Read support for SCF trace files.

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

@@ -320,4 +320,8 @@
          id="org.eclipse.chemclipse.chromatogram.xxd.identifier.supplier.timeranges.feature"
          version="0.0.0"/>
 
+   <includes
+         id="org.eclipse.chemclipse.wsd.converter.supplier.scf.feature"
+         version="0.0.0"/>
+
 </feature>

chemclipse/features/org.eclipse.chemclipse.wsd.converter.supplier.scf.feature/.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>org.eclipse.chemclipse.wsd.converter.supplier.scf.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.wsd.converter.supplier.scf.feature/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=utf8

chemclipse/features/org.eclipse.chemclipse.wsd.converter.supplier.scf.feature/build.properties

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

chemclipse/features/org.eclipse.chemclipse.wsd.converter.supplier.scf.feature/feature.xml

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<feature
+      id="org.eclipse.chemclipse.wsd.converter.supplier.scf.feature"
+      label="SCF Converter"
+      version="0.9.0.qualifier"
+      provider-name="ChemClipse"
+      plugin="org.eclipse.chemclipse.feature.branding"
+      license-feature="org.eclipse.license"
+      license-feature-version="1.0.0.qualifier">
+
+   <description url="http://www.chemclipse.net">
+      SCF DNA sequencing data converter
+   </description>
+
+   <copyright url="http://www.lablicate.com">
+      Copyright (c) 2024 Lablicate GmbH.
+   </copyright>
+
+   <license url="%licenseURL">
+      %license
+   </license>
+
+   <plugin
+         id="org.eclipse.chemclipse.wsd.converter.supplier.scf"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+</feature>

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/.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-17"/>
+	<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.wsd.converter.supplier.scf/.gitignore

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

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/.project

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>org.eclipse.chemclipse.wsd.converter.supplier.scf</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.wsd.converter.supplier.scf/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=utf8

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/.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

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/META-INF/MANIFEST.MF

@@ -0,0 +1,19 @@
+Manifest-Version: 1.0
+Automatic-Module-Name: net.openchrom.wsd.converter.supplier.abif
+Bundle-ManifestVersion: 2
+Bundle-Name: SCF Converter
+Bundle-SymbolicName: org.eclipse.chemclipse.wsd.converter.supplier.scf;singleton:=true
+Bundle-Version: 0.9.0.qualifier
+Bundle-Activator: org.eclipse.chemclipse.wsd.converter.supplier.scf.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.apache.commons.lang3
+Bundle-RequiredExecutionEnvironment: JavaSE-17
+Bundle-ActivationPolicy: lazy

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/OSGI-INF/l10n/bundle_en.properties

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

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/build.properties

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

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/plugin.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+   <extension
+         point="org.eclipse.chemclipse.wsd.converter.chromatogramSupplier">
+      <ChromatogramSupplier
+            description="Reads Staden Trace Files."
+            fileExtension=".scf"
+            filterName="Standard Chromatogram Format (*.scf)"
+            id="org.eclipse.chemclipse.wsd.converter.supplier.scf"
+            importConverter="org.eclipse.chemclipse.wsd.converter.supplier.scf.core.ChromatogramImportConverter"
+            importMagicNumberMatcher="org.eclipse.chemclipse.wsd.converter.supplier.scf.core.MagicNumberMatcher"
+            isExportable="false"
+            isImportable="true">
+      </ChromatogramSupplier>
+   </extension>
+</plugin>

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/src/org/eclipse/chemclipse/wsd/converter/supplier/scf/Activator.java

@@ -0,0 +1,45 @@
+/*******************************************************************************
+ * 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:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.wsd.converter.supplier.scf;
+
+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;
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/src/org/eclipse/chemclipse/wsd/converter/supplier/scf/PathResolver.java

@@ -0,0 +1,45 @@
+/*******************************************************************************
+ * 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:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.wsd.converter.supplier.scf;
+
+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/test.scf
+	 * 
+	 * @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;
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/src/org/eclipse/chemclipse/wsd/converter/supplier/scf/core/ChromatogramImportConverter.java

@@ -0,0 +1,68 @@
+/*******************************************************************************
+ * 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.scf.core;
+
+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.scf.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<IChromatogramWSD> {
+
+	private static final Logger logger = Logger.getLogger(ChromatogramImportConverter.class);
+	private static final String DESCRIPTION = "SCF Import Converter";
+
+	@Override
+	public IProcessingInfo<IChromatogramWSD> convert(File file, IProgressMonitor monitor) {
+
+		IProcessingInfo<IChromatogramWSD> processingInfo = super.validate(file);
+		if(!processingInfo.hasErrorMessages()) {
+			IChromatogramWSDReader reader = new ChromatogramReader();
+			monitor.subTask(ConverterMessages.importChromatogram);
+			try {
+				IChromatogramWSD chromatogram = reader.read(file, monitor);
+				processingInfo.setProcessingResult(chromatogram);
+			} catch(IOException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath()));
+			}
+		}
+		return processingInfo;
+	}
+
+	@Override
+	public IProcessingInfo<IChromatogramOverview> convertOverview(File file, IProgressMonitor monitor) {
+
+		IProcessingInfo<IChromatogramOverview> processingInfo = super.validate(file);
+		if(!processingInfo.hasErrorMessages()) {
+			IChromatogramWSDReader reader = new ChromatogramReader();
+			monitor.subTask(ConverterMessages.importChromatogramOverview);
+			try {
+				IChromatogramOverview chromatogramOverview = reader.readOverview(file, monitor);
+				processingInfo.setProcessingResult(chromatogramOverview);
+			} catch(IOException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath()));
+			}
+		}
+		return processingInfo;
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.wsd.converter.supplier.scf/src/org/eclipse/chemclipse/wsd/converter/supplier/scf/core/MagicNumberMatcher.java

@@ -0,0 +1,31 @@
+/*******************************************************************************
+ * 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.scf.core;
+
+import java.io.File;
+
+import org.eclipse.chemclipse.converter.core.AbstractMagicNumberMatcher;
+import org.eclipse.chemclipse.converter.core.IMagicNumberMatcher;
+
+public class MagicNumberMatcher extends AbstractMagicNumberMatcher implements IMagicNumberMatcher {
+
+	private static final byte[] MAGIC_CODE = new byte[]{(byte)'.', (byte)'s', (byte)'c', (byte)'f'};
+
+	@Override
+	public boolean checkFileFormat(File file) {
+
+		if(!checkFileExtension(file, ".scf")) {
+			return false;
+		}
+		return checkMagicCode(file, MAGIC_CODE);
+	}
+}