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Add named wavelengths for the DAD chromatogram overlay
1 parent 96beeca commit da1b5d7

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Lines changed: 2305 additions & 6 deletions

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

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

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

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

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

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

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

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

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

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/*******************************************************************************
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* Copyright (c) 2020 Lablicate GmbH.
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*
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* All rights reserved.
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* This program and the accompanying materials are made available under the
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* terms of the Eclipse Public License v1.0 which accompanies this distribution,
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* and is available at http://www.eclipse.org/legal/epl-v10.html
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*
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* Contributors:
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* Philip Wenig - initial API and implementation
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*******************************************************************************/
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package org.eclipse.chemclipse.support.util;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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public class NamedWavelengthListUtil {
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public static final String SEPARATOR_TOKEN = ";";
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public static final String SEPARATOR_ENTRY = "|";
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public static final String SEPARATOR_TRACE = " ";
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public String createList(String[] items) {
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List<String> list = getValues(items);
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String values = "";
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for(String value : list) {
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values = values.concat(value + SEPARATOR_TOKEN);
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}
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return values;
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}
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public String[] parseString(String stringList) {
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String[] decodedArray;
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if(stringList.contains(SEPARATOR_TOKEN)) {
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decodedArray = stringList.split(SEPARATOR_TOKEN);
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} else {
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decodedArray = new String[]{stringList};
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}
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return decodedArray;
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}
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public List<String> getList(String preferenceEntry) {
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List<String> values = new ArrayList<String>();
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if(preferenceEntry != "") {
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String[] items = parseString(preferenceEntry);
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if(items.length > 0) {
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for(String item : items) {
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values.add(item);
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}
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}
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}
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Collections.sort(values);
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return values;
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}
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private List<String> getValues(String[] items) {
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List<String> values = new ArrayList<String>();
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if(items != null) {
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int size = items.length;
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for(int i = 0; i < size; i++) {
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values.add(items[i]);
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}
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}
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return values;
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}
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}

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