Fields of BioParticipant and BioReactant unmodifiable

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java

@@ -49,9 +49,9 @@ import java.util.Objects;
  */
 public abstract class BioParticipant extends BioEntity {
 
-	private BioPhysicalEntity physicalEntity;
+	private final BioPhysicalEntity physicalEntity;
 	
-	private Double quantity;
+	private final Double quantity;
 
 	/**
 	 * Constructor
@@ -63,7 +63,13 @@ public abstract class BioParticipant extends BioEntity {
 	public BioParticipant(String id, @Nonnull BioPhysicalEntity physicalEntity, Double quantity) {
 		super(id);
 		this.physicalEntity=physicalEntity;
-		this.setQuantity(quantity);
+		if(Double.isNaN(quantity) || Double.isInfinite(quantity) || quantity <= 0)
+		{
+			ErrorUtils.error("Illegal argument for "+quantity+" "+this.getPhysicalEntity().getId()+": the quantity must be finite and positive");
+			throw new IllegalArgumentException();
+		}
+
+		this.quantity = quantity;
 	}
 
 
@@ -77,18 +83,6 @@ public abstract class BioParticipant extends BioEntity {
 	}
 	
 
-	/**
-	 * <p>Setter for the field <code>physicalEntity</code>.</p>
-	 *
-	 * @param physicalEntity the physicalEntity to set
-	 */
-	public void setPhysicalEntity(BioPhysicalEntity physicalEntity) {
-		this.physicalEntity = physicalEntity;
-	}
-	
-	
-
-
 	/**
 	 * <p>Getter for the field <code>quantity</code>.</p>
 	 *
@@ -99,22 +93,6 @@ public abstract class BioParticipant extends BioEntity {
 	}
 
 
-	/**
-	 * <p>Setter for the field <code>quantity</code>.</p>
-	 *
-	 * @param quantity the quantity to set
-	 */
-	public void setQuantity(Double quantity) {
-		
-		if(Double.isNaN(quantity) || Double.isInfinite(quantity) || quantity <= 0)
-		{
-			ErrorUtils.error("Illegal argument for "+quantity+" "+this.getPhysicalEntity().getId()+": the quantity must be finite and positive");
-			throw new IllegalArgumentException();
-		}
-		
-		this.quantity = quantity;
-	}
-
 	/** {@inheritDoc} */
 	@Override
 	public boolean equals(Object o) {

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java

@@ -50,7 +50,7 @@ import java.util.Objects;
  */
 public class BioReactant extends BioParticipant {
 
-	private BioCompartment location = null;
+	private final BioCompartment location;
 
 	/**
 	 * Constructor
@@ -61,7 +61,7 @@ public class BioReactant extends BioParticipant {
 	 */
 	public BioReactant(@Nonnull BioMetabolite metabolite, Double stoichiometry, @Nonnull BioCompartment location) {
 		super(metabolite.getId()+"__"+stoichiometry+"__"+location.getId(), metabolite, stoichiometry);
-		this.setLocation(location);
+		this.location = location;
 	}
 
 	/**
@@ -73,15 +73,6 @@ public class BioReactant extends BioParticipant {
 		return location;
 	}
 
-	/**
-	 * Set location
-	 *
-	 * @param location a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment}
-	 */
-	protected void setLocation(BioCompartment location) {
-		this.location = location;
-	}
-
 	/**
 	 * Get the associated metabolite
 	 *

met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipantTest.java

@@ -48,9 +48,7 @@ public class BioParticipantTest {
 	@Test(expected = IllegalArgumentException.class)
 	public void testSetNaNQuantity() {
 
-		BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), 2.0);
-		Double nan = Double.NaN;
-		p.setQuantity(nan);
+		BioParticipant p = new BioParticipantFake(new BioMetabolite("test"),  Double.NaN);
 
 	}
 	
@@ -60,9 +58,7 @@ public class BioParticipantTest {
 	@Test(expected = IllegalArgumentException.class)
 	public void testSetInfiniteQuantity() {
 
-		BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), 2.0);
-		Double inf = Double.POSITIVE_INFINITY;
-		p.setQuantity(inf);
+		BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), Double.POSITIVE_INFINITY);
 	}
 	
 	/**
@@ -71,12 +67,9 @@ public class BioParticipantTest {
 	@Test(expected = IllegalArgumentException.class)
 	public void testSetNegativeOrNullQuantity() {
 
-		BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), 2.0);
-		Double n = 0.0;
-		p.setQuantity(n);
-		
-		n = -10.0;
-		p.setQuantity(n);
+		new BioParticipantFake(new BioMetabolite("test"), 0.0);
+
+		new BioParticipantFake(new BioMetabolite("test"), -10.0);
 	}
 
 }

met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactionTest.java

@@ -56,7 +56,7 @@ public class BioReactionTest {
 	public static BioMetabolite l1, l2, r1, r2;
 	public static BioReactant l1Reactant, l2Reactant, r1Reactant, r2Reactant;
 
-	public static BioReaction reaction;
+	public static BioReaction reaction, reaction2;
 
 	public static BioGene g1, g2, g3;
 
@@ -79,8 +79,9 @@ public class BioReactionTest {
 		r2Reactant = new BioReactant(r2, 1.0, cpt2);
 
 		reaction = new BioReaction("testreaction");
+		reaction2 = new BioReaction("testreaction2");
 
-		network.add(reaction, cpt1, cpt2, l1, l2, r1, r2);
+		network.add(reaction, reaction2, cpt1, cpt2, l1, l2, r1, r2);
 
 		network.affectToCompartment(cpt1, l1, l2);
 		network.affectToCompartment(cpt2, r1, r2);
@@ -88,6 +89,9 @@ public class BioReactionTest {
 		network.affectLeft(reaction, l1Reactant, l2Reactant);
 		network.affectRight(reaction, r1Reactant, r2Reactant);
 
+		network.affectLeft(reaction2, l1Reactant);
+		network.affectRight(reaction2, l2Reactant);
+
 		BioEnzyme e1 = new BioEnzyme("e1");
 		BioProtein p1 = new BioProtein("p1");
 		BioProtein p2 = new BioProtein("p2");
@@ -136,11 +140,8 @@ public class BioReactionTest {
 		// Positive test
 		assertTrue("Must be a transport reaction", reaction.isTransportReaction());
 
-		// Negative Test
-		r1Reactant.setLocation(cpt1);
-		r2Reactant.setLocation(cpt1);
 
-		assertFalse("Must not be a transport reaction", reaction.isTransportReaction());
+		assertFalse("Must not be a transport reaction", reaction2.isTransportReaction());
 	}
 
 	/**