fileReader.read(charBuffer); + final String header = new String(charBuffer); + if(header.contains(XmlReader110.VERSION)) { + chromatogramReader = new ChromatogramReaderVersion110(); + } else { + throw new UnknownVersionException(); + } + } + return chromatogramReader; + } + + @Override + public IChromatogramWSD read(File file, IProgressMonitor monitor) throws IOException { + + IChromatogramWSDReader reader = getReader(file); + return reader.read(file, monitor); + } + + @Override + public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) throws IOException { + + IChromatogramWSDReader reader = getReader(file); + return reader.read(file, monitor); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/io/ChromatogramWriter.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/io/ChromatogramWriter.java new file mode 100644 index 0000000000..fe21e4d266 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/io/ChromatogramWriter.java @@ -0,0 +1,40 @@ +/******************************************************************************* + * Copyright (c) 2014, 2024 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 + * Matthias Mailänder - add support for saving version 1.10 + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.converter.io; + +import java.io.File; +import java.io.IOException; + +import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException; +import org.eclipse.chemclipse.converter.io.AbstractChromatogramWriter; +import org.eclipse.chemclipse.wsd.converter.io.IChromatogramWSDWriter; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.io.ChromatogramWriterVersion110; +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; +import org.eclipse.core.runtime.IProgressMonitor; + +public class ChromatogramWriter extends AbstractChromatogramWriter implements IChromatogramWSDWriter { + + @Override + public void writeChromatogram(File file, IChromatogramWSD chromatogram, IProgressMonitor monitor) throws FileIsNotWriteableException, IOException { + + final IChromatogramWSDWriter chromatogramWriter = getChromatogramWriter(); + if(chromatogramWriter != null) { + chromatogramWriter.writeChromatogram(file, chromatogram, monitor); + } + } + + private IChromatogramWSDWriter getChromatogramWriter() { + + return new ChromatogramWriterVersion110(); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java new file mode 100644 index 0000000000..92bb0449ea --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java @@ -0,0 +1,177 @@ +/******************************************************************************* + * Copyright (c) 2024 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.wsd.converter.supplier.mzml.io; + +import java.io.File; +import java.io.IOException; +import java.util.zip.DataFormatException; + +import javax.xml.parsers.ParserConfigurationException; + +import org.apache.commons.lang3.tuple.Pair; +import org.eclipse.chemclipse.converter.io.AbstractChromatogramReader; +import org.eclipse.chemclipse.logging.core.Logger; +import org.eclipse.chemclipse.model.core.IChromatogramOverview; +import org.eclipse.chemclipse.wsd.converter.io.IChromatogramWSDReader; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.IVendorChromatogram; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.IVendorScan; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.IVendorScanSignal; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.VendorChromatogram; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.VendorScan; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.VendorScanSignal; +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.BinaryReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.MetadataReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ChromatogramType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.RunType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumType; +import org.eclipse.core.runtime.IProgressMonitor; +import org.xml.sax.SAXException; + +import jakarta.xml.bind.JAXBException; + +public class ChromatogramReaderVersion110 extends AbstractChromatogramReader implements IChromatogramWSDReader { + + private static final Logger logger = Logger.getLogger(ChromatogramReaderVersion110.class); + + @Override + public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) throws IOException { + + IVendorChromatogram chromatogram = null; + try { + chromatogram = new VendorChromatogram(); + chromatogram.setFile(file); + MzMLType mzML = XmlReader110.getMzML(file); + chromatogram = (IVendorChromatogram)MetadataReader110.readMetadata(mzML, chromatogram); + RunType run = mzML.getRun(); + readSingleWavelengthSignal(run, chromatogram); + } catch(ParserConfigurationException e) { + logger.warn(e); + } catch(SAXException e) { + logger.warn(e); + } catch(JAXBException e) { + logger.warn(e); + } + return chromatogram; + } + + @Override + public IChromatogramWSD read(File file, IProgressMonitor monitor) throws IOException { + + IVendorChromatogram chromatogram = null; + try { + chromatogram = new VendorChromatogram(); + chromatogram.setFile(file); + MzMLType mzML = XmlReader110.getMzML(file); + chromatogram = (IVendorChromatogram)MetadataReader110.readMetadata(mzML, chromatogram); + RunType run = mzML.getRun(); + readSingleWavelengthSignal(run, chromatogram); + readFullSpectrum(run, chromatogram); + } catch(ParserConfigurationException e) { + logger.warn(e); + } catch(SAXException e) { + logger.warn(e); + } catch(JAXBException e) { + logger.warn(e); + } catch(DataFormatException e) { + logger.warn(e); + } + return chromatogram; + } + + private void readFullSpectrum(RunType run, IVendorChromatogram chromatogram) throws DataFormatException { + + int i = 1; + for(SpectrumType spectrum : run.getSpectrumList().getSpectrum()) { + double[] wavelengths = new double[0]; + double[] intensities = new double[0]; + for(BinaryDataArrayType binaryDataArrayType : spectrum.getBinaryDataArrayList().getBinaryDataArray()) { + Pair binaryData = BinaryReader110.parseBinaryData(binaryDataArrayType); + if(binaryData.getKey().equals("wavelength")) { + wavelengths = binaryData.getValue(); + } else if(binaryData.getKey().equals("intensity")) { + intensities = binaryData.getValue(); + } + } + IVendorScan scan = (IVendorScan)chromatogram.getSupplierScan(i); + scan.deleteScanSignals(); // otherwise the total signal is added upon + addSpectrum(wavelengths, intensities, scan); + i++; + } + } + + private void readSingleWavelengthSignal(RunType run, IVendorChromatogram chromatogram) { + + double[] retentionTimes = new double[0]; + double[] intensities = new double[0]; + float lowestWavelength = 0f; + float highestWavelength = 0f; + try { + for(ChromatogramType chromatogramType : run.getChromatogramList().getChromatogram()) { + for(CVParamType cvParam : chromatogramType.getCvParam()) { + if(cvParam.getAccession().equals("MS:1000618") && cvParam.getName().equals("highest observed wavelength")) { + highestWavelength = Float.parseFloat(cvParam.getValue()); + } else if(cvParam.getAccession().equals("MS:1000619") && cvParam.getName().equals("lowest observed wavelength")) { + lowestWavelength = Float.parseFloat(cvParam.getValue()); + } else if(cvParam.getAccession().equals("MS:1000812") && cvParam.getName().equals("absorption chromatogram")) { + for(BinaryDataArrayType binaryDataArrayType : chromatogramType.getBinaryDataArrayList().getBinaryDataArray()) { + Pair binaryData = BinaryReader110.parseBinaryData(binaryDataArrayType); + if(binaryData.getKey().equals("time")) { + retentionTimes = binaryData.getValue(); + } else if(binaryData.getKey().equals("intensity")) { + intensities = binaryData.getValue(); + } + } + } + } + } + if(lowestWavelength != highestWavelength) { + logger.warn("Not a single wavelength chromatogram."); + } + float wavelength = Math.max(lowestWavelength, highestWavelength); + addScans(wavelength, intensities, retentionTimes, chromatogram); + } catch(DataFormatException e) { + logger.warn(e); + } + } + + private void addScans(float wavelength, double[] intensities, double[] retentionTimes, IVendorChromatogram chromatogram) { + + int rt = Math.min(retentionTimes.length, intensities.length); + for(int i = 0; i < rt; i++) { + IVendorScan scan = new VendorScan(); + int retentionTime = (int)(retentionTimes[i]); + scan.setRetentionTime(retentionTime); + float intensity = (float)intensities[i]; + IVendorScanSignal signal = new VendorScanSignal(); + signal.setAbsorbance(intensity); + signal.setWavelength(wavelength); + scan.addScanSignal(signal); + chromatogram.addScan(scan); + } + } + + private void addSpectrum(double[] wavelengths, double[] intensities, IVendorScan scan) { + + int max = Math.min(wavelengths.length, intensities.length); + for(int i = 0; i < max; i++) { + IVendorScanSignal signal = new VendorScanSignal(); + signal.setAbsorbance((float)intensities[i]); + signal.setWavelength((float)wavelengths[i]); + scan.addScanSignal(signal); + } + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/io/ChromatogramWriterVersion110.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/io/ChromatogramWriterVersion110.java new file mode 100644 index 0000000000..6a06042eca --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/io/ChromatogramWriterVersion110.java @@ -0,0 +1,327 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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.wsd.converter.supplier.mzml.io; + +import java.io.File; +import java.io.IOException; +import java.math.BigInteger; +import java.util.List; + +import javax.xml.datatype.DatatypeConfigurationException; +import javax.xml.datatype.XMLGregorianCalendar; + +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.IChromatogram; +import org.eclipse.chemclipse.model.core.IChromatogramOverview; +import org.eclipse.chemclipse.model.core.IScan; +import org.eclipse.chemclipse.wsd.converter.io.IChromatogramWSDWriter; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.Activator; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.preferences.PreferenceSupplier; +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; +import org.eclipse.chemclipse.wsd.model.core.IScanSignalWSD; +import org.eclipse.chemclipse.wsd.model.core.IScanWSD; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlWriter110; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ChromatogramListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ChromatogramType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.DataProcessingListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.DataProcessingType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.FileDescriptionType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.InstrumentConfigurationListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.InstrumentConfigurationType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ObjectFactory; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ParamGroupType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ProcessingMethodType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.RunType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareRefType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SourceFileListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SourceFileType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumType; +import org.eclipse.core.runtime.IProgressMonitor; + +import jakarta.xml.bind.JAXBContext; +import jakarta.xml.bind.JAXBException; +import jakarta.xml.bind.Marshaller; + +public class ChromatogramWriterVersion110 extends AbstractChromatogramWriter implements IChromatogramWSDWriter { + + private static final Logger logger = Logger.getLogger(ChromatogramWriterVersion110.class); + + @Override + public void writeChromatogram(File file, IChromatogramWSD chromatogram, IProgressMonitor monitor) throws FileIsNotWriteableException, IOException { + + try { + JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class); + Marshaller marshaller = jaxbContext.createMarshaller(); + // + RunType run = new RunType(); + SoftwareListType softwareList = XmlWriter110.createSoftwareList(); + InstrumentConfigurationListType instrumentConfigurationList = createInstrumentConfigurationList(softwareList.getSoftware().get(0)); + run.setDefaultInstrumentConfigurationRef(instrumentConfigurationList.getInstrumentConfiguration().get(0)); + SourceFileListType sourceFileList = createSourceFileList(chromatogram); + run.setDefaultSourceFileRef(sourceFileList.getSourceFile().get(0)); + run.setId(chromatogram.getName()); + // + DataProcessingListType dataProcessingList = createDataProcessingList(softwareList.getSoftware().get(0)); + SpectrumListType spectrumList = new SpectrumListType(); + spectrumList.setDefaultDataProcessingRef(dataProcessingList.getDataProcessing().get(0)); + ChromatogramListType chromatogramList = new ChromatogramListType(); + chromatogramList.setDefaultDataProcessingRef(dataProcessingList.getDataProcessing().get(0)); + chromatogramList.setCount(BigInteger.valueOf(1)); // TODO export referenced chromatograms + // + int scans = chromatogram.getNumberOfScans(); + spectrumList.setCount(BigInteger.valueOf(scans)); + float[] totalSignals = new float[scans]; + float[] retentionTimes = new float[scans]; + writeScans(chromatogram, totalSignals, retentionTimes, spectrumList); + run.setSpectrumList(spectrumList); + // + BinaryDataArrayListType binaryDataArrayList = new BinaryDataArrayListType(); + binaryDataArrayList.setCount(BigInteger.valueOf(2)); + boolean compression = PreferenceSupplier.getChromatogramSaveCompression(); + // + BinaryDataArrayType totalSignalsBinaryDataArrayType = XmlWriter110.createBinaryData(totalSignals, compression); + totalSignalsBinaryDataArrayType.getCvParam().add(XmlWriter110.createIntensityArrayType()); + binaryDataArrayList.getBinaryDataArray().add(totalSignalsBinaryDataArrayType); + // + BinaryDataArrayType retentionTimesBinaryDataArrayType = XmlWriter110.createBinaryData(retentionTimes, compression); + retentionTimesBinaryDataArrayType.getCvParam().add(XmlWriter110.createRetentionTimeType()); + binaryDataArrayList.getBinaryDataArray().add(retentionTimesBinaryDataArrayType); + // + ChromatogramType defaultPDA = new ChromatogramType(); + float wavelength = chromatogram.getWavelengths().iterator().next(); // TODO: not default wavelength + defaultPDA.setId(wavelength + "nm"); + defaultPDA.setIndex(BigInteger.valueOf(0)); + defaultPDA.getCvParam().add(createAbsorptionChromatogramType()); + defaultPDA.setDefaultArrayLength(totalSignals.length); + defaultPDA.setBinaryDataArrayList(binaryDataArrayList); + chromatogramList.getChromatogram().add(defaultPDA); + run.setChromatogramList(chromatogramList); + // + XMLGregorianCalendar date = XmlWriter110.createDate(chromatogram); + if(date != null) { + run.setStartTimeStamp(date); + } + MzMLType mzML = new MzMLType(); + mzML.setId(chromatogram.getFile().getName()); + // + CVListType cvList = new CVListType(); + cvList.setCount(BigInteger.valueOf(2)); + cvList.getCv().add(XmlWriter110.MS); + cvList.getCv().add(XmlWriter110.UO); + mzML.setCvList(cvList); + // + mzML.setFileDescription(createFileDescription(chromatogram, sourceFileList)); + mzML.setInstrumentConfigurationList(instrumentConfigurationList); + mzML.setSoftwareList(softwareList); + mzML.setDataProcessingList(dataProcessingList); + mzML.setVersion(XmlReader110.VERSION); + mzML.setRun(run); + marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, "http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd"); + marshaller.marshal(mzML, file); + } catch(JAXBException e) { + logger.warn(e); + } catch(DatatypeConfigurationException e) { + logger.warn(e); + } + } + + private void writeScans(IChromatogramWSD chromatogram, float[] totalSignals, float[] retentionTimes, SpectrumListType spectrumList) { + + int i = 0; + for(IScan scan : chromatogram.getScans()) { + SpectrumType spectrum = new SpectrumType(); + spectrum.setId("scan=" + scan.getScanNumber()); + spectrum.setIndex(BigInteger.valueOf((scan.getScanNumber() - 1))); + // TIC + totalSignals[i] = scan.getTotalSignal(); + retentionTimes[i] = (float)(scan.getRetentionTime() / IChromatogramOverview.SECOND_CORRELATION_FACTOR); + i++; + spectrum.getCvParam().add(createAbsorptionType()); + spectrum.getCvParam().add(createProfileType()); + IScanWSD scanWSD = (IScanWSD)scan; + // full spectra + // + spectrum.getCvParam().add(createHighestObservedWavelength(scanWSD)); + spectrum.getCvParam().add(createLowestObservedWavelength(scanWSD)); + // + List scanSignals = scanWSD.getScanSignals(); + float[] wavelength = new float[scanSignals.size()]; + float[] absorbance = new float[scanSignals.size()]; + int j = 0; + for(IScanSignalWSD scanSignal : scanSignals) { + wavelength[j] = scanSignal.getWavelength(); + absorbance[j] = scanSignal.getAbsorbance(); + j++; + } + BinaryDataArrayListType binaryDataArrayList = new BinaryDataArrayListType(); + binaryDataArrayList.setCount(BigInteger.valueOf(2)); + // + boolean compression = PreferenceSupplier.getChromatogramSaveCompression(); + BinaryDataArrayType wavelengthsBinaryDataArrayType = XmlWriter110.createBinaryData(wavelength, compression); + wavelengthsBinaryDataArrayType.getCvParam().add(createWavelengthType()); + binaryDataArrayList.getBinaryDataArray().add(wavelengthsBinaryDataArrayType); + // + BinaryDataArrayType absorbancesBinaryDataArrayType = XmlWriter110.createBinaryData(absorbance, compression); + absorbancesBinaryDataArrayType.getCvParam().add(XmlWriter110.createIntensityArrayType()); + binaryDataArrayList.getBinaryDataArray().add(absorbancesBinaryDataArrayType); + // + spectrum.setBinaryDataArrayList(binaryDataArrayList); + spectrum.setDefaultArrayLength(wavelength.length); + spectrumList.getSpectrum().add(spectrum); + } + } + + private CVParamType createWavelengthType() { + + CVParamType cvParam = new CVParamType(); + cvParam.setCvRef(XmlWriter110.MS); + cvParam.setAccession("MS:1000617"); + cvParam.setName("wavelength array"); + setUnitNanometer(cvParam); + return cvParam; + } + + private CVParamType createHighestObservedWavelength(IScanWSD scanWSD) { + + CVParamType cvParam = new CVParamType(); + cvParam.setCvRef(XmlWriter110.MS); + cvParam.setAccession("MS:1000618"); + cvParam.setName("highest observed wavelength"); + cvParam.setValue(String.valueOf(scanWSD.getWavelengthBounds().getHighestWavelength().getWavelength())); + setUnitNanometer(cvParam); + return cvParam; + } + + private CVParamType createLowestObservedWavelength(IScanWSD scanWSD) { + + CVParamType cvParam = new CVParamType(); + cvParam.setCvRef(XmlWriter110.MS); + cvParam.setAccession("MS:1000619"); + cvParam.setName("lowest observed wavelength"); + cvParam.setValue(String.valueOf(scanWSD.getWavelengthBounds().getLowestWavelength().getWavelength())); + setUnitNanometer(cvParam); + return cvParam; + } + + private void setUnitNanometer(CVParamType cvParam) { + + cvParam.setUnitAccession("UO:0000018"); + cvParam.setUnitName("nanometer"); + cvParam.setUnitCvRef(XmlWriter110.UO); + } + + private CVParamType createProfileType() { + + CVParamType cvParam = new CVParamType(); + cvParam.setCvRef(XmlWriter110.MS); + cvParam.setAccession("MS:1000128"); + cvParam.setName("profile spectrum"); + cvParam.setValue(""); + return cvParam; + } + + private CVParamType createAbsorptionChromatogramType() { + + CVParamType cvParam = new CVParamType(); + cvParam.setCvRef(XmlWriter110.MS); + cvParam.setAccession("MS:1000812"); + cvParam.setName("absorption chromatogram"); + cvParam.setValue(""); + return cvParam; + } + + private SourceFileListType createSourceFileList(IChromatogram chromatogram) { + + SourceFileListType sourceFileListType = new SourceFileListType(); + sourceFileListType.setCount(BigInteger.valueOf(1)); + SourceFileType sourceFile = XmlWriter110.createSourceFile(chromatogram); + if(chromatogram.getConverterId().equals("org.eclipse.chemclipse.xxd.converter.supplier.chemclipse")) { + CVParamType cvParamFileFormat = new CVParamType(); + cvParamFileFormat.setCvRef(XmlWriter110.MS); + cvParamFileFormat.setAccession("MS:1003374"); + cvParamFileFormat.setName("Open Chromatography Binary OCB format"); + cvParamFileFormat.setValue(""); + sourceFile.getCvParam().add(cvParamFileFormat); + sourceFileListType.setCount(BigInteger.valueOf(2)); + } + sourceFileListType.getSourceFile().add(sourceFile); + return sourceFileListType; + } + + private FileDescriptionType createFileDescription(IChromatogramWSD chromatogram, SourceFileListType sourceFiles) { + + FileDescriptionType fileDescriptionType = new FileDescriptionType(); + fileDescriptionType.setSourceFileList(sourceFiles); + ParamGroupType fileContent = new ParamGroupType(); + fileContent.getCvParam().add(createAbsorptionType()); + fileDescriptionType.setFileContent(fileContent); + ParamGroupType paramGroupType = XmlWriter110.getOperator(chromatogram); + if(paramGroupType != null) { + fileDescriptionType.getContact().add(paramGroupType); + } + return fileDescriptionType; + } + + private CVParamType createAbsorptionType() { + + CVParamType cvParamSpectrum = new CVParamType(); + cvParamSpectrum.setCvRef(XmlWriter110.MS); + cvParamSpectrum.setAccession("MS:1000806"); + cvParamSpectrum.setName("absorption spectrum"); + cvParamSpectrum.setValue(""); + return cvParamSpectrum; + } + + private InstrumentConfigurationListType createInstrumentConfigurationList(SoftwareType software) { + + InstrumentConfigurationListType instrumentConfigurationList = new InstrumentConfigurationListType(); + instrumentConfigurationList.setCount(BigInteger.valueOf(1)); + InstrumentConfigurationType instrumentConfiguration = new InstrumentConfigurationType(); + instrumentConfiguration.setId("unknown"); + SoftwareRefType softwareRef = new SoftwareRefType(); + softwareRef.setRef(software); + instrumentConfiguration.setSoftwareRef(softwareRef); + instrumentConfigurationList.getInstrumentConfiguration().add(instrumentConfiguration); + return instrumentConfigurationList; + } + + private DataProcessingListType createDataProcessingList(SoftwareType software) { + + DataProcessingListType dataProcessingList = new DataProcessingListType(); + dataProcessingList.setCount(BigInteger.valueOf(1)); + DataProcessingType dataProcessing = new DataProcessingType(); + dataProcessing.setId(Activator.getContext().getBundle().getSymbolicName()); + ProcessingMethodType processingMethod = new ProcessingMethodType(); + processingMethod.setSoftwareRef(software); + processingMethod.setOrder(BigInteger.valueOf(1)); + CVParamType exportParam = new CVParamType(); + exportParam.setCvRef(XmlWriter110.MS); + exportParam.setAccession("MS:1000544"); + exportParam.setName("Conversion to mzML"); + exportParam.setValue(""); + processingMethod.getCvParam().add(exportParam); + dataProcessing.getProcessingMethod().add(processingMethod); + dataProcessingList.getDataProcessing().add(dataProcessing); + return dataProcessingList; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorChromatogram.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorChromatogram.java new file mode 100644 index 0000000000..71300b15ef --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorChromatogram.java @@ -0,0 +1,17 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.model; + +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; + +public interface IVendorChromatogram extends IChromatogramWSD { +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorScan.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorScan.java new file mode 100644 index 0000000000..af96d43f0c --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorScan.java @@ -0,0 +1,17 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.model; + +import org.eclipse.chemclipse.wsd.model.core.IScanWSD; + +public interface IVendorScan extends IScanWSD { +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorScanSignal.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorScanSignal.java new file mode 100644 index 0000000000..d17a9e9596 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/IVendorScanSignal.java @@ -0,0 +1,17 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.model; + +import org.eclipse.chemclipse.wsd.model.core.IScanSignalWSD; + +public interface IVendorScanSignal extends IScanSignalWSD { +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorChromatogram.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorChromatogram.java new file mode 100644 index 0000000000..7332061b48 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorChromatogram.java @@ -0,0 +1,24 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.model; + +import org.eclipse.chemclipse.wsd.model.core.AbstractChromatogramWSD; + +@SuppressWarnings("serial") +public class VendorChromatogram extends AbstractChromatogramWSD implements IVendorChromatogram { + + @Override + public String getName() { + + return extractNameFromFile("mzML HPLC-DAD"); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorScan.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorScan.java new file mode 100644 index 0000000000..4ce80bd97e --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorScan.java @@ -0,0 +1,19 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.model; + +import org.eclipse.chemclipse.wsd.model.core.AbstractScanWSD; + +public class VendorScan extends AbstractScanWSD implements IVendorScan { + + private static final long serialVersionUID = -4577378416225112598L; +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorScanSignal.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorScanSignal.java new file mode 100644 index 0000000000..9699a1b36d --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/model/VendorScanSignal.java @@ -0,0 +1,24 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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: + * Philip Wenig - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.model; + +import org.eclipse.chemclipse.wsd.model.core.AbstractScanSignalWSD; + +public class VendorScanSignal extends AbstractScanSignalWSD implements IVendorScanSignal { + + private static final long serialVersionUID = -1231272201935129319L; + + public VendorScanSignal() { + + super(); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/preferences/PreferenceSupplier.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/preferences/PreferenceSupplier.java new file mode 100644 index 0000000000..a221a46b8e --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.mzml/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/preferences/PreferenceSupplier.java @@ -0,0 +1,62 @@ +/******************************************************************************* + * Copyright (c) 2021, 2024 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 + * Philip Wenig - preference initializer + *******************************************************************************/ +package org.eclipse.chemclipse.wsd.converter.supplier.mzml.preferences; + +import org.eclipse.chemclipse.support.preferences.AbstractPreferenceSupplier; +import org.eclipse.chemclipse.support.preferences.IPreferenceSupplier; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.Activator; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110; + +public class PreferenceSupplier extends AbstractPreferenceSupplier implements IPreferenceSupplier { + + public static final String P_CHROMATOGRAM_VERSION_SAVE = "chromatogramVersionSave"; + public static final String DEF_CHROMATOGRAM_VERSION_SAVE = XmlReader110.VERSION; + public static final String P_CHROMATOGRAM_SAVE_COMPRESSION = "chromatogramSaveCompression"; + public static final boolean DEF_CHROMATOGRAM_SAVE_COMPRESSION = true; + + public static IPreferenceSupplier INSTANCE() { + + return INSTANCE(PreferenceSupplier.class); + } + + @Override + public String getPreferenceNode() { + + return Activator.getContext().getBundle().getSymbolicName(); + } + + @Override + public void initializeDefaults() { + + putDefault(P_CHROMATOGRAM_VERSION_SAVE, DEF_CHROMATOGRAM_VERSION_SAVE); + putDefault(P_CHROMATOGRAM_SAVE_COMPRESSION, Boolean.toString(DEF_CHROMATOGRAM_SAVE_COMPRESSION)); + } + + public static String getChromatogramVersionSave() { + + return INSTANCE().get(P_CHROMATOGRAM_VERSION_SAVE, DEF_CHROMATOGRAM_VERSION_SAVE); + } + + public static String[][] getChromatogramVersions() { + + String[][] elements = new String[1][2]; + elements[0][0] = XmlReader110.VERSION; + elements[0][1] = XmlReader110.VERSION; + return elements; + } + + public static boolean getChromatogramSaveCompression() { + + return INSTANCE().getBoolean(P_CHROMATOGRAM_SAVE_COMPRESSION, DEF_CHROMATOGRAM_SAVE_COMPRESSION); + } +} \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.classpath b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.classpath new file mode 100644 index 0000000000..81fe078c20 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.classpath @@ -0,0 +1,7 @@ + + + + + + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.gitignore b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.gitignore new file mode 100644 index 0000000000..5e56e040ec --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.gitignore @@ -0,0 +1 @@ +/bin diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.project b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.project new file mode 100644 index 0000000000..e310f6aabe --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.project @@ -0,0 +1,28 @@ + + + org.eclipse.chemclipse.xxd.converter.supplier.mzml + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.pde.ManifestBuilder + + + + + org.eclipse.pde.SchemaBuilder + + + + + + org.eclipse.pde.PluginNature + org.eclipse.jdt.core.javanature + + diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.settings/org.eclipse.core.resources.prefs b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 0000000000..801fab74d0 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +encoding/=utf8 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.settings/org.eclipse.jdt.core.prefs b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000000..9154beff79 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,7 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=17 +org.eclipse.jdt.core.compiler.compliance=17 +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.source=17 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/META-INF/MANIFEST.MF new file mode 100644 index 0000000000..5c44cb6b87 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/META-INF/MANIFEST.MF @@ -0,0 +1,25 @@ +Manifest-Version: 1.0 +Automatic-Module-Name: org.eclipse.chemclipse.xxd.converter.supplier.mzml +Eclipse-RegisterBuddy: org.eclipse.chemclipse.model, org.eclipse.chemclipse.msd.model +Bundle-ManifestVersion: 2 +Bundle-Name: mzML +Bundle-SymbolicName: org.eclipse.chemclipse.xxd.converter.supplier.mzml;singleton:=true +Bundle-Version: 0.9.0.qualifier +Bundle-Activator: org.eclipse.chemclipse.xxd.converter.supplier.mzml.Activator +Bundle-Vendor: ChemClipse +Require-Bundle: org.eclipse.core.runtime, + org.eclipse.chemclipse.logging;bundle-version="0.8.0", + org.eclipse.chemclipse.converter;bundle-version="0.8.0", + org.eclipse.chemclipse.model;bundle-version="0.8.0", + org.eclipse.chemclipse.support;bundle-version="0.8.0", + org.apache.commons.commons-codec;bundle-version="1.15.0", + org.apache.commons.lang3;bundle-version="3.13.0" +Bundle-RequiredExecutionEnvironment: JavaSE-17 +Bundle-ActivationPolicy: lazy +Import-Package: jakarta.xml.bind, + jakarta.xml.bind.annotation, + jakarta.xml.bind.annotation.adapters +Export-Package: org.eclipse.chemclipse.xxd.converter.supplier.mzml.converter, + org.eclipse.chemclipse.xxd.converter.supplier.mzml.io, + org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10, + org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110 diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/OSGI-INF/l10n/bundle_en.properties b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/OSGI-INF/l10n/bundle_en.properties new file mode 100644 index 0000000000..597fd0bfba --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/OSGI-INF/l10n/bundle_en.properties @@ -0,0 +1 @@ +#Properties file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/build.properties b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/build.properties new file mode 100644 index 0000000000..b26f6d363a --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/build.properties @@ -0,0 +1,5 @@ +source.. = src/ +output.. = bin/ +bin.includes = META-INF/,\ + .,\ + OSGI-INF/ \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/Activator.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/Activator.java new file mode 100644 index 0000000000..1007e5df79 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/Activator.java @@ -0,0 +1,43 @@ +/******************************************************************************* + * Copyright (c) 2013, 2024 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 org.eclipse.chemclipse.xxd.converter.supplier.mzml; + +import org.osgi.framework.BundleActivator; +import org.osgi.framework.BundleContext; + +public class Activator implements BundleActivator { + + private static BundleContext context; + + public static BundleContext getContext() { + + return context; + } + + /* + * (non-Javadoc) + * @see org.osgi.framework.BundleActivator#start(org.osgi.framework.BundleContext) + */ + public void start(BundleContext bundleContext) throws Exception { + + Activator.context = bundleContext; + } + + /* + * (non-Javadoc) + * @see org.osgi.framework.BundleActivator#stop(org.osgi.framework.BundleContext) + */ + public void stop(BundleContext bundleContext) throws Exception { + + Activator.context = null; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/MagicNumberMatcher.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/converter/MagicNumberMatcher.java similarity index 89% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/MagicNumberMatcher.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/converter/MagicNumberMatcher.java index cf5be0d3ca..a168d1ed44 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/MagicNumberMatcher.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/converter/MagicNumberMatcher.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2016, 2023 Lablicate GmbH. + * Copyright (c) 2016, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -10,7 +10,7 @@ * Dr. Philip Wenig - initial API and implementation * Matthias Mailänder - auto detection for MALDI files *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.converter; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.converter; import java.io.File; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryReader10.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/BinaryReader10.java similarity index 91% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryReader10.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/BinaryReader10.java index 65313b0270..1afe2ce38d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryReader10.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/BinaryReader10.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2021, 2023 Lablicate GmbH. + * Copyright (c) 2021, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.io; import java.math.BigInteger; import java.nio.ByteBuffer; @@ -21,8 +21,8 @@ import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.BinaryDataArrayType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.CVParamType; public class BinaryReader10 { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryReader110.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/BinaryReader110.java similarity index 73% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryReader110.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/BinaryReader110.java index 233ecb810d..5566243553 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/BinaryReader110.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/BinaryReader110.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2021, 2023 Lablicate GmbH. + * Copyright (c) 2021, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.io; import java.math.BigInteger; import java.nio.ByteBuffer; @@ -21,8 +21,8 @@ import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.BinaryDataArrayType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; public class BinaryReader110 { @@ -46,31 +46,23 @@ public static Pair parseBinaryData(BinaryDataArrayType binaryD boolean doublePrecision = false; float multiplicator = 1f; for(CVParamType cvParam : binaryDataArrayType.getCvParam()) { - if(cvParam.getAccession().equals("MS:1000574")) { - if(cvParam.getName().equals("zlib compression")) { - compressed = true; - } + if(cvParam.getAccession().equals("MS:1000574") && cvParam.getName().equals("zlib compression")) { + compressed = true; } if(cvParam.getAccession().equals("MS:1000521") && cvParam.getName().equals("32-bit float")) { doublePrecision = false; } else if(cvParam.getAccession().equals("MS:1000523") && cvParam.getName().equals("64-bit float")) { doublePrecision = true; } - if(cvParam.getAccession().equals("MS:1000514")) { - if(cvParam.getName().equals("m/z array")) { - content = "m/z"; - } - } - if(cvParam.getAccession().equals("MS:1000515")) { - if(cvParam.getName().equals("intensity array")) { - content = "intensity"; - } - } - if(cvParam.getAccession().equals("MS:1000595")) { - if(cvParam.getName().equals("time array")) { - content = "time"; - multiplicator = XmlReader110.getTimeMultiplicator(cvParam); - } + if(cvParam.getAccession().equals("MS:1000514") && cvParam.getName().equals("m/z array")) { + content = "m/z"; + } else if(cvParam.getAccession().equals("MS:1000617") && cvParam.getName().equals("wavelength array")) { + content = "wavelength"; + } else if(cvParam.getAccession().equals("MS:1000515") && cvParam.getName().equals("intensity array")) { + content = "intensity"; + } else if(cvParam.getAccession().equals("MS:1000595") && cvParam.getName().equals("time array")) { + content = "time"; + multiplicator = XmlReader110.getTimeMultiplicator(cvParam); } } if(compressed) { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/MetadataReader110.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/MetadataReader110.java new file mode 100644 index 0000000000..863766dbb8 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/MetadataReader110.java @@ -0,0 +1,66 @@ +/******************************************************************************* + * Copyright (c) 2024 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.xxd.converter.supplier.mzml.io; + +import org.eclipse.chemclipse.model.core.IChromatogram; +import org.eclipse.chemclipse.support.history.EditInformation; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.DataProcessingType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.InstrumentConfigurationType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ParamGroupType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ProcessingMethodType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SampleListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SampleType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareType; + +public class MetadataReader110 { + + public static IChromatogram readMetadata(MzMLType mzML, IChromatogram chromatogram) { + + for(ParamGroupType contact : mzML.getFileDescription().getContact()) { + for(CVParamType cvParam : contact.getCvParam()) { + if(chromatogram.getOperator().isEmpty()) { + chromatogram.setOperator(cvParam.getValue()); + } else { + chromatogram.setOperator(String.join(", ", chromatogram.getOperator(), cvParam.getValue())); + } + } + } + SampleListType sampleList = mzML.getSampleList(); + if(sampleList != null) { + for(SampleType sample : sampleList.getSample()) { + if(sample.getName() != null) { + chromatogram.setSampleName(sample.getName()); + } + } + } + for(InstrumentConfigurationType instrument : mzML.getInstrumentConfigurationList().getInstrumentConfiguration()) { + for(CVParamType cvParam : instrument.getCvParam()) { + if(cvParam.getAccession().equals("MS:1000554")) { + chromatogram.setInstrument(cvParam.getName()); + } + } + } + for(DataProcessingType dataProcessing : mzML.getDataProcessingList().getDataProcessing()) { + for(ProcessingMethodType processingMethod : dataProcessing.getProcessingMethod()) { + SoftwareType software = (SoftwareType)processingMethod.getSoftwareRef(); + for(CVParamType cvParam : processingMethod.getCvParam()) { + String operation = cvParam.getName(); + String editor = software.getId() + " " + software.getVersion(); + chromatogram.getEditHistory().add(new EditInformation(operation, editor)); + } + } + } + return chromatogram; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader10.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlReader10.java similarity index 84% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader10.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlReader10.java index a01bc9f953..dd5ecdcd73 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader10.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlReader10.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2021, 2023 Lablicate GmbH. + * Copyright (c) 2021, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.io; import java.io.File; import java.io.IOException; @@ -18,9 +18,9 @@ import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.CVParamType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.MzMLType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model.ObjectFactory; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.ObjectFactory; import org.w3c.dom.Document; import org.w3c.dom.NodeList; import org.xml.sax.SAXException; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader110.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlReader110.java similarity index 85% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader110.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlReader110.java index 560039c21d..78154369cb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader110.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlReader110.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2021, 2023 Lablicate GmbH. + * Copyright (c) 2021, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.io; import java.io.File; import java.io.IOException; @@ -19,9 +19,9 @@ import javax.xml.parsers.ParserConfigurationException; import org.eclipse.chemclipse.model.core.IChromatogramOverview; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.CVParamType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.MzMLType; -import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model.ObjectFactory; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ObjectFactory; import org.w3c.dom.Document; import org.w3c.dom.NodeList; import org.xml.sax.SAXException; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlWriter110.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlWriter110.java new file mode 100644 index 0000000000..500e0e1463 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/XmlWriter110.java @@ -0,0 +1,242 @@ +/******************************************************************************* + * Copyright (c) 2024 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.xxd.converter.supplier.mzml.io; + +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.math.BigInteger; +import java.nio.ByteBuffer; +import java.nio.ByteOrder; +import java.nio.DoubleBuffer; +import java.nio.FloatBuffer; +import java.util.Date; +import java.util.GregorianCalendar; +import java.util.zip.Deflater; + +import javax.xml.datatype.DatatypeConfigurationException; +import javax.xml.datatype.DatatypeFactory; +import javax.xml.datatype.XMLGregorianCalendar; + +import org.apache.commons.codec.digest.DigestUtils; +import org.eclipse.chemclipse.logging.core.Logger; +import org.eclipse.chemclipse.model.core.IChromatogram; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.BinaryDataArrayType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ParamGroupType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareListType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareType; +import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SourceFileType; +import org.eclipse.core.runtime.IProduct; +import org.eclipse.core.runtime.Platform; +import org.osgi.framework.Version; + +import jakarta.xml.bind.DatatypeConverter; + +public class XmlWriter110 { + + public static final CVType MS = createMS(); + public static final CVType UO = createUO(); + // + private static final Logger logger = Logger.getLogger(XmlWriter110.class); + + public static ParamGroupType getOperator(IChromatogram chromatogram) { + + if(!chromatogram.getOperator().isEmpty()) { + ParamGroupType paramGroupType = new ParamGroupType(); + CVParamType cvParam = new CVParamType(); + cvParam.setCvRef(XmlWriter110.MS); + cvParam.setAccession("MS:1000586"); + cvParam.setName("contact name"); + cvParam.setValue(chromatogram.getOperator()); + paramGroupType.getCvParam().add(cvParam); + return paramGroupType; + } + return null; + } + + public static SoftwareListType createSoftwareList() { + + SoftwareListType softwareList = new SoftwareListType(); + softwareList.setCount(BigInteger.valueOf(1)); + SoftwareType software = new SoftwareType(); + IProduct product = Platform.getProduct(); + software.setId("Unknown"); + if(product != null) { + software.setId(product.getName()); + Version version = product.getDefiningBundle().getVersion(); + software.setVersion(version.getMajor() + "." + version.getMinor() + "." + version.getMicro()); + if(product.getName().equals("ChemClipse")) { + CVParamType cvParamSoftware = new CVParamType(); + cvParamSoftware.setCvRef(XmlWriter110.MS); + cvParamSoftware.setAccession("MS:1003376"); + cvParamSoftware.setName("ChemClipse"); + cvParamSoftware.setValue(""); + software.getCvParam().add(cvParamSoftware); + } + if(product.getName().equals("OpenChrom")) { + CVParamType cvParamSoftware = new CVParamType(); + cvParamSoftware.setCvRef(XmlWriter110.MS); + cvParamSoftware.setAccession("MS:1003377"); + cvParamSoftware.setName("OpenChrom"); + cvParamSoftware.setValue(""); + software.getCvParam().add(cvParamSoftware); + } + } + softwareList.getSoftware().add(software); + return softwareList; + } + + public static CVParamType createIntensityArrayType() { + + CVParamType cvParamTotalSignals = new CVParamType(); + cvParamTotalSignals.setCvRef(XmlWriter110.MS); + cvParamTotalSignals.setAccession("MS:1000515"); + cvParamTotalSignals.setName("intensity array"); + cvParamTotalSignals.setUnitCvRef(XmlWriter110.MS); + cvParamTotalSignals.setUnitAccession("MS:1000131"); + cvParamTotalSignals.setUnitName("number of counts"); + return cvParamTotalSignals; + } + + public static CVParamType createRetentionTimeType() { + + CVParamType cvParamRetentionTime = new CVParamType(); + cvParamRetentionTime.setCvRef(XmlWriter110.MS); + cvParamRetentionTime.setAccession("MS:1000595"); + cvParamRetentionTime.setName("time array"); + cvParamRetentionTime.setUnitAccession("UO:0000010"); + cvParamRetentionTime.setUnitName("second"); + return cvParamRetentionTime; + } + + public static XMLGregorianCalendar createDate(IChromatogram chromatogram) throws DatatypeConfigurationException { + + Date date = chromatogram.getDate(); + if(date != null) { + GregorianCalendar calendar = new GregorianCalendar(); + calendar.setTime(date); + return DatatypeFactory.newInstance().newXMLGregorianCalendar(calendar); + } + return null; + } + + public static BinaryDataArrayType createBinaryData(float[] values, boolean compression) { + + FloatBuffer floatBuffer = FloatBuffer.wrap(values); + ByteBuffer byteBuffer = ByteBuffer.allocate(floatBuffer.capacity() * Float.BYTES); + byteBuffer.order(ByteOrder.LITTLE_ENDIAN); + byteBuffer.asFloatBuffer().put(floatBuffer); + BinaryDataArrayType binaryDataArrayType = createBinaryDataArray(byteBuffer, compression); + CVParamType cvParamData = new CVParamType(); + cvParamData.setCvRef(XmlWriter110.MS); + cvParamData.setAccession("MS:1000521"); + cvParamData.setName("32-bit float"); + binaryDataArrayType.getCvParam().add(cvParamData); + return binaryDataArrayType; + } + + public static BinaryDataArrayType createBinaryData(double[] values, boolean compression) { + + DoubleBuffer doubleBuffer = DoubleBuffer.wrap(values); + ByteBuffer byteBuffer = ByteBuffer.allocate(doubleBuffer.capacity() * Double.BYTES); + byteBuffer.order(ByteOrder.LITTLE_ENDIAN); + byteBuffer.asDoubleBuffer().put(doubleBuffer); + BinaryDataArrayType binaryDataArrayType = createBinaryDataArray(byteBuffer, compression); + CVParamType cvParamData = new CVParamType(); + cvParamData.setCvRef(XmlWriter110.MS); + cvParamData.setAccession("MS:1000523"); + cvParamData.setName("64-bit float"); + binaryDataArrayType.getCvParam().add(cvParamData); + return binaryDataArrayType; + } + + private static BinaryDataArrayType createBinaryDataArray(ByteBuffer byteBuffer, boolean compression) { + + BinaryDataArrayType binaryDataArrayType = new BinaryDataArrayType(); + if(compression) { + CVParamType cvParamCompression = new CVParamType(); + cvParamCompression.setCvRef(XmlWriter110.MS); + cvParamCompression.setAccession("MS:1000574"); + cvParamCompression.setName("zlib compression"); + binaryDataArrayType.getCvParam().add(cvParamCompression); + Deflater compresser = new Deflater(); + compresser.setInput(byteBuffer.array()); + compresser.finish(); + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + byte[] readBuffer = new byte[1024]; + while(!compresser.finished()) { + int compressCount = compresser.deflate(readBuffer); + if(compressCount > 0) { + outputStream.write(readBuffer, 0, compressCount); + } + } + byte[] outputByteArray = outputStream.toByteArray(); + String characters = DatatypeConverter.printBase64Binary(outputByteArray); + binaryDataArrayType.setEncodedLength(BigInteger.valueOf(characters.length())); + binaryDataArrayType.setBinary(outputByteArray); + compresser.end(); + } else { + binaryDataArrayType.setBinary(byteBuffer.array()); + } + return binaryDataArrayType; + } + + private static CVType createMS() { + + CVType cvTypeMS = new CVType(); + cvTypeMS.setId("MS"); + cvTypeMS.setFullName("Proteomics Standards Initiative Mass Spectrometry Ontology"); + cvTypeMS.setVersion("4.1.123"); + cvTypeMS.setURI("https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.123/psi-ms.obo"); + return cvTypeMS; + } + + private static CVType createUO() { + + CVType cvTypeUnit = new CVType(); + cvTypeUnit.setId("UO"); + cvTypeUnit.setFullName("Unit Ontology"); + cvTypeUnit.setVersion("2023:05:23"); + cvTypeUnit.setURI("https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/v2023-05-23/unit-ontology.obo"); + return cvTypeUnit; + } + + public static SourceFileType createSourceFile(IChromatogram chromatogram) { + + File file = chromatogram.getFile(); + SourceFileType sourceFile = new SourceFileType(); + sourceFile.setLocation(file.getAbsolutePath()); + sourceFile.setId(file.getName()); + sourceFile.setName(file.getName()); + // + CVParamType cvParamSHA1 = new CVParamType(); + cvParamSHA1.setCvRef(XmlWriter110.MS); + cvParamSHA1.setAccession("MS:1000569"); + cvParamSHA1.setName("SHA-1"); + cvParamSHA1.setValue(calculateSHA1(file)); + sourceFile.getCvParam().add(cvParamSHA1); + return sourceFile; + } + + private static String calculateSHA1(File file) { + + try (FileInputStream fis = new FileInputStream(file)) { + return DigestUtils.sha1Hex(fis); + } catch(IOException e) { + logger.warn(e); + } + return ""; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionListType.java index 076d633da0..4b71586696 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionSettingsListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionSettingsListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionSettingsListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionSettingsListType.java index 38f8e73324..3f17c0a514 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionSettingsListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionSettingsListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionSettingsType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionSettingsType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionSettingsType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionSettingsType.java index 79ff0f9164..bea7efa5ea 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionSettingsType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionSettingsType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionType.java index 0d19ba35ff..4caf995b4d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/AcquisitionType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/AcquisitionType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/BinaryDataArrayListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/BinaryDataArrayListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/BinaryDataArrayListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/BinaryDataArrayListType.java index 3d72416d32..f02e3f4daa 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/BinaryDataArrayListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/BinaryDataArrayListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/BinaryDataArrayType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/BinaryDataArrayType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/BinaryDataArrayType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/BinaryDataArrayType.java index 906627d02a..00d82e7332 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/BinaryDataArrayType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/BinaryDataArrayType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVListType.java index b6e406eafb..3f499d5ec3 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVParamType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVParamType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVParamType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVParamType.java index 79b0d1db7e..f8eab017f2 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVParamType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVParamType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVType.java index 3726b958da..20078d42fa 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/CVType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/CVType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ChromatogramListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ChromatogramListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ChromatogramListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ChromatogramListType.java index d8b1e201ae..374602848c 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ChromatogramListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ChromatogramListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ChromatogramType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ChromatogramType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ChromatogramType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ChromatogramType.java index 0c0fda0dd3..8a3b6173e7 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ChromatogramType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ChromatogramType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ComponentListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ComponentListType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ComponentListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ComponentListType.java index d26e180675..a11faa8f73 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ComponentListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ComponentListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ComponentType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ComponentType.java similarity index 89% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ComponentType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ComponentType.java index f94169af7f..2d0dea871f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ComponentType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ComponentType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/DataProcessingListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/DataProcessingListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/DataProcessingListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/DataProcessingListType.java index a854dd7752..81075d0150 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/DataProcessingListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/DataProcessingListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/DataProcessingType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/DataProcessingType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/DataProcessingType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/DataProcessingType.java index 6345bf6f3b..80247e43f7 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/DataProcessingType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/DataProcessingType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/FileDescriptionType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/FileDescriptionType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/FileDescriptionType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/FileDescriptionType.java index 7c7b1dbb85..4559c996b5 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/FileDescriptionType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/FileDescriptionType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/InstrumentConfigurationListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/InstrumentConfigurationListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/InstrumentConfigurationListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/InstrumentConfigurationListType.java index e1924fe26f..78d898bcf3 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/InstrumentConfigurationListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/InstrumentConfigurationListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/InstrumentConfigurationType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/InstrumentConfigurationType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/InstrumentConfigurationType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/InstrumentConfigurationType.java index 5cf23555b8..a89d45e519 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/InstrumentConfigurationType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/InstrumentConfigurationType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/MzMLType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/MzMLType.java similarity index 97% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/MzMLType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/MzMLType.java index 936c4a882f..128bfe0f46 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/MzMLType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/MzMLType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.io.Serializable; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ObjectFactory.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ObjectFactory.java similarity index 98% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ObjectFactory.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ObjectFactory.java index cab09d6bab..6a0b3cdaf9 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ObjectFactory.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ObjectFactory.java @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import javax.xml.namespace.QName; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ParamGroupType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ParamGroupType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ParamGroupType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ParamGroupType.java index 052622d86d..29982a6bbd 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ParamGroupType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ParamGroupType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/PrecursorListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/PrecursorListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/PrecursorListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/PrecursorListType.java index c00d1a6ab3..3f151c36d8 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/PrecursorListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/PrecursorListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/PrecursorType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/PrecursorType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/PrecursorType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/PrecursorType.java index 5a51c1486f..101392d669 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/PrecursorType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/PrecursorType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ProcessingMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ProcessingMethodType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ProcessingMethodType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ProcessingMethodType.java index b059078ab7..8f2b5fae43 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ProcessingMethodType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ProcessingMethodType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupListType.java index b1a4e28955..436feff475 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupRefType.java similarity index 91% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupRefType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupRefType.java index feb3cf997f..ec415bf493 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupRefType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupRefType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupType.java index 0fe6b14ccc..58c99d4131 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ReferenceableParamGroupType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ReferenceableParamGroupType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/RunType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/RunType.java similarity index 96% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/RunType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/RunType.java index 8d1b9b8d3a..f7bf6b990d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/RunType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/RunType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import javax.xml.datatype.XMLGregorianCalendar; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SampleListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SampleListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SampleListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SampleListType.java index df12773697..0d4b2dc274 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SampleListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SampleListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SampleType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SampleType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SampleType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SampleType.java index bc5bbed8aa..11fbe9cc54 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SampleType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SampleType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanType.java index ecdd3ba1cf..50bfae5d2d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanWindowListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanWindowListType.java similarity index 91% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanWindowListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanWindowListType.java index 48165ce69e..9f1f0e71a7 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanWindowListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanWindowListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanWindowType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanWindowType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanWindowType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanWindowType.java index 3c10096405..a09d1b908f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/ScanWindowType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/ScanWindowType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SelectedIonListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SelectedIonListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SelectedIonListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SelectedIonListType.java index d43b956df5..87d8b1cc8e 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SelectedIonListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SelectedIonListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareListType.java index fe8df789e2..6a2c503ba5 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareParamType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareParamType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareParamType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareParamType.java index 8becf8ece3..2df9c22829 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareParamType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareParamType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareRefType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareRefType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareRefType.java index 3ecb61f084..9851b67815 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareRefType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareRefType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareType.java index 189b9dc76b..f5362a4a45 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SoftwareType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SoftwareType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileListType.java index a80ac60ccf..5cea7ebc1d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileRefListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileRefListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileRefListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileRefListType.java index 563dc3c781..2877a2129b 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileRefListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileRefListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileRefType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileRefType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileRefType.java index 0ee51198b9..efc9210388 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileRefType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileRefType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileType.java index 257d5e098a..7122372976 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SourceFileType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SourceFileType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumDescriptionType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumDescriptionType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumDescriptionType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumDescriptionType.java index 64a8451a4f..b236634ecb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumDescriptionType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumDescriptionType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumListType.java index 71df8744bb..57d58f44d1 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumType.java similarity index 96% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumType.java index b74449e34d..1ccb399014 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/SpectrumType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/SpectrumType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/TargetListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/TargetListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/TargetListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/TargetListType.java index 53bf430013..73a3f0f5bb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/TargetListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/TargetListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/UserParamType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/UserParamType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/UserParamType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/UserParamType.java index 36ae4c2587..c3d17cff16 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v10/model/UserParamType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v10/UserParamType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Matthias Mailänder - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v10.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/AnalyzerComponentType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/AnalyzerComponentType.java similarity index 86% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/AnalyzerComponentType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/AnalyzerComponentType.java index ea59783589..06589c7582 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/AnalyzerComponentType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/AnalyzerComponentType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/BinaryDataArrayListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/BinaryDataArrayListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/BinaryDataArrayListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/BinaryDataArrayListType.java index c3760f55a3..419a371dcd 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/BinaryDataArrayListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/BinaryDataArrayListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/BinaryDataArrayType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/BinaryDataArrayType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/BinaryDataArrayType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/BinaryDataArrayType.java index becee5992e..ea90e2fa78 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/BinaryDataArrayType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/BinaryDataArrayType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2022 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVListType.java similarity index 91% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVListType.java index 8e986eacad..831c8cafb0 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVParamType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVParamType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVParamType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVParamType.java index 121d83ac19..8aa71b2c27 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVParamType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVParamType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVType.java index b673b41661..a5f6aaa322 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/CVType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/CVType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ChromatogramListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ChromatogramListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ChromatogramListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ChromatogramListType.java index ba6a26552c..b9bb29753d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ChromatogramListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ChromatogramListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ChromatogramType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ChromatogramType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ChromatogramType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ChromatogramType.java index 9123200c33..29a8fdcfe2 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ChromatogramType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ChromatogramType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ComponentListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ComponentListType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ComponentListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ComponentListType.java index 32ab427bc4..d6f7bafa9c 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ComponentListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ComponentListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ComponentType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ComponentType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ComponentType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ComponentType.java index 2301e7c477..fc76ca2232 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ComponentType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ComponentType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DataProcessingListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DataProcessingListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DataProcessingListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DataProcessingListType.java index fb7edbbf46..a5d29896a7 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DataProcessingListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DataProcessingListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DataProcessingType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DataProcessingType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DataProcessingType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DataProcessingType.java index 6673987eca..15ea6faa64 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DataProcessingType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DataProcessingType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DetectorComponentType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DetectorComponentType.java similarity index 86% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DetectorComponentType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DetectorComponentType.java index 3a6fe1cfac..d265c88df0 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/DetectorComponentType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/DetectorComponentType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/FileDescriptionType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/FileDescriptionType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/FileDescriptionType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/FileDescriptionType.java index cc427cf43c..04e9769874 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/FileDescriptionType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/FileDescriptionType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/InstrumentConfigurationListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/InstrumentConfigurationListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/InstrumentConfigurationListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/InstrumentConfigurationListType.java index d8b64b9993..7cc4ad32bf 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/InstrumentConfigurationListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/InstrumentConfigurationListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/InstrumentConfigurationType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/InstrumentConfigurationType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/InstrumentConfigurationType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/InstrumentConfigurationType.java index 718c995ad9..7065f97dd1 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/InstrumentConfigurationType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/InstrumentConfigurationType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/MzMLType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/MzMLType.java similarity index 96% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/MzMLType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/MzMLType.java index 75a579aed3..3644729530 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/MzMLType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/MzMLType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.io.Serializable; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ObjectFactory.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ObjectFactory.java similarity index 97% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ObjectFactory.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ObjectFactory.java index 0d7a87ebe7..428e4e2047 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ObjectFactory.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ObjectFactory.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlRegistry; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ParamGroupType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ParamGroupType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ParamGroupType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ParamGroupType.java index 4aaeb13cdb..9140c31dd0 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ParamGroupType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ParamGroupType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/PrecursorListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/PrecursorListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/PrecursorListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/PrecursorListType.java index edbcd3513c..954ebf9937 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/PrecursorListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/PrecursorListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/PrecursorType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/PrecursorType.java similarity index 95% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/PrecursorType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/PrecursorType.java index 44fae0b282..6ee31f6a87 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/PrecursorType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/PrecursorType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProcessingMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProcessingMethodType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProcessingMethodType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProcessingMethodType.java index 2dc74d94b0..5e7a3bd258 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProcessingMethodType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProcessingMethodType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProductListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProductListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProductListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProductListType.java index 22fc0faee8..810c0d7538 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProductListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProductListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProductType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProductType.java similarity index 88% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProductType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProductType.java index 4462dbfd5f..da23d6cd50 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ProductType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ProductType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupListType.java index b5a90df683..77752051e3 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupRefType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupRefType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupRefType.java index 3e680a1260..6d895abfbe 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupRefType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupRefType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupType.java index 99195b1d5c..727f5520c1 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ReferenceableParamGroupType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ReferenceableParamGroupType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/RunType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/RunType.java similarity index 96% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/RunType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/RunType.java index 3a23fc36d4..30175d720d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/RunType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/RunType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import javax.xml.datatype.XMLGregorianCalendar; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SampleListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SampleListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SampleListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SampleListType.java index 1d5b49f69f..9a04694a01 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SampleListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SampleListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SampleType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SampleType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SampleType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SampleType.java index f4f7238e38..c6f24e6a5a 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SampleType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SampleType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanListType.java similarity index 91% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanListType.java index 6898a1cfb9..8748390757 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanSettingsListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanSettingsListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanSettingsListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanSettingsListType.java index 3f98dd9cf6..497cc6df01 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanSettingsListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanSettingsListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanSettingsType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanSettingsType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanSettingsType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanSettingsType.java index 50ba9b8133..4fb1a1461e 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanSettingsType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanSettingsType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanType.java index 9d371eedc0..a395dabe87 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanWindowListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanWindowListType.java similarity index 91% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanWindowListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanWindowListType.java index 9847b5c4df..a5b5ae2f3b 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/ScanWindowListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/ScanWindowListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.util.ArrayList; import java.util.List; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SelectedIonListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SelectedIonListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SelectedIonListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SelectedIonListType.java index 06f479f471..b1d68d8cd1 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SelectedIonListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SelectedIonListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareListType.java index b592007cc7..59e5ed7ee3 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareRefType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareRefType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareRefType.java index c9598e2b5c..7f7bdb891f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareRefType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareRefType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareType.java index 7d011dde56..2f0914b858 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SoftwareType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SoftwareType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceComponentType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceComponentType.java similarity index 86% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceComponentType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceComponentType.java index f97394aea1..9d33bb5749 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceComponentType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceComponentType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileListType.java index 4f62ff425d..1f486f9b42 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileRefListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileRefListType.java similarity index 91% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileRefListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileRefListType.java index 8677f76bc0..ab83f59e04 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileRefListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileRefListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileRefType.java similarity index 90% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileRefType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileRefType.java index e4dc42ce64..b00a6ac8bb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileRefType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileRefType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileType.java index dd5a53fa68..d55e5de7f8 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SourceFileType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SourceFileType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SpectrumListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SpectrumListType.java similarity index 93% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SpectrumListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SpectrumListType.java index 08a3523f61..bd0f892375 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SpectrumListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SpectrumListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2023 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SpectrumType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SpectrumType.java similarity index 96% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SpectrumType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SpectrumType.java index be073237bf..2ad932fb19 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/SpectrumType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/SpectrumType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2022 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/TargetListType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/TargetListType.java similarity index 92% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/TargetListType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/TargetListType.java index c070a33dce..fa5cba59e7 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/TargetListType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/TargetListType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import java.math.BigInteger; import java.util.ArrayList; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/UserParamType.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/UserParamType.java similarity index 94% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/UserParamType.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/UserParamType.java index b82274c921..97983ec72d 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/UserParamType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/UserParamType.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2015, 2018 Lablicate GmbH. + * Copyright (c) 2015, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -9,7 +9,7 @@ * Contributors: * Dr. Philip Wenig - initial API and implementation *******************************************************************************/ -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlAccessType; import jakarta.xml.bind.annotation.XmlAccessorType; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/package-info.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/package-info.java similarity index 87% rename from chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/package-info.java rename to chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/package-info.java index 1bc0caedc1..dc9be0f551 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/v110/model/package-info.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/model/v110/package-info.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright (c) 2023 Lablicate GmbH. + * Copyright (c) 2023, 2024 Lablicate GmbH. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 @@ -10,7 +10,7 @@ * Matthias Mailänder - initial API and implementation *******************************************************************************/ @XmlSchema(namespace = "http://psi.hupo.org/ms/mzml", elementFormDefault = XmlNsForm.QUALIFIED, xmlns = {@XmlNs(namespaceURI = "http://psi.hupo.org/ms/mzml", prefix = "")}) -package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model; +package org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110; import jakarta.xml.bind.annotation.XmlNs; import jakarta.xml.bind.annotation.XmlNsForm; diff --git a/chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverterTinyProteoWizard10_ITest.java b/chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverterTinyProteoWizard10_ITest.java index 7b9e6b991e..ecdf386e1d 100644 --- a/chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverterTinyProteoWizard10_ITest.java +++ b/chemclipse/tests/org.eclipse.chemclipse.msd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverterTinyProteoWizard10_ITest.java @@ -96,7 +96,7 @@ public void testMaxIonAbundance() { } @Test - public void testFirstScan() { + public void testFirstScan() { IRegularMassSpectrum massSpectrum = (IRegularMassSpectrum)chromatogram.getScan(1); assertEquals("Ions", 15, massSpectrum.getNumberOfIons()); diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.classpath b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.classpath new file mode 100644 index 0000000000..81fe078c20 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.classpath @@ -0,0 +1,7 @@ + + + + + + + diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.gitignore b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.gitignore new file mode 100644 index 0000000000..5e56e040ec --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.gitignore @@ -0,0 +1 @@ +/bin diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.project b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.project new file mode 100644 index 0000000000..480971910c --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.project @@ -0,0 +1,28 @@ + + + org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.pde.ManifestBuilder + + + + + org.eclipse.pde.SchemaBuilder + + + + + + org.eclipse.pde.PluginNature + org.eclipse.jdt.core.javanature + + diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.settings/org.eclipse.core.resources.prefs b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 0000000000..801fab74d0 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,2 @@ +eclipse.preferences.version=1 +encoding/=utf8 diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.settings/org.eclipse.jdt.core.prefs b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000000..9154beff79 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,7 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=17 +org.eclipse.jdt.core.compiler.compliance=17 +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.source=17 diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/META-INF/MANIFEST.MF b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/META-INF/MANIFEST.MF new file mode 100644 index 0000000000..b5ea65b740 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/META-INF/MANIFEST.MF @@ -0,0 +1,14 @@ +Manifest-Version: 1.0 +Automatic-Module-Name: org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test +Bundle-ManifestVersion: 2 +Bundle-Name: mzML DAD Test +Bundle-SymbolicName: org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test +Bundle-Version: 0.9.0.qualifier +Bundle-Vendor: ChemClipse +Fragment-Host: org.eclipse.chemclipse.wsd.converter.supplier.mzml;bundle-version="0.8.0" +Bundle-RequiredExecutionEnvironment: JavaSE-17 +Require-Bundle: org.junit;bundle-version="4.11.0", + org.eclipse.chemclipse.rcp.app.test;bundle-version="0.9.0", + com.sun.xml.bind.jaxb-core;bundle-version="4.0.1", + com.sun.xml.bind.jaxb-impl;bundle-version="4.0.1", + org.glassfish.hk2.osgi-resource-locator;bundle-version="1.0.3" diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/build.properties b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/build.properties new file mode 100644 index 0000000000..34d2e4d2da --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/build.properties @@ -0,0 +1,4 @@ +source.. = src/ +output.. = bin/ +bin.includes = META-INF/,\ + . diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/TestPathHelper.java b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/TestPathHelper.java new file mode 100644 index 0000000000..8102b3efb8 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/TestPathHelper.java @@ -0,0 +1,17 @@ +/******************************************************************************* + * Copyright (c) 2024 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.wsd.converter.supplier.mzml; + +public class TestPathHelper extends PathResolver { + + public static final String TESTFILE_PDA_HANDCRAFTED = "testData/PDA.mzML"; +} diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramImportConverterHandCrafted110_ITest.java b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramImportConverterHandCrafted110_ITest.java new file mode 100644 index 0000000000..1744bfb68a --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/src/org/eclipse/chemclipse/wsd/converter/supplier/mzml/converter/ChromatogramImportConverterHandCrafted110_ITest.java @@ -0,0 +1,107 @@ +/******************************************************************************* + * Copyright (c) 2024 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.wsd.converter.supplier.mzml.converter; + +import java.io.File; + +import org.eclipse.chemclipse.processing.core.IProcessingInfo; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.TestPathHelper; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.IVendorChromatogram; +import org.eclipse.chemclipse.wsd.converter.supplier.mzml.model.VendorChromatogram; +import org.eclipse.chemclipse.wsd.model.core.IChromatogramWSD; +import org.eclipse.chemclipse.wsd.model.core.IScanWSD; +import org.eclipse.core.runtime.NullProgressMonitor; +import org.junit.Test; + +import junit.framework.TestCase; + +public class ChromatogramImportConverterHandCrafted110_ITest extends TestCase { + + private IVendorChromatogram chromatogram; + + @Override + protected void setUp() throws Exception { + + super.setUp(); + File importFile = new File(TestPathHelper.getAbsolutePath(TestPathHelper.TESTFILE_PDA_HANDCRAFTED)); + ChromatogramImportConverter converter = new ChromatogramImportConverter(); + IProcessingInfo processingInfo = converter.convert(importFile, new NullProgressMonitor()); + chromatogram = (VendorChromatogram)processingInfo.getProcessingResult(); + } + + @Test + public void testSample() { + + assertEquals("Sample1", chromatogram.getSampleName()); + } + + @Test + public void testOperator() { + + assertEquals("William Pennington, Higglesworth University, 12 Higglesworth Avenue, 12045, HI, USA, http://www.higglesworth.edu/, wpennington@higglesworth.edu, dort, Drek'Thar, da", chromatogram.getOperator()); + } + + @Test + public void testEditHistory() { + + assertEquals("Conversion to mzML", chromatogram.getEditHistory().get(0).getDescription()); + } + + @Test + public void testNumberOfScans() { + + assertEquals("NumberOfScans", 15, chromatogram.getNumberOfScans()); + } + + @Test + public void testStartRetentionTime() { + + assertEquals("Start RT", 0, chromatogram.getStartRetentionTime()); + } + + @Test + public void testStopRetentionTime() { + + assertEquals("Stop RT", 14000, chromatogram.getStopRetentionTime()); + } + + @Test + public void testTotalSignal() { + + assertEquals("Total Signal", 225.0f, chromatogram.getTotalSignal()); + } + + @Test + public void testMaxAbsorption() { + + assertEquals("Max Signal", 120.0f, chromatogram.getMaxSignal()); + } + + @Test + public void testScans() { + + IScanWSD pdaSpectrum = (IScanWSD)chromatogram.getScan(1); + assertEquals("Scans", 15, pdaSpectrum.getNumberOfScanSignals()); + assertEquals(15f, pdaSpectrum.getScanSignal(0).getAbsorbance()); + assertEquals(0f, pdaSpectrum.getScanSignal(0).getWavelength()); + assertEquals(14f, pdaSpectrum.getScanSignal(1).getAbsorbance()); + assertEquals(1f, pdaSpectrum.getScanSignal(1).getWavelength()); + assertEquals(13f, pdaSpectrum.getScanSignal(2).getAbsorbance()); + assertEquals(2f, pdaSpectrum.getScanSignal(2).getWavelength()); + assertEquals(12f, pdaSpectrum.getScanSignal(3).getAbsorbance()); + assertEquals(3f, pdaSpectrum.getScanSignal(3).getWavelength()); + assertEquals(11f, pdaSpectrum.getScanSignal(4).getAbsorbance()); + assertEquals(4f, pdaSpectrum.getScanSignal(4).getWavelength()); + assertEquals(10f, pdaSpectrum.getScanSignal(5).getAbsorbance()); + assertEquals(5f, pdaSpectrum.getScanSignal(5).getWavelength()); + } +} diff --git a/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/testData/PDA.mzML b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/testData/PDA.mzML new file mode 100644 index 0000000000..9e8f5f583e --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.wsd.converter.supplier.mzml.fragment.test/testData/PDA.mzML @@ -0,0 +1,190 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkAAAAAAAAAkQAAAAAAAACZAAAAAAAAAKEAAAAAAAAAqQAAAAAAAACxA + + + + + + + AAAAAAAALkAAAAAAAAAsQAAAAAAAACpAAAAAAAAAKEAAAAAAAAAmQAAAAAAAACRAAAAAAAAAIkAAAAAAAAAgQAAAAAAAABxAAAAAAAAAGEAAAAAAAAAUQAAAAAAAABBAAAAAAAAACEAAAAAAAAAAQAAAAAAAAPA/ + + + + + + + + + + + + + + + + AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkAAAAAAAAAkQAAAAAAAACZAAAAAAAAAKEAAAAAAAAAqQAAAAAAAACxA + + + + + + AAAAAAAALkAAAAAAAAAsQAAAAAAAACpAAAAAAAAAKEAAAAAAAAAmQAAAAAAAACRAAAAAAAAAIkAAAAAAAAAgQAAAAAAAABxAAAAAAAAAGEAAAAAAAAAUQAAAAAAAABBAAAAAAAAACEAAAAAAAAAAQAAAAAAAAPA/ + + + + + + + +