- ModelPolisher now uses the JSBML-1.2 snapshot

- Undid changes to SBMLFix, as they are now obsolete

pom.xml

@@ -75,6 +75,11 @@
 				<enabled>true</enabled>
 			</releases>
 		</repository>
+		<repository>
+			<id>JSBML</id>
+			<name>The JSBML repository</name>
+			<url>http://jsbml.sourceforge.net/m2repo_snapshots/</url>
+		</repository>
 		<!-- Local libraries are an in-project repository -->
 		<!-- Add the dependencies and put them in -->
 		<!-- ${project.basedir}/lib/groupId/artifactId/version/ -->
@@ -92,7 +97,7 @@
 		<dependency>
 			<groupId>org.sbml.jsbml</groupId>
 			<artifactId>jsbml</artifactId>
-			<version>1.1</version>
+			<version>1.2-SNAPSHOT</version>
 		</dependency>
 
 		<dependency>
@@ -142,8 +147,6 @@
 			</resource>
 		</resources>
 
-
-
 		<plugins>
 
 			<!-- Download source code in Eclipse, best practice [OPTIONAL!] -->
@@ -212,8 +215,6 @@
 			</plugin>
 
 		</plugins>
-
-
 	</build>
 
 </project>

src/edu/ucsd/sbrg/util/SBMLFix.java

@@ -263,18 +263,7 @@ private static void createFluxObjective(String modelDescriptor, Reaction r,
     logger.info(MessageFormat.format(
       "Added flux objective for reaction ''{0}'' with coefficient {1,number} to model {2}.",
       r.getId(), coeff, modelDescriptor));
-    String rId = null;
-    // o.createFluxObjective(null, null, coeff, r);
-    rId = r != null ? r.getId() : null;
-    FluxObjective fluxObjective =
-      new FluxObjective(null, null, o.getLevel(), o.getVersion());
-    if (!Double.isNaN(coeff)) {
-      fluxObjective.setCoefficient(coeff);
-    }
-    if (rId != null) {
-      fluxObjective.setReaction(rId);
-    }
-    o.getListOfFluxObjectives().add(fluxObjective);
+    o.createFluxObjective(null, null, coeff, r);
   }