Merge pull request #911 from Mailaender/mmass-msd

Added an import converter for mMass .msd files

chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mmass.feature/.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>org.eclipse.chemclipse.msd.converter.supplier.mmass.feature</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.pde.FeatureBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.FeatureNature</nature>
+	</natures>
+</projectDescription>

chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mmass.feature/build.properties

@@ -0,0 +1 @@
+bin.includes = feature.xml

chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mmass.feature/feature.xml

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<feature
+      id="org.eclipse.chemclipse.msd.converter.supplier.mmass.feature"
+      label="mMass Converter"
+      version="0.9.0.qualifier"
+      provider-name="ChemClipse"
+      plugin="org.eclipse.chemclipse.feature.branding">
+
+   <description url="http://www.mmass.org/">
+      This is the mMass .msd file converter.
+   </description>
+
+   <copyright url="http://www.chemclipse.net/">
+      Copyright (c) 2022 Lablicate GmbH.
+   </copyright>
+
+   <license url="http://www.eclipse.org/legal/epl-v10.html">
+      Copyright (c) 2022 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
+   </license>
+
+   <plugin
+         id="org.eclipse.chemclipse.msd.converter.supplier.mmass"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+</feature>

chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mzml.feature/feature.xml

@@ -1,9 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <feature
       id="org.eclipse.chemclipse.msd.converter.supplier.mzml.feature"
-      label="MSD mzML"
+      label="mzML Converter"
       version="0.9.0.qualifier"
-      provider-name="ChemClipse" plugin="org.eclipse.chemclipse.feature.branding">
+      provider-name="ChemClipse"
+      plugin="org.eclipse.chemclipse.feature.branding">
 
    <description url="http://www.chemclipse.net/plugins/converter/mzml/">
       This is the mzML chromatogram converter.

chemclipse/features/org.eclipse.chemclipse.rcp.app.compilation.core.feature/feature.xml

@@ -3,7 +3,8 @@
       id="org.eclipse.chemclipse.rcp.app.compilation.core.feature"
       label="ChemClipse Core"
       version="0.9.0.qualifier"
-      provider-name="ChemClipse" plugin="org.eclipse.chemclipse.feature.branding">
+      provider-name="ChemClipse"
+      plugin="org.eclipse.chemclipse.feature.branding">
 
    <description url="http://www.chemclipse.net">
       This is the ChemClipse core feature.
@@ -232,18 +233,18 @@ http://www.eclipse.org/legal/epl-v10.html
    <includes
          id="org.eclipse.chemclipse.msd.classifier.supplier.molpeak.feature"
          version="0.0.0"/>
-         
+
    <includes
          id="org.eclipse.chemclipse.xxd.converter.supplier.ascii.feature"
          version="0.0.0"/>
 
    <includes
          id="org.eclipse.chemclipse.csd.converter.supplier.arw.feature"
          version="0.0.0"/>
-         
+
    <includes
          id="org.eclipse.chemclipse.wsd.converter.supplier.arw.feature"
-         version="0.0.0"/>         
+         version="0.0.0"/>
 
    <includes
          id="org.eclipse.chemclipse.xxd.converter.supplier.zip.feature"
@@ -269,4 +270,8 @@ http://www.eclipse.org/legal/epl-v10.html
          id="org.eclipse.chemclipse.msd.converter.supplier.sirius.feature"
          version="0.0.0"/>
 
+   <includes
+         id="org.eclipse.chemclipse.msd.converter.supplier.mmass.feature"
+         version="0.0.0"/>
+
 </feature>

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/.classpath

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/.gitignore

@@ -0,0 +1 @@
+/bin

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/.project

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>org.eclipse.chemclipse.msd.converter.supplier.mmass</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ManifestBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.SchemaBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.PluginNature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/.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=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.8

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/META-INF/MANIFEST.MF

@@ -0,0 +1,22 @@
+Manifest-Version: 1.0
+Automatic-Module-Name: org.eclipse.chemclipse.msd.converter.supplier.mzml
+Eclipse-RegisterBuddy: org.eclipse.chemclipse.model, org.eclipse.chemclipse.msd.model
+Bundle-ManifestVersion: 2
+Bundle-Name: mMass Converter
+Bundle-SymbolicName: org.eclipse.chemclipse.msd.converter.supplier.mmass;singleton:=true
+Bundle-Version: 0.9.0.qualifier
+Bundle-Activator: org.eclipse.chemclipse.msd.converter.supplier.mmass.Activator
+Bundle-Vendor: ChemClipse
+Require-Bundle: org.eclipse.core.runtime,
+ org.eclipse.chemclipse.msd.converter;bundle-version="0.8.0",
+ org.eclipse.chemclipse.msd.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.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.codec;bundle-version="1.9.0"
+Bundle-RequiredExecutionEnvironment: JavaSE-1.8
+Bundle-ActivationPolicy: lazy
+Import-Package: org.apache.commons.lang3.tuple;version="3.1.0",
+ org.eclipse.chemclipse.xxd.converter.supplier.io.exception

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/OSGI-INF/l10n/bundle_en.properties

@@ -0,0 +1 @@
+#Properties file

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/build.properties

@@ -0,0 +1,6 @@
+source.. = src/
+output.. = bin/
+bin.includes = META-INF/,\
+               .,\
+               plugin.xml,\
+               OSGI-INF/

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/plugin.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+   <extension
+         point="org.eclipse.chemclipse.msd.converter.massSpectrumSupplier">
+      <MassSpectrumSupplier
+            description="Reads mMass .msd Mass Spectra"
+            exportConverter="org.eclipse.chemclipse.msd.converter.supplier.mmass.converter.MassSpectrumExportConverter"
+            fileExtension=".msd"
+            filterName="mMass Mass Spectrum (*.msd)"
+            id="org.eclipse.chemclipse.msd.converter.supplier.mmass"
+            importConverter="org.eclipse.chemclipse.msd.converter.supplier.mmass.converter.MassSpectrumImportConverter"
+            importMagicNumberMatcher="org.eclipse.chemclipse.msd.converter.supplier.mmass.converter.MassSpectrumMagicNumberMatcher"
+            isExportable="false"
+            isImportable="true">
+      </MassSpectrumSupplier>
+   </extension>
+</plugin>

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/Activator.java

@@ -0,0 +1,43 @@
+/*******************************************************************************
+ * Copyright (c) 2013, 2022 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.mmass;
+
+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;
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/converter/MassSpectrumExportConverter.java

@@ -0,0 +1,45 @@
+/*******************************************************************************
+ * Copyright (c) 2022 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.mmass.converter;
+
+import java.io.File;
+
+import org.eclipse.chemclipse.msd.converter.massspectrum.AbstractMassSpectrumExportConverter;
+import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
+import org.eclipse.chemclipse.msd.model.core.IScanMSD;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.chemclipse.processing.core.ProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+
+public class MassSpectrumExportConverter extends AbstractMassSpectrumExportConverter {
+
+	private static final String DESCRIPTION = "mMass .msd Mass Spectra Export Converter";
+
+	@Override
+	public IProcessingInfo<IMassSpectra> convert(File file, IScanMSD massSpectrum, boolean append, IProgressMonitor monitor) {
+
+		return getProcessingInfo();
+	}
+
+	@Override
+	public IProcessingInfo<IMassSpectra> convert(File file, IMassSpectra massSpectra, boolean append, IProgressMonitor monitor) {
+
+		return getProcessingInfo();
+	}
+
+	private IProcessingInfo<IMassSpectra> getProcessingInfo() {
+
+		IProcessingInfo<IMassSpectra> processingInfo = new ProcessingInfo<>();
+		processingInfo.addErrorMessage(DESCRIPTION, "It's not possible to export mass spectra as mMass .msd yet.");
+		return processingInfo;
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/converter/MassSpectrumImportConverter.java

@@ -0,0 +1,62 @@
+/*******************************************************************************
+ * Copyright (c) 2022 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.mmass.converter;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+import org.eclipse.chemclipse.converter.exceptions.FileIsEmptyException;
+import org.eclipse.chemclipse.converter.exceptions.FileIsNotReadableException;
+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.mmass.converter.io.MassSpectrumReader;
+import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+
+public class MassSpectrumImportConverter extends AbstractMassSpectrumImportConverter {
+
+	private static final Logger logger = Logger.getLogger(MassSpectrumImportConverter.class);
+	private static final String DESCRIPTION = "mMass .msd annotated Mass Spectrum Import";
+
+	@Override
+	public IProcessingInfo<IMassSpectra> convert(File file, IProgressMonitor monitor) {
+
+		IProcessingInfo<IMassSpectra> processingInfo = super.validate(file);
+		if(!processingInfo.hasErrorMessages()) {
+			try {
+				IMassSpectraReader massSpectraReader = new MassSpectrumReader();
+				IMassSpectra massSpectra = massSpectraReader.read(file, monitor);
+				if(massSpectra != null && massSpectra.size() > 0) {
+					processingInfo.setProcessingResult(massSpectra);
+				} else {
+					processingInfo.addErrorMessage(DESCRIPTION, "No mass spectra are stored." + file.getAbsolutePath());
+				}
+			} catch(FileNotFoundException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "The file couldn't be found: " + file.getAbsolutePath());
+			} catch(FileIsNotReadableException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "The file is not readable: " + file.getAbsolutePath());
+			} catch(FileIsEmptyException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "The file is empty: " + file.getAbsolutePath());
+			} catch(IOException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "Something has gone completely wrong: " + file.getAbsolutePath());
+			}
+		}
+		return processingInfo;
+	}
+}