Model contain SbmlFunction collection

model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java

@@ -157,14 +157,12 @@ public interface BioEntity extends Serializable {
    */
   void setVisibilityLevel(Integer zoomLevelVisibility);
 
-	/**
-	 * Returns semantic zoom level visibility.
-	 * 
-	 * @return semantic zoom level visibility
-	 */
-    String getVisibilityLevel();
-
-    String getElementId();
+  /**
+   * Returns semantic zoom level visibility.
+   * 
+   * @return semantic zoom level visibility
+   */
+  String getVisibilityLevel();
 
   /**
    * Returns the {@link Model} where BioEntity is located.

model/src/main/java/lcsb/mapviewer/model/map/SbmlFunction.java

+package lcsb.mapviewer.model.map;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.IndexColumn;
+
+/**
+ * Representation of a single SBML function
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+@Entity
+@Table(name = "sbml_function")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlFunction implements Serializable {
+
+  /**
+   * Default class logger.
+   */
+  @SuppressWarnings("unused")
+  private static Logger logger = Logger.getLogger(SbmlFunction.class);
+
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Unique database identifier.
+   */
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  @Column(name = "idDb", unique = true, nullable = false)
+  private int id;
+
+  private String functionId;
+
+  private String name;
+  
+  @Column(columnDefinition = "TEXT")
+  private String definition;
+
+  @ElementCollection
+  @CollectionTable(name = "sbml_function_arguments", joinColumns = @JoinColumn(name = "sbml_function_iddb"))
+  @IndexColumn(name = "idx")
+  @Column(name = "argument_name")
+  private List<String> arguments = new ArrayList<>();
+
+  /**
+   * Constructor required by hibernate.
+   */
+  SbmlFunction() {
+    super();
+  }
+
+  public SbmlFunction(String functionId) {
+    this.functionId = functionId;
+  }
+
+  public String getFunctionId() {
+    return functionId;
+  }
+
+  public void setFunctionId(String functionId) {
+    this.functionId = functionId;
+  }
+
+  public String getName() {
+    return name;
+  }
+
+  public void setName(String name) {
+    this.name = name;
+  }
+
+  public List<String> getArguments() {
+    return arguments;
+  }
+
+  public void setArguments(List<String> arguments) {
+    this.arguments = arguments;
+  }
+
+  public String getDefinition() {
+    return definition;
+  }
+
+  public void setDefinition(String definition) {
+    this.definition = definition;
+  }
+
+
+}

model/src/main/java/lcsb/mapviewer/model/map/model/Model.java

@@ -8,6 +8,7 @@ import java.util.Set;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.SbmlFunction;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
 import lcsb.mapviewer.model.map.layout.BlockDiagram;
@@ -588,4 +589,8 @@ public interface Model {
    *          layout to remove
    */
   void removeLayout(Layout dbLayout);
+
+  Set<SbmlFunction> getFunctions();
+
+  void addFunctions(Collection<SbmlFunction> parseXmlFunctionCollection);
 }

model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java

@@ -27,6 +27,7 @@ import org.hibernate.annotations.CascadeType;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.SbmlFunction;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
 import lcsb.mapviewer.model.map.layout.BlockDiagram;
 import lcsb.mapviewer.model.map.layout.ElementGroup;
@@ -101,6 +102,16 @@ public class ModelData implements Serializable {
   @OneToMany(mappedBy = "model", orphanRemoval = true)
   private Set<Reaction> reactions = new HashSet<>();
 
+  /**
+   * Collection of SBML functions in the map.
+   * 
+   * @see SbmlFunction
+   * 
+   */
+  @Cascade({ CascadeType.ALL })
+  @OneToMany(mappedBy = "model", orphanRemoval = true)
+  private Set<SbmlFunction> functions = new HashSet<>();
+
   /**
    * When the map was created.
    */
@@ -110,7 +121,7 @@ public class ModelData implements Serializable {
    * Width of the map.
    */
   private Double width;
-  
+
   /**
    * Height of the map.
    */
@@ -120,7 +131,7 @@ public class ModelData implements Serializable {
    * X coordinate that should be used when initially showing map.
    */
   private Double defaultCenterX;
-  
+
   /**
    * Y coordinate that should be used when initially showing map.
    */
@@ -732,4 +743,8 @@ public class ModelData implements Serializable {
   public void setDefaultZoomLevel(Integer defaultZoomLevel) {
     this.defaultZoomLevel = defaultZoomLevel;
   }
+
+  public Set<SbmlFunction> getFunctions() {
+    return functions;
+  }
 }
\ No newline at end of file

model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java

@@ -16,6 +16,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.SbmlFunction;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
 import lcsb.mapviewer.model.map.layout.BlockDiagram;
@@ -652,4 +653,14 @@ public class ModelFullIndexed implements Model {
   public void setDefaultZoomLevel(Integer defaultZoomLevel) {
     modelData.setDefaultZoomLevel(defaultZoomLevel);
   }
+
+  @Override
+  public Set<SbmlFunction> getFunctions() {
+    return modelData.getFunctions();
+  }
+
+  @Override
+  public void addFunctions(Collection<SbmlFunction> functions) {
+    modelData.getFunctions().addAll(functions);
+  }
 }

model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java

@@ -889,10 +889,4 @@ public class Reaction implements BioEntity {
     }
 
   }
-
-  @Override
-  public String getElementId() {
-    return getIdReaction();
-  }
-
 }

model/src/test/java/lcsb/mapviewer/model/map/SbmlFunctionTest.java

+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.Test;
+
+public class SbmlFunctionTest {
+
+  @Test
+  public void testConstructor() {
+    String id = "function_i";
+    SbmlFunction function = new SbmlFunction(id);
+    assertEquals(id, function.getFunctionId());
+  }
+  
+  @Test
+  public void testSetName() {
+    String name = "name";
+    SbmlFunction function = new SbmlFunction("");
+    function.setName(name);
+    assertEquals(name, function.getName());
+  }
+
+  @Test
+  public void testSetDefinition() {
+    String definition = "<lambda><bvar><ci> x </ci></bvar></lambda>";
+    SbmlFunction function = new SbmlFunction("");
+    function.setDefinition(definition);
+    assertEquals(definition, function.getDefinition());
+  }
+
+  @Test
+  public void testGetArguments() {
+    List<String> arguments = new ArrayList<>();
+    arguments.add("x");
+    
+    SbmlFunction function = new SbmlFunction("");
+    function.setArguments(arguments);
+    assertEquals(arguments, function.getArguments());
+  }
+
+}