Add named wavelengths for the DAD chromatogram overlay

chemclipse/plugins/org.eclipse.chemclipse.model/META-INF/MANIFEST.MF

@@ -53,7 +53,8 @@ Export-Package: org.eclipse.chemclipse.model.baseline,
  org.eclipse.chemclipse.model.traces,
  org.eclipse.chemclipse.model.types,
  org.eclipse.chemclipse.model.updates,
- org.eclipse.chemclipse.model.versioning
+ org.eclipse.chemclipse.model.versioning,
+ org.eclipse.chemclipse.model.wavelengths
 Import-Package: org.osgi.service.component.annotations;version="1.2.0"
 Service-Component: OSGI-INF/org.eclipse.chemclipse.model.supplier.IMeasurementFilterProcessTypeSupplier.xml,
  OSGI-INF/org.eclipse.chemclipse.model.supplier.IPeakFilterProcessTypeSupplier.xml

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/wavelengths/NamedWavelength.java

@@ -0,0 +1,44 @@
+/*******************************************************************************
+ * Copyright (c) 2020, 2021 Lablicate GmbH.
+ * 
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.model.wavelengths;
+
+public class NamedWavelength {
+
+	private String identifier = "";
+	private String wavelength = "";
+
+	public NamedWavelength(String identifier, String wavelength) {
+
+		this.identifier = identifier;
+		this.wavelength = wavelength;
+	}
+
+	public String getIdentifier() {
+
+		return identifier;
+	}
+
+	public void setIdentifier(String identifier) {
+
+		this.identifier = identifier;
+	}
+
+	public String getWavelengths() {
+
+		return wavelength;
+	}
+
+	public void setWavelengths(String wavelength) {
+
+		this.wavelength = wavelength;
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/wavelengths/NamedWavelengthUtil.java

@@ -0,0 +1,31 @@
+/*******************************************************************************
+ * Copyright (c) 2021 Lablicate GmbH.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.model.wavelengths;
+
+public class NamedWavelengthUtil {
+
+	private static final String TRADITIONAL = "Traditional Wavelengths";
+	private static final String MERCURY_LAMP = "Low Pressure Mercury Lamp";
+	private static final String ZINC_LAMP = "Zinc Lamp";
+	//
+
+	public static final String getDefaultWavelengths() {
+
+		NamedWavelengths namedWavelengths = new NamedWavelengths();
+		//
+		namedWavelengths.add(new NamedWavelength(TRADITIONAL, "214 254 280 365"));
+		namedWavelengths.add(new NamedWavelength(MERCURY_LAMP, "254")); // 253.7 nm
+		namedWavelengths.add(new NamedWavelength(ZINC_LAMP, "214"));
+		//
+		return namedWavelengths.save();
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/wavelengths/NamedWavelengths.java

@@ -0,0 +1,214 @@
+/*******************************************************************************
+ * Copyright (c) 2020, 2021 Lablicate GmbH.
+ * 
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Philip Wenig - initial API and implementation
+ * Matthias Mailänder - adapted for DAD
+ *******************************************************************************/
+package org.eclipse.chemclipse.model.wavelengths;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.eclipse.chemclipse.logging.core.Logger;
+import org.eclipse.chemclipse.support.util.NamedWavelengthListUtil;
+
+public class NamedWavelengths {
+
+	private static final Logger logger = Logger.getLogger(NamedWavelengths.class);
+	//
+	private NamedWavelengthListUtil namedWavelengthListUtil = new NamedWavelengthListUtil();
+	private final Map<String, NamedWavelength> namedWavelengthMap = new HashMap<>();
+
+	public NamedWavelengths() {
+
+	}
+
+	/**
+	 * Initializes this named Wavelengths from the given settings.
+	 * 
+	 * @param namedWavelengths
+	 */
+	public NamedWavelengths(String namedWavelengths) {
+
+		load(namedWavelengths);
+	}
+
+	public void addAll(Collection<NamedWavelength> namedWavelengths) {
+
+		for(NamedWavelength namedWavelength : namedWavelengths) {
+			add(namedWavelength);
+		}
+	}
+
+	public void add(NamedWavelength namedWavelength) {
+
+		namedWavelengthMap.put(namedWavelength.getIdentifier(), namedWavelength);
+	}
+
+	public void remove(String identifier) {
+
+		namedWavelengthMap.remove(identifier);
+	}
+
+	public void remove(List<NamedWavelength> namedWavelengths) {
+
+		for(NamedWavelength namedWavelength : namedWavelengths) {
+			remove(namedWavelength);
+		}
+	}
+
+	public void remove(NamedWavelength namedWavelength) {
+
+		if(namedWavelength != null) {
+			namedWavelengthMap.remove(namedWavelength.getIdentifier());
+		}
+	}
+
+	public NamedWavelength get(String identifier) {
+
+		return namedWavelengthMap.get(identifier);
+	}
+
+	public Set<String> keySet() {
+
+		return namedWavelengthMap.keySet();
+	}
+
+	public Collection<NamedWavelength> values() {
+
+		return namedWavelengthMap.values();
+	}
+
+	public void clear() {
+
+		namedWavelengthMap.clear();
+	}
+
+	public String extractNamedWavelength(NamedWavelength namedWavelength) {
+
+		StringBuilder builder = new StringBuilder();
+		extractNamedWavelength(namedWavelength, builder);
+		return builder.toString();
+	}
+
+	public NamedWavelength extractNamedWavelength(String item) {
+
+		NamedWavelength namedWavelength = null;
+		//
+		if(!"".equals(item)) {
+			String[] values = item.split("\\" + NamedWavelengthListUtil.SEPARATOR_ENTRY);
+			String identifier = ((values.length > 0) ? values[0].trim() : "");
+			String Wavelengths = ((values.length > 1) ? values[1].trim() : "");
+			namedWavelength = new NamedWavelength(identifier, Wavelengths);
+		}
+		//
+		return namedWavelength;
+	}
+
+	public void load(String timeRanges) {
+
+		loadSettings(timeRanges);
+	}
+
+	public void loadDefault(String timeRanges) {
+
+		loadSettings(timeRanges);
+	}
+
+	public String save() {
+
+		StringBuilder builder = new StringBuilder();
+		Iterator<NamedWavelength> iterator = values().iterator();
+		while(iterator.hasNext()) {
+			NamedWavelength namedWavelength = iterator.next();
+			extractNamedWavelength(namedWavelength, builder);
+			if(iterator.hasNext()) {
+				builder.append(NamedWavelengthListUtil.SEPARATOR_TOKEN);
+			}
+		}
+		return builder.toString().trim();
+	}
+
+	public void importItems(File file) {
+
+		try (BufferedReader bufferedReader = new BufferedReader(new FileReader(file))) {
+			String line;
+			while((line = bufferedReader.readLine()) != null) {
+				NamedWavelength template = extractNamedWavelength(line);
+				if(template != null) {
+					add(template);
+				}
+			}
+		} catch(FileNotFoundException e) {
+			logger.warn(e);
+		} catch(IOException e) {
+			logger.warn(e);
+		}
+	}
+
+	public boolean exportItems(File file) {
+
+		try (PrintWriter printWriter = new PrintWriter(file)) {
+			/*
+			 * Sort the items.
+			 */
+			List<NamedWavelength> namedWavelengths = new ArrayList<>(values());
+			Collections.sort(namedWavelengths, (r1, r2) -> r1.getIdentifier().compareTo(r2.getIdentifier()));
+			//
+			Iterator<NamedWavelength> iterator = namedWavelengths.iterator();
+			while(iterator.hasNext()) {
+				StringBuilder builder = new StringBuilder();
+				NamedWavelength template = iterator.next();
+				extractNamedWavelength(template, builder);
+				printWriter.println(builder.toString());
+			}
+			printWriter.flush();
+			return true;
+		} catch(FileNotFoundException e) {
+			logger.warn(e);
+			return false;
+		}
+	}
+
+	private void loadSettings(String timeRanges) {
+
+		if(!"".equals(timeRanges)) {
+			String[] items = namedWavelengthListUtil.parseString(timeRanges);
+			if(items.length > 0) {
+				for(String item : items) {
+					NamedWavelength namedWavelength = extractNamedWavelength(item);
+					if(namedWavelength != null) {
+						add(namedWavelength);
+					}
+				}
+			}
+		}
+	}
+
+	private void extractNamedWavelength(NamedWavelength namedWavelength, StringBuilder builder) {
+
+		builder.append(namedWavelength.getIdentifier());
+		builder.append(" ");
+		builder.append(NamedWavelengthListUtil.SEPARATOR_ENTRY);
+		builder.append(" ");
+		builder.append(namedWavelength.getWavelengths());
+	}
+}

chemclipse/plugins/org.eclipse.chemclipse.support/src/org/eclipse/chemclipse/support/util/NamedWavelengthListUtil.java

@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright (c) 2020 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.support.util;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class NamedWavelengthListUtil {
+
+	public static final String SEPARATOR_TOKEN = ";";
+	public static final String SEPARATOR_ENTRY = "|";
+	public static final String SEPARATOR_TRACE = " ";
+
+	public String createList(String[] items) {
+
+		List<String> list = getValues(items);
+		String values = "";
+		for(String value : list) {
+			values = values.concat(value + SEPARATOR_TOKEN);
+		}
+		return values;
+	}
+
+	public String[] parseString(String stringList) {
+
+		String[] decodedArray;
+		if(stringList.contains(SEPARATOR_TOKEN)) {
+			decodedArray = stringList.split(SEPARATOR_TOKEN);
+		} else {
+			decodedArray = new String[]{stringList};
+		}
+		return decodedArray;
+	}
+
+	public List<String> getList(String preferenceEntry) {
+
+		List<String> values = new ArrayList<String>();
+		if(preferenceEntry != "") {
+			String[] items = parseString(preferenceEntry);
+			if(items.length > 0) {
+				for(String item : items) {
+					values.add(item);
+				}
+			}
+		}
+		Collections.sort(values);
+		return values;
+	}
+
+	private List<String> getValues(String[] items) {
+
+		List<String> values = new ArrayList<String>();
+		if(items != null) {
+			int size = items.length;
+			for(int i = 0; i < size; i++) {
+				values.add(items[i]);
+			}
+		}
+		return values;
+	}
+}