feat: add Parameter and FunctionDefinition support to AntimonySerializer

core/src/org/sbml/jsbml/util/AntimonySerializer.java

@@ -14,6 +14,8 @@
 import org.sbml.jsbml.AlgebraicRule;
 import org.sbml.jsbml.Event;
 import org.sbml.jsbml.EventAssignment;
+import org.sbml.jsbml.Parameter;
+import org.sbml.jsbml.FunctionDefinition;
 
 /**
  * Utility class to serialize SBML models and components into the Antimony scripting language.
@@ -46,6 +48,10 @@ public static String toAntimony(SBase element) {
             return toAntimony((Rule) element);
         } else if (element instanceof Event) {
             return toAntimony((Event) element);
+        } else if (element instanceof Parameter) {
+            return toAntimony((Parameter) element);
+        } else if (element instanceof FunctionDefinition) {
+            return toAntimony((FunctionDefinition) element);
         }
 
         return "// Unsupported SBML component for Antimony serialization.";
@@ -94,6 +100,18 @@ public static String toAntimony(Model model) {
         }
         ant.append("\n");
 
+        ant.append("  // Parameters\n");
+        for (Parameter p : model.getListOfParameters()) {
+            ant.append("  ").append(toAntimony(p)).append("\n");
+        }
+        ant.append("\n");
+
+        ant.append("  // Function Definitions\n");
+        for (FunctionDefinition fd : model.getListOfFunctionDefinitions()) {
+            ant.append("  ").append(toAntimony(fd)).append("\n");
+        }
+        ant.append("\n");
+
         ant.append(END).append("\n");
 
         return ant.toString();
@@ -298,4 +316,53 @@ public static String toAntimony(Event e) {
         ant.append(";");
         return ant.toString();
     }
+
+    /**
+     * Converts an individual SBML Parameter into an Antimony string.
+     */
+    public static String toAntimony(Parameter p) {
+        if (p == null) return "";
+        StringBuilder ant = new StringBuilder();
+
+        ant.append(p.getId());
+        if (p.isSetValue()) {
+            ant.append(" = ").append(p.getValue());
+        }
+        ant.append(";");
+        return ant.toString();
+    }
+
+    /**
+     * Converts an individual SBML FunctionDefinition into an Antimony string.
+     */
+    public static String toAntimony(FunctionDefinition fd) {
+        if (fd == null || !fd.isSetMath()) return "";
+        StringBuilder ant = new StringBuilder();
+
+        ant.append("function ").append(fd.getId()).append("(");
+
+        ASTNode math = fd.getMath();
+        if (math.isLambda()) {
+            // In JSBML, all children except the last one are the bound variables (bvars)
+            int numBvars = math.getChildCount() - 1; 
+
+            for (int i = 0; i < numBvars; i++) {
+                // Fetch the child node directly
+                ant.append(math.getChild(i).getName());
+                if (i < numBvars - 1) {
+                    ant.append(", ");
+                }
+            }
+            ant.append(")\n  ");
+
+            // The last child is the actual math body of the function
+            if (math.getChildCount() > 0) {
+                ASTNode body = math.getChild(math.getChildCount() - 1);
+                ant.append(ASTNode.formulaToString(body));
+            }
+        }
+
+        ant.append("\n").append(END).append("\n");
+        return ant.toString();
+    }
 }

core/test/org/sbml/jsbml/util/AntimonySerializerTest.java

@@ -23,7 +23,8 @@
 import org.sbml.jsbml.Trigger;
 import org.sbml.jsbml.Delay;
 import org.sbml.jsbml.Priority;
-
+import org.sbml.jsbml.Parameter;
+import org.sbml.jsbml.FunctionDefinition;
 /**
  * Tests for the {@link AntimonySerializer} Phase 1 LLM utility.
  * 
@@ -288,4 +289,36 @@ public void testAdvancedEventOptions() {
         String expected = "E2: at 5 after x, priority = 1, t0 = false, persistent = false: S1 = 0;";
         assertEquals("Should serialize advanced event options", expected, AntimonySerializer.toAntimony(e));
     }
+    @Test
+    public void testToAntimonyParameter() {
+        // Test a parameter with a value
+        Parameter p1 = new Parameter();
+        p1.setId("k1");
+        p1.setValue(0.5);
+        String result1 = AntimonySerializer.toAntimony(p1);
+        assertEquals("k1 = 0.5;", result1);
+
+        // Test a parameter without a value
+        Parameter p2 = new Parameter();
+        p2.setId("k2");
+        String result2 = AntimonySerializer.toAntimony(p2);
+        assertEquals("k2;", result2);
+    }
+
+    @Test
+    public void testToAntimonyFunctionDefinition() throws Exception {
+        FunctionDefinition fd = new FunctionDefinition();
+        fd.setId("multiply");
+
+        // In JSBML, parseFormula converts the string into a proper ASTNode tree
+        ASTNode math = ASTNode.parseFormula("lambda(x, y, x * y)"); 
+        fd.setMath(math);
+
+        String result = AntimonySerializer.toAntimony(fd);
+
+        // The expected Antimony output (removed spaces around the asterisk)
+        String expected = "function multiply(x, y)\n  x*y\n" + AntimonyConstants.END + "\n";
+
+        assertEquals(expected, result);
+    }
 }