merged core into project

.gitignore

@@ -5,3 +5,4 @@
 .settings
 .project
 .classpath
+/schema/

build.gradle

@@ -25,7 +25,6 @@ repositories {
 }
 
 dependencies {
-	compile 'ch.psi:ch.psi.fda.core:2.3.4'
 	compile 'ch.psi:jcae:2.4.1'
 	compile 'com.google.inject:guice:3.0'
 	compile 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:2.5.1'
@@ -39,6 +38,7 @@ dependencies {
 	compile 'org.freehep:freehep-xdr:2.0.4'
 	compile 'ch.psi:plot:2.1-SNAPSHOT'
 	
+	compile 'com.google.guava:guava:>15.0'
 	
 	compile 'com.sun.mail:javax.mail:1.5.0'
 	compile 'javax.inject:javax.inject:1'
@@ -58,14 +58,16 @@ task sourcesJar(type: Jar, dependsOn: classes) {
     from sourceSets.main.allSource
 }
 
+/*
 task javadocJar(type: Jar, dependsOn: javadoc) {
     classifier = 'javadoc'
     from javadoc.destinationDir
 }
+*/
 
 artifacts {
     archives sourcesJar
-    archives javadocJar
+    //archives javadocJar
 }
 
 jaxb{

src/main/java/ch/psi/fda/DescriptorProvider.java

@@ -0,0 +1,17 @@
+package ch.psi.fda;
+
+import java.io.File;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+import ch.psi.fda.vdescriptor.VDescriptor;
+
+public interface DescriptorProvider {
+
+	public void load(File ... files );
+	
+	public EDescriptor getEDescriptor();
+	public VDescriptor getVDescriptor();
+	
+	public Class<?> getEDescriptorClass();
+	
+}

src/main/java/ch/psi/fda/EContainer.java

@@ -0,0 +1,28 @@
+package ch.psi.fda;
+
+public interface EContainer {
+
+	/**
+	 * Initialize execution container like required resources, etc.
+	 */
+	public void initialize();
+	
+	/**
+	 * Executes the logic implemented by the ExecutionContainer
+	 * Execute is a blocking function and must not return before the actual logic is executed
+	 */
+	public void execute();
+	
+	/**
+	 * Try to abort the execution of the logic
+	 */
+	public void abort();
+	
+	public boolean isActive();
+	
+	/**
+	 * Destroy execution container and free all allocated resources
+	 */
+	public void destroy();
+	
+}

src/main/java/ch/psi/fda/EContainerFactory.java

@@ -0,0 +1,22 @@
+package ch.psi.fda;
+
+import ch.psi.fda.edescriptor.EDescriptor;
+
+import com.google.common.eventbus.EventBus;
+
+public interface EContainerFactory {
+
+	/**
+	 * Check whether the factory supports 
+	 * @param descriptor
+	 * @return
+	 */
+	public boolean supportsEDescriptor(EDescriptor descriptor);
+	
+	/**
+	 * Create the execution container based on the passed descriptor
+	 * @param descriptor
+	 * @return
+	 */
+	public EContainer getEContainer(EDescriptor descriptor, EventBus bus);
+}

src/main/java/ch/psi/fda/edescriptor/EDescriptor.java

@@ -0,0 +1,15 @@
+package ch.psi.fda.edescriptor;
+
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlTransient;
+
+/**
+ * Execution container descriptor
+ */
+@XmlRootElement
+@XmlTransient
+public interface EDescriptor {
+
+	
+	// TODO Need to contain what need to be streamed
+}

src/main/java/ch/psi/fda/messages/ControlMessage.java

@@ -0,0 +1,29 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.messages;
+
+
+/**
+ * A control message that is not holding any data but
+ * control information (like end of loop, etc.)
+ */
+public abstract class ControlMessage extends Message{
+	private static final long serialVersionUID = 1L;
+}

src/main/java/ch/psi/fda/messages/DataMessage.java

@@ -0,0 +1,105 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.messages;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Message holding data
+ */
+public class DataMessage extends Message{
+	
+	private static final long serialVersionUID = 1L;
+	
+	private final List<Object> data;
+	private List<Metadata> metadata;
+	
+//	public DataMessage(){
+//		this.data = new ArrayList<Object>();
+//		this.metadata = new ArrayList<>();
+//	}
+//	
+	public DataMessage(List<Metadata> metadata){
+		this.data = new ArrayList<Object>();
+		this.metadata = metadata;
+	}
+	
+	public List<Object> getData(){
+		return(data);
+	}
+	public List<Metadata> getMetadata(){
+		return metadata;
+	}
+	public void setMetadata(List<Metadata> metadata){
+		this.metadata = metadata;
+	}
+	
+	// Utility functions
+	
+	@SuppressWarnings("unchecked")
+	public <T> T getData(String id){
+		int i=0;
+		for(Metadata m: metadata){
+			if(m.getId().equals(id)){
+				return (T) data.get(i);
+			}
+			i++;
+		}
+		throw new IllegalArgumentException("No data found for id: "+id);
+	}
+	
+	public Metadata getMetadata(String id){
+		for(Metadata m: metadata){
+			if(m.getId().equals(id)){
+				return m;
+			}
+		}
+		throw new IllegalArgumentException("No data found for id: "+id);
+	}
+	
+	@Override
+	public String toString() {
+		StringBuffer b = new StringBuffer();
+		b.append("Message [ ");
+		for (Object o : data) {
+			if (o.getClass().isArray()) {
+				// If the array object is of type double[] display its content
+				if (o instanceof double[]) {
+					double[] oa = (double[]) o;
+					b.append("[ ");
+					for (double o1 : oa) {
+						b.append(o1);
+						b.append(" ");
+					}
+					b.append("]");
+				} else {
+					b.append(o.toString());
+				}
+			} else {
+				b.append(o);
+			}
+			
+			b.append(" ");
+		}
+		b.append("]");
+		return b.toString();
+	}
+}

src/main/java/ch/psi/fda/messages/EndOfStreamMessage.java

@@ -0,0 +1,52 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.messages;
+
+/**
+ * Message that is send at the end of the action loop inside an ActionLoop implementation
+ * of just to indicate that a particular stream has finished
+ */
+public class EndOfStreamMessage extends ControlMessage {
+	
+	private static final long serialVersionUID = 1L;
+	
+	/**
+	 * Intersect flag - flag to indicate that stream should be intersected
+	 * after this message.
+	 */
+	private final boolean iflag;
+	
+	public EndOfStreamMessage(){
+		this(false);
+	}
+	
+	public EndOfStreamMessage(boolean iflag){
+		this.iflag = iflag;
+	}
+	
+	public boolean isIflag(){
+		return(iflag);
+	}
+
+	@Override
+	public String toString() {
+		return "Message[ c message: end of stream ]";
+	}
+}

src/main/java/ch/psi/fda/messages/Message.java

@@ -0,0 +1,29 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.messages;
+
+import java.io.Serializable;
+
+/**
+ * Message that can be put to the data queue
+ */
+public abstract class Message implements Serializable{
+	private static final long serialVersionUID = 1L;
+}

src/main/java/ch/psi/fda/messages/Metadata.java

@@ -0,0 +1,58 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.messages;
+
+import java.io.Serializable;
+
+/**
+ * Metadata of a component of a message. Each component has a global id.
+ * Optionally the component can also belong to a dimension. However, depending on the 
+ * view the number of the dimension might vary. Therefore the dimension number
+ * might change during the lifetime of a message (component).
+ */
+public class Metadata implements Serializable{
+
+	private static final long serialVersionUID = 1L;
+
+	private final String id;
+	private int dimension;
+	
+	public Metadata(String id){
+		this.id = id;
+		this.dimension = 0;
+	}
+	
+	public Metadata(String id, int dimension){
+		this.id = id;
+		this.dimension = dimension;
+	}
+
+	public void setDimension(int dimension){
+		this.dimension = dimension;
+	}
+	
+	public int getDimension() {
+		return dimension;
+	}
+
+	public String getId() {
+		return id;
+	}
+}

src/main/java/ch/psi/fda/messages/StreamDelimiterMessage.java

@@ -0,0 +1,67 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.messages;
+
+/**
+ * Message that is send at the end of the action loop inside an ActionLoop implementation
+ */
+public class StreamDelimiterMessage extends ControlMessage{
+	private static final long serialVersionUID = 1L;
+	/**
+	 * Number of the dimension this delimiter belongs to.
+	 */
+	private final int number;
+	
+	/**
+	 * Intersect flag - flag to indicate that stream should be intersected
+	 * after this message.
+	 */
+	private final boolean iflag;
+	
+	/**
+	 * @param number	Number of the dimension this delimiter belongs to
+	 */
+	public StreamDelimiterMessage(int number){
+		this(number, false);
+	}
+	
+	/**
+	 * @param number
+	 * @param iflag		Flag to indicate that data is grouped
+	 */
+	public StreamDelimiterMessage(int number, boolean iflag){
+		this.number = number;
+		this.iflag = iflag;
+	}
+
+	public int getNumber() {
+		return number;
+	}
+	
+	public boolean isIflag(){
+		return iflag;
+	}
+	
+	@Override
+	public String toString() {
+		// TODO Auto-generated method stub
+		return "Message [ c message: delimiter dimension "+number+" ]";
+	}
+}

src/main/java/ch/psi/fda/serializer/SerializerTXT.java

@@ -0,0 +1,224 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.serializer;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import com.google.common.eventbus.Subscribe;
+
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+
+/**
+ * Serialize data received by a DataQueue
+ */
+public class SerializerTXT {
+
+	private static final Logger logger = Logger.getLogger(SerializerTXT.class.getName());
+
+	private File file;
+	private boolean appendSuffix = true;
+
+	private boolean first = true;
+	private File outfile;
+
+	private int icount;
+	private String basename;
+	private String extension;
+	private boolean newfile;
+	private boolean dataInBetween;
+	private BufferedWriter writer;
+	private StringBuffer b;
+	private StringBuffer b1;
+	private boolean showDimensionHeader = true;
+
+	public SerializerTXT(File file) {
+		this.file = file;
+	}
+
+	/**
+	 * @param metadata
+	 * @param file
+	 * @param appendSuffix
+	 *            Flag whether to append a _0000 suffix after the original file
+	 *            name
+	 */
+	public SerializerTXT(File file, boolean appendSuffix) {
+		this.file = file;
+		this.appendSuffix = appendSuffix;
+	}
+
+	@Subscribe
+	public void onMessage(Message message) {
+		try {
+			if (first) {
+				first = false;
+				// Write header
+
+				icount = 0;
+				newfile = true;
+				dataInBetween = false;
+				writer = null;
+
+				// Get basename of the file
+				basename = this.file.getAbsolutePath(); // Determine file name
+				extension = basename.replaceAll("^.*\\.", ""); // Determine
+																// extension
+				basename = basename.replaceAll("\\." + extension + "$", "");
+			}
+
+			if (message instanceof DataMessage) {
+				dataInBetween = true;
+				if (newfile) {
+
+					b = new StringBuffer();
+					b1 = new StringBuffer();
+					b.append("#");
+					b1.append("#");
+					for (Metadata c : ((DataMessage) message).getMetadata()) {
+
+						b.append(c.getId());
+						b.append("\t");
+
+						b1.append(c.getDimension());
+						b1.append("\t");
+					}
+					b.setCharAt(b.length() - 1, '\n');
+					b1.setCharAt(b1.length() - 1, '\n');
+
+					// Open new file and write header
+					// Construct file name
+					if (appendSuffix) {
+						outfile = new File(String.format("%s_%04d.%s", basename, icount, extension));
+					}
+					else {
+						outfile = new File(String.format("%s.%s", basename, extension));
+					}
+
+					// Open file
+					logger.fine("Open new data file: " + outfile.getAbsolutePath());
+					writer = new BufferedWriter(new FileWriter(outfile));
+
+					// Write header
+					writer.write(b.toString());
+					if (showDimensionHeader) {
+						writer.write(b1.toString());
+					}
+
+					newfile = false;
+				}
+
+				// Write message to file - each message will result in one line
+				DataMessage m = (DataMessage) message;
+				StringBuffer buffer = new StringBuffer();
+				for (Object o : m.getData()) {
+					if (o.getClass().isArray()) {
+						// If the array object is of type double[] display its
+						// content
+						if (o instanceof double[]) {
+							double[] oa = (double[]) o;
+							for (double o1 : oa) {
+								buffer.append(o1);
+								buffer.append(" "); // Use space instead of tab
+							}
+							buffer.replace(buffer.length() - 1, buffer.length() - 1, "\t"); // Replace
+																							// last
+																							// space
+																							// with
+																							// tab
+						}
+						else if (o instanceof Object[]) {
+							// TODO need to be recursive ...
+							Object[] oa = (Object[]) o;
+							for (Object o1 : oa) {
+								buffer.append(o1);
+								buffer.append(" "); // Use space instead of tab
+							}
+							buffer.replace(buffer.length() - 1, buffer.length() - 1, "\t"); // Replace
+																							// last
+																							// space
+																							// with
+																							// tab
+						}
+						else {
+							buffer.append("-"); // Not supported
+						}
+					}
+					else {
+						buffer.append(o);
+						buffer.append("\t");
+					}
+				}
+
+				if (buffer.length() > 0) {
+					buffer.deleteCharAt(buffer.length() - 1); // Remove last
+																// character
+																// (i.e. \t)
+					buffer.append("\n"); // Append newline
+				}
+				writer.write(buffer.toString());
+			}
+			else if (message instanceof StreamDelimiterMessage) {
+				StreamDelimiterMessage m = (StreamDelimiterMessage) message;
+				logger.info("Delimiter - number: " + m.getNumber() + " iflag: " + m.isIflag());
+				if (m.isIflag() && appendSuffix) {
+					// Only increase iflag counter if there was data in between
+					// subsequent StreamDelimiterMessages.
+					if (dataInBetween) {
+						icount++;
+					}
+					dataInBetween = false;
+
+					// Set flag to open new file
+					newfile = true;
+
+					// Close file
+					writer.close();
+				}
+			}
+			else if (message instanceof EndOfStreamMessage) {
+				if (writer != null) {
+					// Close file
+					writer.close(); // If the stream was closed previously this
+									// has no effect
+				}
+			}
+		} catch (IOException e) {
+			logger.log(Level.SEVERE, "Data serializer had a problem writing to the specified file", e);
+			throw new RuntimeException("Data serializer had a problem writing to the specified file", e);
+		}
+	}
+
+	public boolean isShowDimensionHeader() {
+		return showDimensionHeader;
+	}
+
+	public void setShowDimensionHeader(boolean showDimensionHeader) {
+		this.showDimensionHeader = showDimensionHeader;
+	}
+}

src/main/java/ch/psi/fda/vdescriptor/LinePlot.java

@@ -0,0 +1,53 @@
+package ch.psi.fda.vdescriptor;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement(name="lineplot")
+public class LinePlot extends Plot {
+	private List<Series> data = new ArrayList<>();
+	
+	private Double minX;
+	private Double maxX;
+        private Integer maxSeries;
+
+	public LinePlot(){
+	}
+	
+	public LinePlot(String title){
+		setTitle(title);
+	}
+	
+	@XmlElement
+	public List<Series> getData() {
+		return data;
+	}
+	public void setData(List<Series> data) {
+		this.data = data;
+	}
+	@XmlAttribute
+	public Double getMinX() {
+		return minX;
+	}
+	public void setMinX(Double minX) {
+		this.minX = minX;
+	}
+	@XmlAttribute
+	public Double getMaxX() {
+		return maxX;
+	}
+	public void setMaxX(Double maxX) {
+		this.maxX = maxX;
+	}
+	@XmlAttribute
+	public Integer getMaxSeries() {
+		return maxSeries;
+	}
+	public void setMaxSeries(Integer maxSeries) {
+		this.maxSeries = maxSeries;
+	}
+}

src/main/java/ch/psi/fda/vdescriptor/MatrixPlot.java

@@ -0,0 +1,87 @@
+package ch.psi.fda.vdescriptor;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlSchemaType;
+
+@XmlRootElement(name="matrixplot")
+public class MatrixPlot extends Plot {
+	
+	private List<Series> data = new ArrayList<>();
+	private Double minX;
+	private Double maxX;
+	private Integer nX;
+	
+	private Double minY;
+	private Double maxY;
+	private Integer nY;
+        
+        private String type;
+	
+	public MatrixPlot(){
+	}
+	
+	public MatrixPlot(String title){
+		setTitle(title);
+	}
+
+	public List<Series> getData() {
+		return data;
+	}
+	public void setData(List<Series> data) {
+		this.data = data;
+	}
+	@XmlAttribute
+	@XmlSchemaType(name = "float")
+	public Double getMinX() {
+		return minX;
+	}
+	public void setMinX(Double minX) {
+		this.minX = minX;
+	}
+	@XmlAttribute
+	public Double getMaxX() {
+		return maxX;
+	}
+	public void setMaxX(Double maxX) {
+		this.maxX = maxX;
+	}
+	@XmlAttribute
+	public Integer getnX() {
+		return nX;
+	}
+	public void setnX(Integer nX) {
+		this.nX = nX;
+	}
+	@XmlAttribute
+	public Double getMinY() {
+		return minY;
+	}
+	public void setMinY(Double minY) {
+		this.minY = minY;
+	}
+	@XmlAttribute
+	public Double getMaxY() {
+		return maxY;
+	}
+	public void setMaxY(Double maxY) {
+		this.maxY = maxY;
+	}
+	@XmlAttribute
+	public Integer getnY() {
+		return nY;
+	}
+	public void setnY(Integer nY) {
+		this.nY = nY;
+	}
+	@XmlAttribute
+	public String getType() {            
+            return type;
+	}
+	public void setType(String type) {
+		this.type = type;
+	}
+}

src/main/java/ch/psi/fda/vdescriptor/Plot.java

@@ -0,0 +1,20 @@
+package ch.psi.fda.vdescriptor;
+
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlTransient;
+
+
+@XmlSeeAlso({LinePlot.class, MatrixPlot.class})
+@XmlTransient
+public abstract class Plot {
+	
+	private String title;
+
+	public String getTitle() {
+		return title;
+	}
+	public void setTitle(String title) {
+		this.title = title;
+	}
+	
+}

src/main/java/ch/psi/fda/vdescriptor/Series.java

@@ -0,0 +1,12 @@
+package ch.psi.fda.vdescriptor;
+
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlTransient;
+
+
+@XmlSeeAlso({XYSeries.class, XYZSeries.class})
+@XmlTransient
+public abstract class Series {
+	
+	
+}

src/main/java/ch/psi/fda/vdescriptor/VDescriptor.java

@@ -0,0 +1,28 @@
+package ch.psi.fda.vdescriptor;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElementWrapper;
+import javax.xml.bind.annotation.XmlElements;
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement(name="vdescriptor")
+public class VDescriptor {
+	
+	private List<Plot> plots = new ArrayList<>();
+
+	@XmlElementWrapper
+	@XmlElements({
+        @XmlElement(name="lineplot",type=LinePlot.class),
+        @XmlElement(name="matrixplot",type=MatrixPlot.class),
+    })
+	public List<Plot> getPlots() {
+		return plots;
+	}
+
+	public void setPlots(List<Plot> plots) {
+		this.plots = plots;
+	}
+}

src/main/java/ch/psi/fda/vdescriptor/XYSeries.java

@@ -0,0 +1,42 @@
+package ch.psi.fda.vdescriptor;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement(name="xyseries")
+public class XYSeries extends Series {
+
+	private String x = null;
+	private String y = null;
+        private Integer  maxItemCount = -1;
+	
+	public XYSeries(){
+	}
+	
+	public XYSeries(String x, String y){
+		this.x = x;
+		this.y = y;
+	}
+	
+	@XmlAttribute
+	public String getX() {
+		return x;
+	}
+	public void setX(String x) {
+		this.x = x;
+	}
+	@XmlAttribute
+	public String getY() {
+		return y;
+	}
+	public void setY(String y) {
+		this.y = y;
+	}	        
+	@XmlAttribute
+	public Integer getMaxItemCount() {
+		return maxItemCount;
+	}
+	public void setMaxItemCount(Integer maxCount) {
+		this.maxItemCount = maxCount;
+	}        
+}

src/main/java/ch/psi/fda/vdescriptor/XYZSeries.java

@@ -0,0 +1,43 @@
+package ch.psi.fda.vdescriptor;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement(name="xyzseries")
+public class XYZSeries extends Series {
+
+	private String x = null;
+	private String y = null;
+	private String z = null;
+	
+	public XYZSeries(){
+	}
+	
+	public XYZSeries(String x, String y, String z){
+		this.x = x;
+		this.y = y;
+		this.z = z;
+	}
+	
+	@XmlAttribute
+	public String getX() {
+		return x;
+	}
+	public void setX(String x) {
+		this.x = x;
+	}
+	@XmlAttribute
+	public String getY() {
+		return y;
+	}
+	public void setY(String y) {
+		this.y = y;
+	}
+	@XmlAttribute
+	public String getZ() {
+		return z;
+	}
+	public void setZ(String z) {
+		this.z = z;
+	}
+}

src/main/java/ch/psi/fda/vdescriptor/YSeries.java

@@ -0,0 +1,28 @@
+package ch.psi.fda.vdescriptor;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+
+/**
+ * In a YSeries the Y components hold an data array in which the index i the x and the value the y value.
+ */
+@XmlRootElement(name="yseries")
+public class YSeries extends Series {
+
+	private String y = null;
+	
+	public YSeries(){
+	}
+	
+	public YSeries(String y){
+		this.y = y;
+	}
+	
+	@XmlAttribute
+	public String getY() {
+		return y;
+	}
+	public void setY(String y) {
+		this.y = y;
+	}
+}

src/main/java/ch/psi/fda/vdescriptor/YZSeries.java

@@ -0,0 +1,38 @@
+package ch.psi.fda.vdescriptor;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+
+
+/**
+ * In a YZSeries the Y components hold an data array in which the index i the x and the value the y value.
+ */
+@XmlRootElement(name="yzseries")
+public class YZSeries extends Series {
+
+	private String y = null;
+	private String z = null;
+	
+	public YZSeries(){
+	}
+	
+	public YZSeries(String y, String z){
+		this.y = y;
+		this.z = z;
+	}
+	
+	@XmlAttribute
+	public String getY() {
+		return y;
+	}
+	public void setY(String y) {
+		this.y = y;
+	}
+	@XmlAttribute
+	public String getZ() {
+		return z;
+	}
+	public void setZ(String z) {
+		this.z = z;
+	}
+}

src/test/java/ch/psi/fda/vdescriptor/VDescriptorTest.java

@@ -0,0 +1,43 @@
+package ch.psi.fda.vdescriptor;
+
+import java.io.File;
+import java.util.logging.Logger;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class VDescriptorTest {
+
+	private static final Logger logger = Logger.getLogger(VDescriptorTest.class.getName());
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void test() throws JAXBException {
+		try {
+			JAXBContext context = JAXBContext.newInstance(VDescriptor.class);
+			Unmarshaller u = context.createUnmarshaller();
+
+			VDescriptor descriptor = (VDescriptor) u.unmarshal(new File("src/test/resources/vdescriptor.xml"));
+			for (Plot p : descriptor.getPlots()) {
+				logger.info(p.getClass().getName());
+			}
+		} catch (JAXBException e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+}

src/test/resources/vdescriptor.xml

@@ -0,0 +1,15 @@
+<vdescriptor>
+	<plots>
+		<lineplot>
+			<data>
+				<xyseries x="A" y="B" />
+				<xyseries x="A" y="C" />
+			</data>
+		</lineplot>
+		<matrixplot>
+			<data>
+				<xyzseries x="A" y="B" z="X" />
+			</data>
+		</matrixplot>
+	</plots>
+</vdescriptor>