GSoC - SBML L3V2 models support with some other bug fixes

src/main/java/org/simulator/About.java

@@ -24,7 +24,7 @@
 
 /**
  * This class displays a short about message for this library.
- * 
+ *
  * @author Andreas Dräger
  * @version $Rev$
  * @since 1.1
@@ -67,5 +67,4 @@ public static void main(String[] args) {
       System.out.println(message);
     }
   }
-
 }

src/main/java/org/simulator/comp/CompSimulator.java

@@ -16,78 +16,80 @@
 import java.io.File;
 import java.io.IOException;
 
-
 /**
- * Class for simulating comp models.
- *
- * TODO: support different simulation types (FBA, stochastic), currently limited to ode
+ * Class for simulating models encoded in the SBML comp package.
+ * <p>
+ * This class allows to simulate models encoded in the SBML hierarchical model
+ * composition package comp (http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/comp).
+ * The models are simulated by applying model flattening, i.e., reducing the hierarchical
+ * models to standard (flat) SBML models.
  *
+ * This class currently is limited to SBML core models (ODE).
+ * TODO: support additional simulations (FBA, stochastic)
  *
- * @author Shalin Shah, atthias König
+ * @author Shalin Shah, Matthias König
  * @version $Rev$
  * @since 1.5
  */
 public class CompSimulator {
-    private static Logger logger = Logger.getLogger(CompSimulator.class.getName());
-    private SBMLDocument doc;
-    private SBMLDocument docFlat;
-
-    public CompSimulator(File file) throws IOException, XMLStreamException {
 
-        // Read original SBML file and add meta-info about original ID
-        doc = SBMLReader.read(file);
-        doc = AddMetaInfo.putOrigId(doc);
-
-        // Flatten the model extra information in userObjects
-        CompFlatteningConverter compFlatteningConverter = new CompFlatteningConverter();
-        docFlat = compFlatteningConverter.flatten(doc);
-        assert docFlat != null;
+  private static Logger logger = Logger.getLogger(CompSimulator.class.getName());
+  private SBMLDocument doc;
+  private SBMLDocument docFlat;
+
+  public CompSimulator(File file) throws IOException, XMLStreamException {
+
+    // Read original SBML file and add meta-info about original ID
+    doc = SBMLReader.read(file);
+    doc = AddMetaInfo.putOrigId(doc);
+
+    // Flatten the model extra information in userObjects
+    CompFlatteningConverter compFlatteningConverter = new CompFlatteningConverter();
+    docFlat = compFlatteningConverter.flatten(doc);
+    assert docFlat != null;
+  }
+
+  public SBMLDocument getDoc() {
+    return doc;
+  }
+
+  public SBMLDocument getDocFlat() {
+    return docFlat;
+  }
+
+  public MultiTable solve(double timeEnd, double stepSize)
+      throws DerivativeException, ModelOverdeterminedException {
+    DESSolver solver = new RosenbrockSolver();
+    return solve(timeEnd, stepSize, solver);
+  }
+
+  public MultiTable solve(double timeEnd, double stepSize, DESSolver solver)
+      throws DerivativeException, ModelOverdeterminedException {
+    solver.setStepSize(stepSize);
+
+    // Execute the model using solver
+    Model model = docFlat.getModel();
+    SBMLinterpreter interpreter = new SBMLinterpreter(model);
+    if (solver instanceof AbstractDESSolver) {
+      ((AbstractDESSolver) solver).setIncludeIntermediates(false);
     }
 
+    // Compute the numerical solution of the initial value problem
+    // TODO: Rel-Tolerance, Abs-Tolerance.
+    MultiTable solution = solver.solve(interpreter, interpreter.getInitialValues(), 0d, timeEnd);
 
-    public SBMLDocument getDoc() {
-        return doc;
-    }
-
-    public SBMLDocument getDocFlat() {
-        return docFlat;
-    }
-
-    public MultiTable solve(double timeEnd, double stepSize) throws DerivativeException, ModelOverdeterminedException {
-        DESSolver solver = new RosenbrockSolver();
-        return solve(timeEnd, stepSize, solver);
-    }
+    // If columns other than time exists map ids back to original
+    if (solution.getColumnCount() > 1) {
+      logger.warn("Output contains objects, trying to plot and extract ids:\n");
 
-    public MultiTable solve(double timeEnd, double stepSize, DESSolver solver) throws DerivativeException, ModelOverdeterminedException {
-        solver.setStepSize(stepSize);
-
-        // Execute the model using solver
-        Model model = docFlat.getModel();
-
-        SBMLinterpreter interpreter = new SBMLinterpreter(model);
-        if (solver instanceof AbstractDESSolver) {
-            ((AbstractDESSolver) solver).setIncludeIntermediates(false);
-        }
-
-        // Compute the numerical solution of the initial value problem
-        // TODO: Rel-Tolerance, Abs-Tolerance.
-        MultiTable solution = solver.solve(interpreter, interpreter.getInitialValues(), 0d, timeEnd);
-
-        // If columns other than time exists map ids back to original
-        if(solution.getColumnCount() > 1) {
-            logger.warn("Output contains objects, trying to plot and extract ids:\n");
-            // Map the output ids back to the original model
-            for (int index = 1; index < solution.getColumnCount(); index++) {
-                AbstractTreeNode node = (AbstractTreeNode) doc.getElementBySId(solution.getColumnIdentifier(index));
-
-                if(node.isSetUserObjects()) {
-                    System.out.println("flat id: " + solution.getColumnIdentifier(index) + "\t old id:" +
-                            node.getUserObject(AddMetaInfo.ORIG_ID) + "\t model enclosing it: " + node.getUserObject(AddMetaInfo.MODEL_ID));
-                }
-            }
+      // Map the output ids back to the original model
+      for (int index = 1; index < solution.getColumnCount(); index++) {
+        AbstractTreeNode node = (AbstractTreeNode) doc.getElementBySId(solution.getColumnIdentifier(index));
+        if (node.isSetUserObjects()) {
+          System.out.println("flat id: " + solution.getColumnIdentifier(index) + "\t old id:" + node.getUserObject(AddMetaInfo.ORIG_ID) + "\t model enclosing it: " + node.getUserObject(AddMetaInfo.MODEL_ID));
         }
-
-        return solution;
+      }
     }
-
+    return solution;
+  }
 }

src/main/java/org/simulator/examples/BiomodelsExample.java

@@ -38,7 +38,7 @@
 /**
  * This class can test the simulation of all models from
  * <a href="http://www.ebi.ac.uk/biomodels-main/" target="_blank">BioModels database</a>.
- * 
+ *
  * @author Roland Keller
  * @version $Rev$
  */
@@ -52,6 +52,7 @@ public class BiomodelsExample {
 
   /**
    * Tests the models of biomodels.org using the {@link RosenbrockSolver} as integrator
+   *
    * @param file
    * @param from
    * @param to
@@ -89,14 +90,10 @@ public static void testBiomodels(String file, int from, int to)
         try {
           double time1 = System.nanoTime();
           SBMLinterpreter interpreter = new SBMLinterpreter(model);
-
           if ((solver != null) && (interpreter != null)) {
             solver.setStepSize(0.01);
-
             // solve
-            solver.solve(interpreter,
-              interpreter.getInitialValues(), 0, 10);
-
+            solver.solve(interpreter, interpreter.getInitialValues(), 0, 10);
             if (solver.isUnstable()) {
               logger.warning("unstable!");
               errors++;
@@ -116,27 +113,27 @@ public static void testBiomodels(String file, int from, int to)
     }
     System.out.println("Models: " + nModels);
     System.out.println("Models with errors in simulation: " + errors);
-    System.out.println("Models with correct simulation: "
-        + (nModels - errors));
-    for(int slowModel: slowModels) {
+    System.out.println("Models with correct simulation: " + (nModels - errors));
+    for (int slowModel : slowModels) {
       System.out.println("Slow: #" + slowModel);
     }
   }
 
+
   /**
    * * Input:
    * <ol>
    * <li>directory with models (containing the biomodels),
    * <li>first model to be simulated,
    * <li>last model to be simulated,
    * </ol>
-   * 
+   *
    * @param args
    * @throws IOException
    * @throws URISyntaxException
    */
-  public static void main(String[] args) throws IOException,URISyntaxException {
+  public static void main(String[] args)
+      throws IOException, URISyntaxException {
     testBiomodels(args[0], Integer.parseInt(args[1]), Integer.parseInt(args[2]));
   }
-
 }