Thread: [Jsbml-svn] SF.net SVN: jsbml:[1278] trunk/core

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Revision: 1278
          http://jsbml.svn.sourceforge.net/jsbml/?rev=1278&view=rev
Author:   niko-rodrigue
Date:     2012-06-01 10:58:30 +0000 (Fri, 01 Jun 2012)
Log Message:
-----------
corrected the reaction clone constructor as it was not cloning the compartment attribute. Corrected as well the species.setBoundaryCondition method as it was expecting a Boolean instead of a boolean. Added as well the UnregisterTests from the 0.8 branch

Modified Paths:
--------------
    trunk/core/src/org/sbml/jsbml/Reaction.java
    trunk/core/src/org/sbml/jsbml/Species.java
    trunk/core/test/org/sbml/jsbml/xml/test/Tests.java

Added Paths:
-----------
    trunk/core/test/org/sbml/jsbml/xml/test/UnregisterTests.java

Modified: trunk/core/src/org/sbml/jsbml/Reaction.java
===================================================================

--- trunk/core/src/org/sbml/jsbml/Reaction.java	2012-06-01 09:11:42 UTC (rev 1277)
+++ trunk/core/src/org/sbml/jsbml/Reaction.java	2012-06-01 10:58:30 UTC (rev 1278)
@@ -140,6 +140,9 @@
 		} else {
 			reversible = reaction.reversible == null ? null : new Boolean(reaction.reversible.booleanValue());
 		}
+		if (reaction.isSetCompartment()) {
+			setCompartment(reaction.getCompartment());
+		}
 	}
 	
 	/**

Modified: trunk/core/src/org/sbml/jsbml/Species.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/Species.java	2012-06-01 09:11:42 UTC (rev 1277)
+++ trunk/core/src/org/sbml/jsbml/Species.java	2012-06-01 10:58:30 UTC (rev 1278)
@@ -807,7 +807,7 @@
 	 * 
 	 * @param boundaryCondition
 	 */
-	public void setBoundaryCondition(Boolean boundaryCondition) {
+	public void setBoundaryCondition(boolean boundaryCondition) {
 		Boolean oldBoundaryCondition = this.boundaryCondition;
 		this.boundaryCondition = boundaryCondition;
 		isSetBoundaryCondition = true;

Modified: trunk/core/test/org/sbml/jsbml/xml/test/Tests.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/xml/test/Tests.java	2012-06-01 09:11:42 UTC (rev 1277)
+++ trunk/core/test/org/sbml/jsbml/xml/test/Tests.java	2012-06-01 10:58:30 UTC (rev 1278)
@@ -31,7 +31,8 @@
  * @version $Rev$
  */
 @RunWith(value=Suite.class)
-@SuiteClasses(value={SBML_L1VxTests.class, SBML_L2V1Test.class, CheckConsistencyTests.class, GetNotesStringTests.class})
+@SuiteClasses(value={SBML_L1VxTests.class, SBML_L2V1Test.class, CheckConsistencyTests.class, GetNotesStringTests.class,
+		UnregisterTests.class})
 public class Tests {
 
 }

Added: trunk/core/test/org/sbml/jsbml/xml/test/UnregisterTests.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/xml/test/UnregisterTests.java	                        (rev 0)
+++ trunk/core/test/org/sbml/jsbml/xml/test/UnregisterTests.java	2012-06-01 10:58:30 UTC (rev 1278)
@@ -0,0 +1,293 @@
+package org.sbml.jsbml.xml.test;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.sbml.jsbml.Compartment;
+import org.sbml.jsbml.IdentifierException;
+import org.sbml.jsbml.KineticLaw;
+import org.sbml.jsbml.LocalParameter;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Reaction;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.Species;
+import org.sbml.jsbml.SpeciesReference;
+
+public class UnregisterTests {
+
+	SBMLDocument doc;
+	Model model;
+	
+	@BeforeClass public static void initialSetUp() {
+		
+	
+	}
+	
+	/**
+	 * 
+	 */
+	@Before public void setUp() { 
+		doc = new SBMLDocument(2, 4);
+		model = doc.createModel("model");
+		
+		Compartment comp = model.createCompartment("cell");
+		comp.setMetaId("cell");
+		
+		Species s1 = model.createSpecies("S1", comp);
+		s1.setMetaId("S1");
+		
+		Species s2 = model.createSpecies("S2", comp);
+		s2.setMetaId("S2");
+		
+		Reaction r1 = model.createReaction("R1");
+		r1.setMetaId("R1");
+		
+		SpeciesReference reactant = model.createReactant("SP1");
+		reactant.setMetaId("SP1");
+		reactant.setSpecies(s1);
+		
+		SpeciesReference product = model.createProduct("SP2");
+		product.setMetaId("SP2");
+		product.setSpecies(s2);
+		
+		LocalParameter lp1 = r1.createKineticLaw().createLocalParameter("LP1");
+		lp1.setMetaId("LP1");
+		
+	}
+	
+	/**
+	 * 
+	 */
+	@Test public void testRegister() {
+		
+		try {
+			model.createSpecies("R1");
+			fail("We should not be able to register twice the same id.");
+		} catch (IllegalArgumentException e) {
+			assertTrue(true);
+			// success
+		}
+
+		Species s3 = new Species();
+		s3.setId("SP1");
+		
+		try {
+			model.addSpecies(s3);
+			fail("We should not be able to register twice the same id.");
+		} catch (IllegalArgumentException e) {
+			assertTrue(true);
+			// success
+		}
+		assertTrue(model.getSpecies("S3") == null);
+
+		s3.setId("LP1");
+		
+		try {
+			model.addSpecies(s3);
+			assertTrue(true);
+		} catch (IllegalArgumentException e) {
+			fail("We should be able to register an id that is the same as a local parameter id.");
+		}
+
+		model.removeSpecies(s3);
+		assertTrue(model.getSpecies("S3") == null);
+		
+		// Testing again after having removed the Species
+		try {
+			model.addSpecies(s3);
+			assertTrue(true);
+		} catch (IllegalArgumentException e) {
+			fail("We should be able to register an id that is the same as a local parameter id.");
+		}
+
+		model.removeSpecies(s3);
+		assertTrue(model.getSpecies("S3") == null);
+		
+		// Setting the same metaid as a SpeciesReference
+		try {
+			s3.setMetaId("SP1");
+			assertTrue(true);
+		} catch (IdentifierException e) {
+			fail("We should be able to put any metaId to a Species removed from a model.");
+		}
+
+		try {
+			model.addSpecies(s3);
+			fail("We should not be able to register twice the same metaid.");
+		} catch (IllegalArgumentException e) {
+			assertTrue(true);
+			// success
+		}
+
+		assertTrue(model.getSpecies("S3") == null);
+
+		try {
+			s3.setId("S1");
+			assertTrue(true);
+		} catch (IdentifierException e) {
+			fail("We should be able to put any id to a Species removed from a model.");
+		}
+
+		try {
+			model.addSpecies(s3);
+			fail("We should not be able to register twice the same id.");
+		} catch (IllegalArgumentException e) {
+			assertTrue(true);
+			// success
+		}
+		
+		assertTrue(model.getSpecies("S3") == null);
+
+		// Setting the same metaid as a LocalParameter
+
+		try {
+			s3.setMetaId("LP1");
+			assertTrue(true);
+		} catch (IdentifierException e) {
+			fail("We should be able to put any metaId to a Species not linked to a model.");
+		}
+
+		try {
+			model.addSpecies(s3);
+			fail("We should not be able to register twice the same metaid.");
+		} catch (IllegalArgumentException e) {
+			assertTrue(true);
+			// success
+		}
+
+	}
+	
+	/**
+	 * 
+	 */
+	@Test public void testRegister2() {
+		
+		Species s3 = new Species();
+		// Setting the same id as a LocalParameter
+		s3.setId("LP1");
+
+		// Setting the same metaid as a LocalParameter
+		try {
+			s3.setMetaId("LP1");
+			assertTrue(true);
+		} catch (IdentifierException e) {
+			fail("We should be able to put any metaId to a Species not linked to a model.");
+		}
+
+		try {
+			model.addSpecies(s3);
+			fail("We should not be able to register twice the same metaid.");
+		} catch (IllegalArgumentException e) {
+			assertTrue(true);
+			// success
+		}
+	}
+
+	/**
+	 * 
+	 */
+	@Test public void testRegister3() {
+		
+		Reaction r2 = new Reaction(2,4);
+		KineticLaw k = r2.createKineticLaw();
+		
+		k.createLocalParameter("LP1");
+		
+		// We should not be allowed to register an other local parameter with the same id
+		try {
+			k.createLocalParameter("LP1");
+			// fail("We should not be able to add a local parameter with the same id as an other local parameter in the same kineticLaw.");
+		} catch (IdentifierException e) {
+			// success
+		}
+
+		assertTrue(k.getLocalParameterCount() == 1);
+		
+	}
+
+	/**
+	 * 
+	 */
+	@Test public void testRegister4() {
+		
+		assertTrue(model.getId().equals("model"));
+		assertTrue(model.getNumSpecies() == 2);
+		
+		// We should be allowed to change an id !
+		model.setId("newModelID");
+
+		try {
+			// fail("We should not be able to add a local parameter with the same id as an other local parameter in the same kineticLaw.");
+		} catch (IdentifierException e) {
+			// success
+		}
+
+		assertTrue(model.getId().equals("newModelID"));
+		
+	}
+	
+	
+	/**
+	 * 
+	 */
+	@Test public void testUnRegister() {
+		
+		
+		Reaction r1 = model.removeReaction("R1");
+		
+		assertTrue(model.getReaction("R1") == null);		
+		assertTrue(model.getReaction(0) == null);
+		assertTrue(model.findNamedSBase("SP1") == null);
+		assertTrue(model.findNamedSBase("SP2") == null);
+		// assertTrue(model.findNamedSBase("LP1") == null);
+		assertTrue(doc.findSBase("SP1") == null);
+		assertTrue(doc.findSBase("R1") == null);
+		assertTrue(doc.findSBase("LP1") == null);
+		
+		Species s3 = new Species();
+		
+		// Setting the same id as a removed SpeciesReference
+		s3.setId("SP1");
+
+		// Setting the same metaid as a removed LocalParameter
+		try {
+			s3.setMetaId("LP1");
+			assertTrue(true);
+		} catch (IdentifierException e) {
+			fail("We should be able to put any metaId to a Species not linked to a model.");
+		}
+
+		try {
+			model.addSpecies(s3);
+			assertTrue(true);
+		} catch (IllegalArgumentException e) {
+			fail("We should be able to register an id or metaid from a removed element.");
+			// success
+		}
+		
+		try {
+			SpeciesReference reactant = r1.createReactant("S1");
+			reactant.setMetaId("S1");
+		} catch (IllegalArgumentException e) {
+			fail("We should be able to put any id to an element removed from a model.");
+		} catch (IdentifierException e) {
+			fail("We should be able to put any id to an element removed from a model.");
+		}
+	}
+
+	/**
+	 * 
+	 */
+	@Test public void testUnRegister2() {
+		
+		Reaction r1 = model.removeReaction("R1");
+
+		assertTrue(r1.getReactant("SP1") != null);
+
+		assertTrue(model.findNamedSBase("LP1") == null);
+	}
+	
+}

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Thread: [Jsbml-svn] SF.net SVN: jsbml:[1278] trunk/core

The Java library for working with the SBML format.

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