remove element from reaction node

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

@@ -522,15 +522,6 @@ public class Reaction implements AnnotatedObject {
 	 * @return <code>true</code> if element is part of the reaction,
 	 *         <code>false</code> otherwise
 	 */
-	public boolean containsElement(Element element) {
-		for (ReactionNode node : getReactionNodes()) {
-			if (node.getElement().equals(element)) {
-				return true;
-			}
-		}
-		return false;
-	}
-
 	public boolean containsElement(Alias alias) {
 		for (ReactionNode node : getReactionNodes()) {
 			if (node.getAlias().equals(alias)) {

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

-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-
-/**
- * One of two known types of nodes in the {@link Reaction}. It defines input or
- * output element of the reaction in the map model. {@link #element} and
- * {@link #alias} define which element on the map correspond to this node. There
- * are three known subclasses:
- * <ul>
- * <li> {@link Reactant} - input of the reaction,</li>
- * <li> {@link Product} - output of the reaction,</li>
- * <li> {@link Modifier} - some modifier of the reaction.</li>
- * </ul>
- * 
- * 
- * @author Piotr Gawron
- * 
- */
-@Entity
-@DiscriminatorValue("GENERIC_REACTION_NODE")
-public abstract class ReactionNode extends AbstractNode {
-
-	/**
-	 * 
-	 */
-	private static final long	serialVersionUID	= 1L;
-
-	/**
-	 * {@link Element} that represents this node in the model.
-	 */
-	@ManyToOne
-	private Element				element;
-
-	/**
-	 * {@link SpecisAlias} that represents this node in the model.
-	 */
-	@ManyToOne
-	private Alias	alias;
-
-	/**
-	 * Default constructor.
-	 */
-	protected ReactionNode() {
-		super();
-	}
-
-	/**
-	 * Constructor that creates a copy of the object in the parameter.
-	 * 
-	 * @param node
-	 *          original node
-	 */
-	protected ReactionNode(ReactionNode node) {
-		super(node);
-		this.element = node.getElement();
-		this.alias = node.getAlias();
-	}
-
-	/**
-	 * Constructor that creates node for given {@link #alias} and {@link #element}
-	 * .
-	 * 
-	 * @param alias
-	 *          {@link Alias} to which this node refer to
-	 * @param element
-	 *          {@link Element} to which this node refer to
-	 */
-	public ReactionNode(Alias alias, Element element) {
-		this.alias = alias;
-		this.element = element;
-	}
-
-	/**
-	 * @return the element
-	 * @see #element
-	 */
-	public Element getElement() {
-		return element;
-	}
-
-	/**
-	 * @param element the element to set
-	 * @see #element
-	 */
-	public void setElement(Element element) {
-		this.element = element;
-	}
-
-	/**
-	 * @return the alias
-	 * @see #alias
-	 */
-	public Alias getAlias() {
-		return alias;
-	}
-
-	/**
-	 * @param alias the alias to set
-	 * @see #alias
-	 */
-	public void setAlias(Alias alias) {
-		this.alias = alias;
-	}
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+
+/**
+ * One of two known types of nodes in the {@link Reaction}. It defines input or
+ * output element of the reaction in the map model. {@link #element} and
+ * {@link #alias} define which element on the map correspond to this node. There
+ * are three known subclasses:
+ * <ul>
+ * <li> {@link Reactant} - input of the reaction,</li>
+ * <li> {@link Product} - output of the reaction,</li>
+ * <li> {@link Modifier} - some modifier of the reaction.</li>
+ * </ul>
+ * 
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+@Entity
+@DiscriminatorValue("GENERIC_REACTION_NODE")
+public abstract class ReactionNode extends AbstractNode {
+
+	/**
+	 * 
+	 */
+	private static final long	serialVersionUID	= 1L;
+
+	/**
+	 * {@link SpecisAlias} that represents this node in the model.
+	 */
+	@ManyToOne
+	private Alias	alias;
+
+	/**
+	 * Default constructor.
+	 */
+	protected ReactionNode() {
+		super();
+	}
+
+	/**
+	 * Constructor that creates a copy of the object in the parameter.
+	 * 
+	 * @param node
+	 *          original node
+	 */
+	protected ReactionNode(ReactionNode node) {
+		super(node);
+		this.alias = node.getAlias();
+	}
+
+	/**
+	 * Constructor that creates node for given {@link #alias} and {@link #element}
+	 * .
+	 * 
+	 * @param alias
+	 *          {@link Alias} to which this node refer to
+	 * @param element
+	 *          {@link Element} to which this node refer to
+	 */
+	public ReactionNode(Alias alias, Element element) {
+		this.alias = alias;
+	}
+
+	/**
+	 * @return the alias
+	 * @see #alias
+	 */
+	public Alias getAlias() {
+		return alias;
+	}
+
+	/**
+	 * @param alias the alias to set
+	 * @see #alias
+	 */
+	public void setAlias(Alias alias) {
+		this.alias = alias;
+	}
+
+}

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

@@ -91,11 +91,6 @@ public class ReactionNodeComparator implements Comparator<ReactionNode> {
 			return aliasComparator.compare(arg0.getAlias(), arg1.getAlias());
 		}
 
-		if (elementComparator.compare(arg0.getElement(), arg1.getElement()) != 0) {
-			logger.debug("Element different");
-			return elementComparator.compare(arg0.getElement(), arg1.getElement());
-		}
-
 		return 0;
 	}
 }

model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java

@@ -86,14 +86,6 @@ public class NodeOperatorComparatorTest {
 			operator1 = createNodeOperator();
 			operator2 = createNodeOperator();
 
-			Product product = (Product) operator1.getOutputs().get(0);
-			product.setElement(new GenericProtein());
-			assertTrue(comparator.compare(operator1, operator2) != 0);
-			assertTrue(comparator.compare(operator2, operator1) != 0);
-
-			operator1 = createNodeOperator();
-			operator2 = createNodeOperator();
-
 			reactant = (Reactant) operator1.getInputs().get(0);
 			reactant.getAlias().setName("bla");
 			assertTrue(comparator.compare(operator1, operator2) != 0);

model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java

@@ -85,13 +85,6 @@ public class ReactionNodeComparatorTest {
 			operator1 = createNodeOperator();
 			operator2 = createNodeOperator();
 
-			operator1.setElement(new GenericProtein());
-			assertTrue(comparator.compare(operator1, operator2) != 0);
-			assertTrue(comparator.compare(operator2, operator1) != 0);
-
-			operator1 = createNodeOperator();
-			operator2 = createNodeOperator();
-
 			operator1.getAlias().setName("bla");
 			assertTrue(comparator.compare(operator1, operator2) != 0);
 			assertTrue(comparator.compare(operator2, operator1) != 0);