Systems Biology Markup Language (SBML)

Revision: 12947
          http://sbml.svn.sourceforge.net/sbml/?rev=12947&view=rev
Author:   sarahkeating
Date:     2011-02-18 10:32:43 +0000 (Fri, 18 Feb 2011)

Log Message:
-----------
changed code so that in L3 if an attribute has not been set it will not be written out
Comments on the list seem 100% in favour - if I'm premature I can always revert it :-)

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs
    trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteL3SBML.cs
    trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteSBML.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteL3SBML.java
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteSBML.java
    trunk/libsbml/src/bindings/python/test/sbml/TestWriteL3SBML.py
    trunk/libsbml/src/bindings/python/test/sbml/TestWriteSBML.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteL3SBML.rb
    trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteSBML.rb
    trunk/libsbml/src/sbml/Compartment.cpp
    trunk/libsbml/src/sbml/Event.cpp
    trunk/libsbml/src/sbml/Parameter.cpp
    trunk/libsbml/src/sbml/Reaction.cpp
    trunk/libsbml/src/sbml/Species.cpp
    trunk/libsbml/src/sbml/SpeciesReference.cpp
    trunk/libsbml/src/sbml/Trigger.cpp
    trunk/libsbml/src/sbml/Unit.cpp
    trunk/libsbml/src/sbml/test/TestSBMLConvert.c
    trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp
    trunk/libsbml/src/sbml/test/TestWriteSBML.cpp

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs	2011-02-18 10:32:43 UTC (rev 12947)
@@ -278,7 +278,7 @@
 
     public void test_SBMLConvert_convertToL1_Species_Amount()
     {
-      SBMLDocument d = new  SBMLDocument(2,1);
+      SBMLDocument d = new  SBMLDocument(2,4);
       Model m = d.createModel();
       string sid =  "C";
       Compartment c = new  Compartment(2,4);

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteL3SBML.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteL3SBML.cs	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteL3SBML.cs	2011-02-18 10:32:43 UTC (rev 12947)
@@ -291,6 +291,7 @@
     "  </priority>\n" + 
     "</event>";
       Event e = D.createModel().createEvent();
+      e.setUseValuesFromTriggerTime(true);
       Trigger t = e.createTrigger();
       t.setInitialValue(true);
       t.setPersistent(false);
@@ -320,6 +321,7 @@
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(util_PosInf());
+      p.setConstant(true);
       assertEquals( true, equals(expected,p.toSBML()) );
     }
 
@@ -394,6 +396,7 @@
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(util_NaN());
+      p.setConstant(true);
       assertEquals( true, equals(expected,p.toSBML()) );
     }
 
@@ -403,6 +406,7 @@
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(util_NegInf());
+      p.setConstant(true);
       assertEquals( true, equals(expected,p.toSBML()) );
     }
 
@@ -452,10 +456,10 @@
     {
       string expected = "<reaction id=\"v1\" reversible=\"true\" fast=\"false\">\n" + 
     "  <listOfReactants>\n" + 
-    "    <speciesReference species=\"x0\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"x0\"/>\n" + 
     "  </listOfReactants>\n" + 
     "  <listOfProducts>\n" + 
-    "    <speciesReference species=\"s1\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"s1\"/>\n" + 
     "  </listOfProducts>\n" + 
     "  <listOfModifiers>\n" + 
     "    <modifierSpeciesReference species=\"m1\"/>\n" + 
@@ -482,6 +486,7 @@
       Reaction r = D.getModel().createReaction();
       r.setId("v1");
       r.setReversible(true);
+      r.setFast(false);
       r.createReactant().setSpecies("x0");
       r.createProduct().setSpecies("s1");
       r.createModifier().setSpecies("m1");
@@ -545,7 +550,7 @@
 
     public void test_WriteL3SBML_Trigger()
     {
-      string expected =  "<trigger initialValue=\"true\" persistent=\"true\"/>";
+      string expected =  "<trigger/>";
       Trigger t = D.createModel().createEvent().createTrigger();
       assertEquals( true, equals(expected,t.toSBML()) );
     }
@@ -555,6 +560,7 @@
       string expected =  "<trigger initialValue=\"false\" persistent=\"true\"/>";
       Trigger t = D.createModel().createEvent().createTrigger();
       t.setInitialValue(false);
+      t.setPersistent(true);
       assertEquals( true, equals(expected,t.toSBML()) );
     }
 
@@ -563,6 +569,7 @@
       string expected =  "<trigger initialValue=\"true\" persistent=\"false\"/>";
       Trigger t = D.createModel().createEvent().createTrigger();
       t.setPersistent(false);
+      t.setInitialValue(true);
       assertEquals( true, equals(expected,t.toSBML()) );
     }
 
@@ -597,7 +604,7 @@
 
     public void test_WriteL3SBML_Unit_noValues()
     {
-      string expected = "<unit kind=\"(Invalid UnitKind)\" exponent=\"NaN\"" + " scale=\"2147483647\" multiplier=\"NaN\"/>";
+      string expected =  "<unit/>";
       Unit u = D.createModel().createUnitDefinition().createUnit();
       assertEquals( true, equals(expected,u.toSBML()) );
     }
@@ -612,14 +619,13 @@
     "      <unitDefinition/>\n" + 
     "    </listOfUnitDefinitions>\n" + 
     "    <listOfCompartments>\n" + 
-    "      <compartment constant=\"true\"/>\n" + 
+    "      <compartment/>\n" + 
     "    </listOfCompartments>\n" + 
     "    <listOfSpecies>\n" + 
-    "      <species hasOnlySubstanceUnits=\"false\"" + 
-    " boundaryCondition=\"false\" constant=\"false\"/>\n" + 
+    "      <species/>\n" +
     "    </listOfSpecies>\n" + 
     "    <listOfParameters>\n" + 
-    "      <parameter constant=\"true\"/>\n" + 
+    "      <parameter/>\n" + 
     "    </listOfParameters>\n" + 
     "    <listOfInitialAssignments>\n" + 
     "      <initialAssignment/>\n" + 
@@ -631,10 +637,10 @@
     "      <constraint/>\n" + 
     "    </listOfConstraints>\n" + 
     "    <listOfReactions>\n" + 
-    "      <reaction reversible=\"true\" fast=\"false\"/>\n" + 
+    "      <reaction/>\n" + 
     "    </listOfReactions>\n" + 
     "    <listOfEvents>\n" + 
-    "      <event useValuesFromTriggerTime=\"true\"/>\n" + 
+    "      <event/>\n" + 
     "    </listOfEvents>\n" + 
     "  </model>\n");
       Model m = D.createModel();
@@ -669,6 +675,7 @@
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(3.31);
+      p.setConstant(true);
       assertEquals( true, equals(expected,p.toSBML()) );
     }
 

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteSBML.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteSBML.cs	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteSBML.cs	2011-02-18 10:32:43 UTC (rev 12947)
@@ -817,7 +817,7 @@
 
     public void test_WriteSBML_INF()
     {
-      string expected =  "<parameter id=\"p\" value=\"INF\" constant=\"true\"/>";
+      string expected =  "<parameter id=\"p\" value=\"INF\"/>";
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(util_PosInf());
@@ -992,7 +992,7 @@
 
     public void test_WriteSBML_NaN()
     {
-      string expected =  "<parameter id=\"p\" value=\"NaN\" constant=\"true\"/>";
+      string expected =  "<parameter id=\"p\" value=\"NaN\"/>";
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(util_NaN());
@@ -1001,7 +1001,7 @@
 
     public void test_WriteSBML_NegINF()
     {
-      string expected =  "<parameter id=\"p\" value=\"-INF\" constant=\"true\"/>";
+      string expected =  "<parameter id=\"p\" value=\"-INF\"/>";
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(util_NegInf());
@@ -1969,6 +1969,7 @@
       Parameter p = D.createModel().createParameter();
       p.setId("p");
       p.setValue(3.31);
+      p.setConstant(true);
       assertEquals( true, equals(expected,p.toSBML()) );
     }
 

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteL3SBML.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteL3SBML.java	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteL3SBML.java	2011-02-18 10:32:43 UTC (rev 12947)
@@ -277,6 +277,7 @@
     "  </priority>\n" + 
     "</event>";
     Event e = D.createModel().createEvent();
+    e.setUseValuesFromTriggerTime(true);
     Trigger t = e.createTrigger();
     t.setInitialValue(true);
     t.setPersistent(false);
@@ -306,6 +307,7 @@
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(util_PosInf());
+    p.setConstant(true);
     assertEquals( true, equals(expected,p.toSBML()) );
   }
 
@@ -380,6 +382,7 @@
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(util_NaN());
+    p.setConstant(true);
     assertEquals( true, equals(expected,p.toSBML()) );
   }
 
@@ -389,6 +392,7 @@
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(util_NegInf());
+    p.setConstant(true);
     assertEquals( true, equals(expected,p.toSBML()) );
   }
 
@@ -438,10 +442,10 @@
   {
     String expected = "<reaction id=\"v1\" reversible=\"true\" fast=\"false\">\n" + 
     "  <listOfReactants>\n" + 
-    "    <speciesReference species=\"x0\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"x0\"/>\n" + 
     "  </listOfReactants>\n" + 
     "  <listOfProducts>\n" + 
-    "    <speciesReference species=\"s1\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"s1\"/>\n" + 
     "  </listOfProducts>\n" + 
     "  <listOfModifiers>\n" + 
     "    <modifierSpeciesReference species=\"m1\"/>\n" + 
@@ -468,6 +472,7 @@
     Reaction r = D.getModel().createReaction();
     r.setId("v1");
     r.setReversible(true);
+    r.setFast(false);
     r.createReactant().setSpecies("x0");
     r.createProduct().setSpecies("s1");
     r.createModifier().setSpecies("m1");
@@ -531,7 +536,7 @@
 
   public void test_WriteL3SBML_Trigger()
   {
-    String expected =  "<trigger initialValue=\"true\" persistent=\"true\"/>";
+    String expected =  "<trigger/>";
     Trigger t = D.createModel().createEvent().createTrigger();
     assertEquals( true, equals(expected,t.toSBML()) );
   }
@@ -541,6 +546,7 @@
     String expected =  "<trigger initialValue=\"false\" persistent=\"true\"/>";
     Trigger t = D.createModel().createEvent().createTrigger();
     t.setInitialValue(false);
+    t.setPersistent(true);
     assertEquals( true, equals(expected,t.toSBML()) );
   }
 
@@ -549,6 +555,7 @@
     String expected =  "<trigger initialValue=\"true\" persistent=\"false\"/>";
     Trigger t = D.createModel().createEvent().createTrigger();
     t.setPersistent(false);
+    t.setInitialValue(true);
     assertEquals( true, equals(expected,t.toSBML()) );
   }
 
@@ -583,7 +590,7 @@
 
   public void test_WriteL3SBML_Unit_noValues()
   {
-    String expected = "<unit kind=\"(Invalid UnitKind)\" exponent=\"NaN\"" + " scale=\"2147483647\" multiplier=\"NaN\"/>";
+    String expected =  "<unit/>";
     Unit u = D.createModel().createUnitDefinition().createUnit();
     assertEquals( true, equals(expected,u.toSBML()) );
   }
@@ -598,14 +605,13 @@
     "      <unitDefinition/>\n" + 
     "    </listOfUnitDefinitions>\n" + 
     "    <listOfCompartments>\n" + 
-    "      <compartment constant=\"true\"/>\n" + 
+    "      <compartment/>\n" + 
     "    </listOfCompartments>\n" + 
     "    <listOfSpecies>\n" + 
-    "      <species hasOnlySubstanceUnits=\"false\"" + 
-    " boundaryCondition=\"false\" constant=\"false\"/>\n" + 
+    "      <species/>\n" +
     "    </listOfSpecies>\n" + 
     "    <listOfParameters>\n" + 
-    "      <parameter constant=\"true\"/>\n" + 
+    "      <parameter/>\n" + 
     "    </listOfParameters>\n" + 
     "    <listOfInitialAssignments>\n" + 
     "      <initialAssignment/>\n" + 
@@ -617,10 +623,10 @@
     "      <constraint/>\n" + 
     "    </listOfConstraints>\n" + 
     "    <listOfReactions>\n" + 
-    "      <reaction reversible=\"true\" fast=\"false\"/>\n" + 
+    "      <reaction/>\n" + 
     "    </listOfReactions>\n" + 
     "    <listOfEvents>\n" + 
-    "      <event useValuesFromTriggerTime=\"true\"/>\n" + 
+    "      <event/>\n" + 
     "    </listOfEvents>\n" + 
     "  </model>\n");
     Model m = D.createModel();
@@ -655,6 +661,7 @@
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(3.31);
+    p.setConstant(true);
     assertEquals( true, equals(expected,p.toSBML()) );
   }
 

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteSBML.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteSBML.java	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestWriteSBML.java	2011-02-18 10:32:43 UTC (rev 12947)
@@ -803,10 +803,11 @@
 
   public void test_WriteSBML_INF()
   {
-    String expected =  "<parameter id=\"p\" value=\"INF\" constant=\"true\"/>";
+    String expected =  "<parameter id=\"p\" value=\"INF\"/>";
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(util_PosInf());
+
     assertEquals( true, equals(expected,p.toSBML()) );
   }
 
@@ -978,7 +979,7 @@
 
   public void test_WriteSBML_NaN()
   {
-    String expected =  "<parameter id=\"p\" value=\"NaN\" constant=\"true\"/>";
+    String expected =  "<parameter id=\"p\" value=\"NaN\"/>";
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(util_NaN());
@@ -987,7 +988,7 @@
 
   public void test_WriteSBML_NegINF()
   {
-    String expected =  "<parameter id=\"p\" value=\"-INF\" constant=\"true\"/>";
+    String expected =  "<parameter id=\"p\" value=\"-INF\"/>";
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(util_NegInf());
@@ -1955,6 +1956,7 @@
     Parameter p = D.createModel().createParameter();
     p.setId("p");
     p.setValue(3.31);
+    p.setConstant(true);
     assertEquals( true, equals(expected,p.toSBML()) );
   }
 

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestWriteL3SBML.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestWriteL3SBML.py	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestWriteL3SBML.py	2011-02-18 10:32:43 UTC (rev 12947)
@@ -187,6 +187,7 @@
     "  </priority>\n" + 
     "</event>")
     e = self.D.createModel().createEvent()
+    e.setUseValuesFromTriggerTime(True)
     t = e.createTrigger()
     t.setInitialValue(True)
     t.setPersistent(False)
@@ -214,6 +215,7 @@
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(util_PosInf())
+    p.setConstant(True)
     self.assertEqual( True, self.equals(expected,p.toSBML()) )
     pass  
 
@@ -281,6 +283,7 @@
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NaN())
+    p.setConstant(True)
     self.assertEqual( True, self.equals(expected,p.toSBML()) )
     pass  
 
@@ -289,6 +292,7 @@
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NegInf())
+    p.setConstant(True)
     self.assertEqual( True, self.equals(expected,p.toSBML()) )
     pass  
 
@@ -333,10 +337,10 @@
   def test_WriteL3SBML_Reaction_full(self):
     expected = wrapString("<reaction id=\"v1\" reversible=\"true\" fast=\"false\">\n" + 
     "  <listOfReactants>\n" + 
-    "    <speciesReference species=\"x0\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"x0\"/>\n" + 
     "  </listOfReactants>\n" + 
     "  <listOfProducts>\n" + 
-    "    <speciesReference species=\"s1\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"s1\"/>\n" + 
     "  </listOfProducts>\n" + 
     "  <listOfModifiers>\n" + 
     "    <modifierSpeciesReference species=\"m1\"/>\n" + 
@@ -363,6 +367,7 @@
     r = self.D.getModel().createReaction()
     r.setId("v1")
     r.setReversible(True)
+    r.setFast(False)
     r.createReactant().setSpecies("x0")
     r.createProduct().setSpecies("s1")
     r.createModifier().setSpecies("m1")
@@ -421,7 +426,7 @@
     pass  
 
   def test_WriteL3SBML_Trigger(self):
-    expected =  "<trigger initialValue=\"true\" persistent=\"true\"/>";
+    expected =  "<trigger/>";
     t = self.D.createModel().createEvent().createTrigger()
     self.assertEqual( True, self.equals(expected,t.toSBML()) )
     pass  
@@ -430,6 +435,7 @@
     expected =  "<trigger initialValue=\"false\" persistent=\"true\"/>";
     t = self.D.createModel().createEvent().createTrigger()
     t.setInitialValue(False)
+    t.setPersistent(True)
     self.assertEqual( True, self.equals(expected,t.toSBML()) )
     pass  
 
@@ -437,6 +443,7 @@
     expected =  "<trigger initialValue=\"true\" persistent=\"false\"/>";
     t = self.D.createModel().createEvent().createTrigger()
     t.setPersistent(False)
+    t.setInitialValue(True)
     self.assertEqual( True, self.equals(expected,t.toSBML()) )
     pass  
 
@@ -468,7 +475,7 @@
     pass  
 
   def test_WriteL3SBML_Unit_noValues(self):
-    expected = "<unit kind=\"(Invalid UnitKind)\" exponent=\"NaN\"" + " scale=\"2147483647\" multiplier=\"NaN\"/>";
+    expected =  "<unit/>";
     u = self.D.createModel().createUnitDefinition().createUnit()
     self.assertEqual( True, self.equals(expected,u.toSBML()) )
     pass  
@@ -482,14 +489,13 @@
     "      <unitDefinition/>\n" + 
     "    </listOfUnitDefinitions>\n" + 
     "    <listOfCompartments>\n" + 
-    "      <compartment constant=\"true\"/>\n" + 
+    "      <compartment/>\n" + 
     "    </listOfCompartments>\n" + 
     "    <listOfSpecies>\n" + 
-    "      <species hasOnlySubstanceUnits=\"false\"" + 
-    " boundaryCondition=\"false\" constant=\"false\"/>\n" + 
+    "      <species/>\n" +
     "    </listOfSpecies>\n" + 
     "    <listOfParameters>\n" + 
-    "      <parameter constant=\"true\"/>\n" + 
+    "      <parameter/>\n" + 
     "    </listOfParameters>\n" + 
     "    <listOfInitialAssignments>\n" + 
     "      <initialAssignment/>\n" + 
@@ -501,10 +507,10 @@
     "      <constraint/>\n" + 
     "    </listOfConstraints>\n" + 
     "    <listOfReactions>\n" + 
-    "      <reaction reversible=\"true\" fast=\"false\"/>\n" + 
+    "      <reaction/>\n" + 
     "    </listOfReactions>\n" + 
     "    <listOfEvents>\n" + 
-    "      <event useValuesFromTriggerTime=\"true\"/>\n" + 
+    "      <event/>\n" + 
     "    </listOfEvents>\n" + 
     "  </model>\n")
     m = self.D.createModel()
@@ -537,6 +543,7 @@
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(3.31)
+    p.setConstant(True)
     self.assertEqual( True, self.equals(expected,p.toSBML()) )
     pass  
 

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestWriteSBML.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestWriteSBML.py	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestWriteSBML.py	2011-02-18 10:32:43 UTC (rev 12947)
@@ -675,7 +675,7 @@
     pass  
 
   def test_WriteSBML_INF(self):
-    expected =  "<parameter id=\"p\" value=\"INF\" constant=\"true\"/>";
+    expected =  "<parameter id=\"p\" value=\"INF\"/>";
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(util_PosInf())
@@ -837,7 +837,7 @@
     pass  
 
   def test_WriteSBML_NaN(self):
-    expected =  "<parameter id=\"p\" value=\"NaN\" constant=\"true\"/>";
+    expected =  "<parameter id=\"p\" value=\"NaN\"/>";
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NaN())
@@ -845,7 +845,7 @@
     pass  
 
   def test_WriteSBML_NegINF(self):
-    expected =  "<parameter id=\"p\" value=\"-INF\" constant=\"true\"/>";
+    expected =  "<parameter id=\"p\" value=\"-INF\"/>";
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NegInf())
@@ -1742,6 +1742,7 @@
     p = self.D.createModel().createParameter()
     p.setId("p")
     p.setValue(3.31)
+    p.setConstant(True)
     self.assertEqual( True, self.equals(expected,p.toSBML()) )
     pass  
 

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteL3SBML.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteL3SBML.rb	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteL3SBML.rb	2011-02-18 10:32:43 UTC (rev 12947)
@@ -176,6 +176,7 @@
     "  </priority>\n" + 
     "</event>"
     e = @@d.createModel().createEvent()
+    e.setUseValuesFromTriggerTime(true)
     t = e.createTrigger()
     t.setInitialValue(true)
     t.setPersistent(false)
@@ -203,6 +204,7 @@
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(util_PosInf())
+    p.setConstant(true)
     assert_equal true, equals(expected,p.toSBML())
   end
 
@@ -270,6 +272,7 @@
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NaN())
+    p.setConstant(true)
     assert_equal true, equals(expected,p.toSBML())
   end
 
@@ -278,6 +281,7 @@
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NegInf())
+    p.setConstant(true)
     assert_equal true, equals(expected,p.toSBML())
   end
 
@@ -322,10 +326,10 @@
   def test_WriteL3SBML_Reaction_full
     expected = "<reaction id=\"v1\" reversible=\"true\" fast=\"false\">\n" + 
     "  <listOfReactants>\n" + 
-    "    <speciesReference species=\"x0\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"x0\"/>\n" + 
     "  </listOfReactants>\n" + 
     "  <listOfProducts>\n" + 
-    "    <speciesReference species=\"s1\" constant=\"false\"/>\n" + 
+    "    <speciesReference species=\"s1\"/>\n" + 
     "  </listOfProducts>\n" + 
     "  <listOfModifiers>\n" + 
     "    <modifierSpeciesReference species=\"m1\"/>\n" + 
@@ -352,6 +356,7 @@
     r = @@d.getModel().createReaction()
     r.setId("v1")
     r.setReversible(true)
+    r.setFast(false)
     r.createReactant().setSpecies("x0")
     r.createProduct().setSpecies("s1")
     r.createModifier().setSpecies("m1")
@@ -410,7 +415,7 @@
   end
 
   def test_WriteL3SBML_Trigger
-    expected =  "<trigger initialValue=\"true\" persistent=\"true\"/>";
+    expected =  "<trigger/>";
     t = @@d.createModel().createEvent().createTrigger()
     assert_equal true, equals(expected,t.toSBML())
   end
@@ -419,6 +424,7 @@
     expected =  "<trigger initialValue=\"false\" persistent=\"true\"/>";
     t = @@d.createModel().createEvent().createTrigger()
     t.setInitialValue(false)
+    t.setPersistent(true)
     assert_equal true, equals(expected,t.toSBML())
   end
 
@@ -426,6 +432,7 @@
     expected =  "<trigger initialValue=\"true\" persistent=\"false\"/>";
     t = @@d.createModel().createEvent().createTrigger()
     t.setPersistent(false)
+    t.setInitialValue(true)
     assert_equal true, equals(expected,t.toSBML())
   end
 
@@ -457,7 +464,7 @@
   end
 
   def test_WriteL3SBML_Unit_noValues
-    expected = "<unit kind=\"(Invalid UnitKind)\" exponent=\"NaN\"" + " scale=\"2147483647\" multiplier=\"NaN\"/>";
+    expected =  "<unit/>";
     u = @@d.createModel().createUnitDefinition().createUnit()
     assert_equal true, equals(expected,u.toSBML())
   end
@@ -471,14 +478,13 @@
     "      <unitDefinition/>\n" + 
     "    </listOfUnitDefinitions>\n" + 
     "    <listOfCompartments>\n" + 
-    "      <compartment constant=\"true\"/>\n" + 
+    "      <compartment/>\n" + 
     "    </listOfCompartments>\n" + 
     "    <listOfSpecies>\n" + 
-    "      <species hasOnlySubstanceUnits=\"false\"" + 
-    " boundaryCondition=\"false\" constant=\"false\"/>\n" + 
+    "      <species/>\n" +
     "    </listOfSpecies>\n" + 
     "    <listOfParameters>\n" + 
-    "      <parameter constant=\"true\"/>\n" + 
+    "      <parameter/>\n" + 
     "    </listOfParameters>\n" + 
     "    <listOfInitialAssignments>\n" + 
     "      <initialAssignment/>\n" + 
@@ -490,10 +496,10 @@
     "      <constraint/>\n" + 
     "    </listOfConstraints>\n" + 
     "    <listOfReactions>\n" + 
-    "      <reaction reversible=\"true\" fast=\"false\"/>\n" + 
+    "      <reaction/>\n" + 
     "    </listOfReactions>\n" + 
     "    <listOfEvents>\n" + 
-    "      <event useValuesFromTriggerTime=\"true\"/>\n" + 
+    "      <event/>\n" + 
     "    </listOfEvents>\n" + 
     "  </model>\n")
     m = @@d.createModel()
@@ -526,6 +532,7 @@
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(3.31)
+    p.setConstant(true)
     assert_equal true, equals(expected,p.toSBML())
   end
 

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteSBML.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteSBML.rb	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestWriteSBML.rb	2011-02-18 10:32:43 UTC (rev 12947)
@@ -664,7 +664,7 @@
   end
 
   def test_WriteSBML_INF
-    expected =  "<parameter id=\"p\" value=\"INF\" constant=\"true\"/>";
+    expected =  "<parameter id=\"p\" value=\"INF\"/>";
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(util_PosInf())
@@ -826,7 +826,7 @@
   end
 
   def test_WriteSBML_NaN
-    expected =  "<parameter id=\"p\" value=\"NaN\" constant=\"true\"/>";
+    expected =  "<parameter id=\"p\" value=\"NaN\"/>";
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NaN())
@@ -834,7 +834,7 @@
   end
 
   def test_WriteSBML_NegINF
-    expected =  "<parameter id=\"p\" value=\"-INF\" constant=\"true\"/>";
+    expected =  "<parameter id=\"p\" value=\"-INF\"/>";
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(util_NegInf())
@@ -1735,6 +1735,7 @@
     p = @@d.createModel().createParameter()
     p.setId("p")
     p.setValue(3.31)
+    p.setConstant(true)
     assert_equal true, equals(expected,p.toSBML())
   end
 

Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/Compartment.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -1563,7 +1563,9 @@
     }
     else
     {
-      stream.writeAttribute("constant", mConstant);
+      // in L3 only write it out if it has been set
+      if (isSetConstant())
+        stream.writeAttribute("constant", mConstant);
     }
     //
     // sboTerm: SBOTerm { use="optional" }  (L2v3 ->)

Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/Event.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -1563,7 +1563,9 @@
   }
   else if (level > 2)
   {
-    stream.writeAttribute("useValuesFromTriggerTime", 
+    // in L3 only write it out if it has been set
+    if (isSetUseValuesFromTriggerTime())
+      stream.writeAttribute("useValuesFromTriggerTime", 
                           mUseValuesFromTriggerTime);
   }
 }

Modified: trunk/libsbml/src/sbml/Parameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/Parameter.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/Parameter.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -1140,7 +1140,9 @@
     }
     else if (this->getTypeCode() == SBML_PARAMETER)
     {
-      stream.writeAttribute("constant", mConstant);
+      // in L3 only write it out if it has been set
+      if (isSetConstant())
+        stream.writeAttribute("constant", mConstant);
     }
 
     //

Modified: trunk/libsbml/src/sbml/Reaction.cpp
===================================================================
--- trunk/libsbml/src/sbml/Reaction.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/Reaction.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -1776,7 +1776,9 @@
   }
   else
   {
-    stream.writeAttribute("reversible", mReversible);
+    // in L3 only write it out if it has been set
+    if (isSetReversible())
+      stream.writeAttribute("reversible", mReversible);
   }
 
   //
@@ -1792,7 +1794,9 @@
   }
   else
   {
-    stream.writeAttribute("fast", mFast);
+    // in L3 only write it out if it has been set
+    if (isSetFast())
+      stream.writeAttribute("fast", mFast);
   }
 
   if (level > 2)

Modified: trunk/libsbml/src/sbml/Species.cpp
===================================================================
--- trunk/libsbml/src/sbml/Species.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/Species.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -1728,7 +1728,9 @@
     }
     else if (level > 2)
     {
-      stream.writeAttribute( "hasOnlySubstanceUnits", 
+      // in L3 only write it out if it has been set
+      if (isSetHasOnlySubstanceUnits())
+        stream.writeAttribute( "hasOnlySubstanceUnits", 
                               mHasOnlySubstanceUnits );
     }
   }
@@ -1745,7 +1747,9 @@
   }
   else
   {
-    stream.writeAttribute("boundaryCondition", mBoundaryCondition);
+    // in L3 only write it out if it has been set
+    if (isSetBoundaryCondition())
+      stream.writeAttribute("boundaryCondition", mBoundaryCondition);
   }
 
 
@@ -1770,7 +1774,9 @@
     }
     else if (level > 2)
     {
-      stream.writeAttribute("constant", mConstant);
+      // in L3 only write it out if it has been set
+      if (isSetConstant())
+        stream.writeAttribute("constant", mConstant);
     }
 
     //

Modified: trunk/libsbml/src/sbml/SpeciesReference.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesReference.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/SpeciesReference.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -1663,7 +1663,9 @@
   //
   if (getLevel() > 2)
   {
-    stream.writeAttribute("constant", mConstant);
+    // in L3 only write it out if it has been set
+    if (isSetConstant())
+      stream.writeAttribute("constant", mConstant);
   }
 }
 /** @endcond */

Modified: trunk/libsbml/src/sbml/Trigger.cpp
===================================================================
--- trunk/libsbml/src/sbml/Trigger.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/Trigger.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -636,8 +636,12 @@
 
   if (level > 2)
   {
-    stream.writeAttribute("initialValue", mInitialValue);
-    stream.writeAttribute("persistent", mPersistent);
+    // in L3 only write it out if it has been set
+    if (isSetInitialValue())
+      stream.writeAttribute("initialValue", mInitialValue);
+      // in L3 only write it out if it has been set
+    if (isSetPersistent())
+      stream.writeAttribute("persistent", mPersistent);
   }
 }
 /** @endcond */

Modified: trunk/libsbml/src/sbml/Unit.cpp
===================================================================
--- trunk/libsbml/src/sbml/Unit.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/Unit.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -1798,7 +1798,16 @@
   // kind: UnitKind  { use="required" }  (L1v1, L1v2, L2v1->)
   //
   const string kind = UnitKind_toString(mKind);
-  stream.writeAttribute("kind", kind);
+  if (level < 3)
+  {
+    stream.writeAttribute("kind", kind);
+  }
+  else
+  {
+    // in L3 only write it out if it has been set
+    if (isSetKind())
+      stream.writeAttribute("kind", kind);
+  }
 
   //
   // exponent  { use="optional" default="1" }  (L1v1, L1v2, L2v1->)
@@ -1811,7 +1820,9 @@
   }
   else
   {
-    stream.writeAttribute("exponent", mExponentDouble);
+    // in L3 only write it out if it has been set
+    if (isSetExponent())
+      stream.writeAttribute("exponent", mExponentDouble);
   }
  
   //
@@ -1824,7 +1835,9 @@
   }
   else
   {
-    stream.writeAttribute("scale", mScale);
+    // in L3 only write it out if it has been set
+    if (isSetScale())
+      stream.writeAttribute("scale", mScale);
   }
 
   if (level > 1)
@@ -1839,7 +1852,9 @@
     }
     else
     {
-      stream.writeAttribute("multiplier", mMultiplier);
+      // in L3 only write it out if it has been set
+      if (isSetMultiplier())
+        stream.writeAttribute("multiplier", mMultiplier);
     }
     //
     // offset  { use="optional" default="0" }  (L2v1)

Modified: trunk/libsbml/src/sbml/test/TestSBMLConvert.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestSBMLConvert.c	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/test/TestSBMLConvert.c	2011-02-18 10:32:43 UTC (rev 12947)
@@ -132,7 +132,7 @@
 
 START_TEST (test_SBMLConvert_convertToL1_Species_Amount)
 {
-  SBMLDocument_t *d   = SBMLDocument_createWithLevelAndVersion(2, 1);
+  SBMLDocument_t *d   = SBMLDocument_createWithLevelAndVersion(2, 4);
   Model_t        *m   = SBMLDocument_createModel(d);
   const char     *sid = "C";
   Compartment_t  *c   = Compartment_create(2, 4);

Modified: trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -283,8 +283,7 @@
 
 START_TEST (test_WriteL3SBML_Unit_noValues)
 {
-  const char* expected = "<unit kind=\"(Invalid UnitKind)\" exponent=\"NaN\""
-    " scale=\"2147483647\" multiplier=\"NaN\"/>";
+  const char* expected = "<unit/>";
 
 
   Unit* u = D->createModel()->createUnitDefinition()->createUnit();
@@ -469,10 +468,10 @@
   const char* expected = 
     "<reaction id=\"v1\" reversible=\"true\" fast=\"false\">\n"
     "  <listOfReactants>\n"
-    "    <speciesReference species=\"x0\" constant=\"false\"/>\n"
+    "    <speciesReference species=\"x0\"/>\n"
     "  </listOfReactants>\n"
     "  <listOfProducts>\n"
-    "    <speciesReference species=\"s1\" constant=\"false\"/>\n"
+    "    <speciesReference species=\"s1\"/>\n"
     "  </listOfProducts>\n"
     "  <listOfModifiers>\n"
     "    <modifierSpeciesReference species=\"m1\"/>\n"
@@ -503,6 +502,7 @@
 
   r->setId("v1");
   r->setReversible(true);
+  r->setFast(false);
 
   r->createReactant()->setSpecies("x0");
   r->createProduct ()->setSpecies("s1");
@@ -583,7 +583,7 @@
 
 START_TEST (test_WriteL3SBML_Trigger)
 {
-  const char* expected = "<trigger initialValue=\"true\" persistent=\"true\"/>";
+  const char* expected = "<trigger/>";
 
   Trigger *t = D->createModel()->createEvent()->createTrigger();
   
@@ -598,6 +598,7 @@
 
   Trigger *t = D->createModel()->createEvent()->createTrigger();
   t->setInitialValue(false);
+  t->setPersistent(true);
   
   fail_unless( equals(expected,t->toSBML()) );
 }
@@ -610,6 +611,7 @@
 
   Trigger *t = D->createModel()->createEvent()->createTrigger();
   t->setPersistent(false);
+  t->setInitialValue(true);
   
   fail_unless( equals(expected,t->toSBML()) );
 }
@@ -644,6 +646,7 @@
     "</event>";
 
   Event *e = D->createModel()->createEvent();
+  e->setUseValuesFromTriggerTime(true);
   Trigger *t = e->createTrigger();
   t->setInitialValue(true);
   t->setPersistent(false);
@@ -667,6 +670,7 @@
   Parameter *p = D->createModel()->createParameter();
   p->setId("p");
   p->setValue(util_NaN());
+  p->setConstant(true);
 
 
   fail_unless( equals(expected,p->toSBML()) );
@@ -682,6 +686,7 @@
   Parameter *p = D->createModel()->createParameter();
   p->setId("p");
   p->setValue(util_PosInf());
+  p->setConstant(true);
 
   fail_unless( equals(expected,p->toSBML()) );
 
@@ -698,6 +703,7 @@
   Parameter *p = D->createModel()->createParameter();
   p->setId("p");
   p->setValue(util_NegInf());
+  p->setConstant(true);
 
   fail_unless( equals(expected,p->toSBML()) );
 }
@@ -712,6 +718,7 @@
   Parameter *p = D->createModel()->createParameter();
   p->setId("p");
   p->setValue(3.31);
+  p->setConstant(true);
 
 
   setlocale(LC_NUMERIC, "de_DE");
@@ -877,14 +884,13 @@
     "      <unitDefinition/>\n"
     "    </listOfUnitDefinitions>\n"
     "    <listOfCompartments>\n"
-    "      <compartment constant=\"true\"/>\n"
+    "      <compartment/>\n"
     "    </listOfCompartments>\n"
     "    <listOfSpecies>\n"
-    "      <species hasOnlySubstanceUnits=\"false\""
-    " boundaryCondition=\"false\" constant=\"false\"/>\n"
+    "      <species/>\n"
     "    </listOfSpecies>\n"
     "    <listOfParameters>\n"
-    "      <parameter constant=\"true\"/>\n"
+    "      <parameter/>\n"
     "    </listOfParameters>\n"
     "    <listOfInitialAssignments>\n"
     "      <initialAssignment/>\n"
@@ -896,10 +902,10 @@
     "      <constraint/>\n"
     "    </listOfConstraints>\n"
     "    <listOfReactions>\n"
-    "      <reaction reversible=\"true\" fast=\"false\"/>\n"
+    "      <reaction/>\n"
     "    </listOfReactions>\n"
     "    <listOfEvents>\n"
-    "      <event useValuesFromTriggerTime=\"true\"/>\n"
+    "      <event/>\n"
     "    </listOfEvents>\n"
     "  </model>\n");
 

Modified: trunk/libsbml/src/sbml/test/TestWriteSBML.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestWriteSBML.cpp	2011-02-18 01:34:24 UTC (rev 12946)
+++ trunk/libsbml/src/sbml/test/TestWriteSBML.cpp	2011-02-18 10:32:43 UTC (rev 12947)
@@ -2223,7 +2223,7 @@
 
 START_TEST (test_WriteSBML_NaN)
 {
-  const char* expected = "<parameter id=\"p\" value=\"NaN\" constant=\"true\"/>";
+  const char* expected = "<parameter id=\"p\" value=\"NaN\"/>";
 
   Parameter *p = D->createModel()->createParameter();
   p->setId("p");
@@ -2237,7 +2237,7 @@
 
 START_TEST (test_WriteSBML_INF)
 {
-  const char* expected = "<parameter id=\"p\" value=\"INF\" constant=\"true\"/>";
+  const char* expected = "<parameter id=\"p\" value=\"INF\"/>";
 
   Parameter *p = D->createModel()->createParameter();
   p->setId("p");
@@ -2251,7 +2251,7 @@
 
 START_TEST (test_WriteSBML_NegINF)
 {
-  const char* expected = "<parameter id=\"p\" value=\"-INF\" constant=\"true\"/>";
+  const char* expected = "<parameter id=\"p\" value=\"-INF\"/>";
 
 
   Parameter *p = D->createModel()->createParameter();
@@ -2270,6 +2270,7 @@
   Parameter *p = D->createModel()->createParameter();
   p->setId("p");
   p->setValue(3.31);
+  p->setConstant(true);
 
 
   setlocale(LC_NUMERIC, "de_DE");


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12949
          http://sbml.svn.sourceforge.net/sbml/?rev=12949&view=rev
Author:   sarahkeating
Date:     2011-02-18 13:39:05 +0000 (Fri, 18 Feb 2011)

Log Message:
-----------
improved the internal consistency validator so it will report unset required attributes and elements

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestInternalConsistencyChecks.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInternalConsistencyChecks.java
    trunk/libsbml/src/bindings/python/test/sbml/TestInternalConsistencyChecks.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestInternalConsistencyChecks.rb
    trunk/libsbml/src/sbml/test/TestInternalConsistencyChecks.cpp
    trunk/libsbml/src/validator/constraints/InternalConsistencyConstraints.cpp

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestInternalConsistencyChecks.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestInternalConsistencyChecks.cs	2011-02-18 10:40:28 UTC (rev 12948)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestInternalConsistencyChecks.cs	2011-02-18 13:39:05 UTC (rev 12949)
@@ -1,8 +1,9 @@
 ///  @file    TestInternalConsistencyChecks.cs
-///  @brief   Tests the internal consistency validation.
+///  @brief   Tests the internal consistency validation.
 ///  @author  Frank Bergmann (Csharp conversion)
 ///  @author  Akiya Jouraku (Csharp conversion)
-///  @author  Sarah Keating 
+///  @author  Sarah Keating
+ 
 /// 
 ///  $Id$
 ///  $HeadURL$
@@ -130,6 +131,720 @@
     }
 
 
+    public void test_internal_consistency_check_20306()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      FunctionDefinition fd = m.createFunctionDefinition();
+      fd.setId("fd");
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20306 );
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      fd.setMath(ast);
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20307()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      FunctionDefinition fd = m.createFunctionDefinition();
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      fd.setMath(ast);
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20307 );
+      fd.setId("fd");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20419()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      UnitDefinition ud = m.createUnitDefinition();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20419 );
+      ud.setId("ud");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20421()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      UnitDefinition ud = m.createUnitDefinition();
+      ud.setId("ud");
+      Unit u = ud.createUnit();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 4 );
+      assertTrue( d.getError(0).getErrorId() == 20421 );
+      assertTrue( d.getError(1).getErrorId() == 20421 );
+      assertTrue( d.getError(2).getErrorId() == 20421 );
+      assertTrue( d.getError(3).getErrorId() == 20421 );
+      u.setKind(libsbml.UNIT_KIND_MOLE);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 3 );
+      assertTrue( d.getError(0).getErrorId() == 20421 );
+      assertTrue( d.getError(1).getErrorId() == 20421 );
+      assertTrue( d.getError(2).getErrorId() == 20421 );
+      u.setExponent(1.0);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 2 );
+      assertTrue( d.getError(0).getErrorId() == 20421 );
+      assertTrue( d.getError(1).getErrorId() == 20421 );
+      u.setScale(0);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20421 );
+      u.setMultiplier(1.0);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20517()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Compartment c = m.createCompartment();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 2 );
+      assertTrue( d.getError(0).getErrorId() == 20517 );
+      assertTrue( d.getError(1).getErrorId() == 20517 );
+      c.setId("c");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20517 );
+      c.setConstant(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20623()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Compartment c = m.createCompartment();
+      c.setId("c");
+      c.setConstant(true);
+      Species s = m.createSpecies();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 5 );
+      assertTrue( d.getError(0).getErrorId() == 20623 );
+      assertTrue( d.getError(1).getErrorId() == 20614 );
+      assertTrue( d.getError(2).getErrorId() == 20623 );
+      assertTrue( d.getError(3).getErrorId() == 20623 );
+      assertTrue( d.getError(4).getErrorId() == 20623 );
+      s.setId("s");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 4 );
+      assertTrue( d.getError(0).getErrorId() == 20614 );
+      assertTrue( d.getError(1).getErrorId() == 20623 );
+      assertTrue( d.getError(2).getErrorId() == 20623 );
+      assertTrue( d.getError(3).getErrorId() == 20623 );
+      s.setCompartment("c");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 3 );
+      assertTrue( d.getError(0).getErrorId() == 20623 );
+      assertTrue( d.getError(1).getErrorId() == 20623 );
+      assertTrue( d.getError(2).getErrorId() == 20623 );
+      s.setHasOnlySubstanceUnits(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 2 );
+      assertTrue( d.getError(0).getErrorId() == 20623 );
+      assertTrue( d.getError(1).getErrorId() == 20623 );
+      s.setBoundaryCondition(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20623 );
+      s.setConstant(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20706()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Parameter p = m.createParameter();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 2 );
+      assertTrue( d.getError(0).getErrorId() == 20706 );
+      assertTrue( d.getError(1).getErrorId() == 20706 );
+      p.setId("c");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20706 );
+      p.setConstant(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20804()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      InitialAssignment ia = m.createInitialAssignment();
+      ia.setSymbol("fd");
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20804 );
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      ia.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20805()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      InitialAssignment ia = m.createInitialAssignment();
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      ia.setMath(ast);
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20805 );
+      ia.setSymbol("fd");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20907_alg()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      AlgebraicRule r = m.createAlgebraicRule();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20907 );
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      r.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20907_assign()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      AssignmentRule r = m.createAssignmentRule();
+      r.setVariable("fd");
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20907 );
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      r.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20907_rate()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      RateRule r = m.createRateRule();
+      r.setVariable("fd");
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20907 );
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      r.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20908()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      AssignmentRule r = m.createAssignmentRule();
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      r.setMath(ast);
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20908 );
+      r.setVariable("fd");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_20909()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      RateRule r = m.createRateRule();
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      r.setMath(ast);
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 20909 );
+      r.setVariable("fd");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21007()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Constraint r = m.createConstraint();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21007 );
+      ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+      r.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21101()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Reaction r = m.createReaction();
+      r.setId("r");
+      r.setReversible(true);
+      r.setFast(false);
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21101 );
+      SpeciesReference sr = r.createReactant();
+      sr.setSpecies("s");
+      sr.setConstant(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21110()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Reaction r = m.createReaction();
+      SpeciesReference sr = r.createProduct();
+      sr.setSpecies("s");
+      sr.setConstant(true);
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 3 );
+      assertTrue( d.getError(0).getErrorId() == 21110 );
+      assertTrue( d.getError(1).getErrorId() == 21110 );
+      assertTrue( d.getError(2).getErrorId() == 21110 );
+      r.setId("r");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 2 );
+      assertTrue( d.getError(0).getErrorId() == 21110 );
+      assertTrue( d.getError(1).getErrorId() == 21110 );
+      r.setReversible(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21110 );
+      r.setFast(false);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21116()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Reaction r = m.createReaction();
+      r.setId("r");
+      r.setReversible(true);
+      r.setFast(false);
+      SpeciesReference sr = r.createReactant();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 2 );
+      assertTrue( d.getError(0).getErrorId() == 21116 );
+      assertTrue( d.getError(1).getErrorId() == 21116 );
+      sr.setSpecies("s");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21116 );
+      sr.setConstant(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21117()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Reaction r = m.createReaction();
+      r.setId("r");
+      r.setReversible(true);
+      r.setFast(false);
+      SpeciesReference sr = r.createReactant();
+      sr.setSpecies("s");
+      sr.setConstant(true);
+      ModifierSpeciesReference msr = r.createModifier();
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21117 );
+      msr.setSpecies("s");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21130()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Reaction r = m.createReaction();
+      r.setId("r");
+      r.setReversible(true);
+      r.setFast(false);
+      SpeciesReference sr = r.createReactant();
+      sr.setSpecies("s");
+      sr.setConstant(true);
+      KineticLaw kl = r.createKineticLaw();
+      LocalParameter lp = kl.createLocalParameter();
+      lp.setId("s");
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21130 );
+      ASTNode ast = libsbml.parseFormula("2*x");
+      kl.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21172()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Reaction r = m.createReaction();
+      r.setId("r");
+      r.setReversible(true);
+      r.setFast(false);
+      SpeciesReference sr = r.createReactant();
+      sr.setSpecies("s");
+      sr.setConstant(true);
+      KineticLaw kl = r.createKineticLaw();
+      ASTNode ast = libsbml.parseFormula("2*x");
+      kl.setMath(ast);
+      LocalParameter lp = kl.createLocalParameter();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21172 );
+      lp.setId("pp");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21201()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("s");
+      ASTNode ast = libsbml.parseFormula("2*x");
+      ea.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21201 );
+      Trigger t = r.createTrigger();
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      t.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21203()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      ASTNode ast = libsbml.parseFormula("2*x");
+      Trigger t = r.createTrigger();
+      t.setMath(ast);
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21203 );
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("ea");
+      ea.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21209()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("s");
+      ASTNode ast = libsbml.parseFormula("2*x");
+      ea.setMath(ast);
+      Trigger t = r.createTrigger();
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21209 );
+      t.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21210()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      ASTNode ast = libsbml.parseFormula("2*x");
+      Trigger t = r.createTrigger();
+      t.setMath(ast);
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("ea");
+      ea.setMath(ast);
+      Delay delay = r.createDelay();
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21210 );
+      delay.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21213()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("s");
+      ASTNode ast = libsbml.parseFormula("2*x");
+      Trigger t = r.createTrigger();
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      t.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21213 );
+      ea.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21214()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      EventAssignment ea = r.createEventAssignment();
+      ASTNode ast = libsbml.parseFormula("2*x");
+      ea.setMath(ast);
+      Trigger t = r.createTrigger();
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      t.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21214 );
+      ea.setVariable("s");
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21225()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("s");
+      ASTNode ast = libsbml.parseFormula("2*x");
+      ea.setMath(ast);
+      Trigger t = r.createTrigger();
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      t.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21225 );
+      r.setUseValuesFromTriggerTime(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21226()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("s");
+      ASTNode ast = libsbml.parseFormula("2*x");
+      ea.setMath(ast);
+      Trigger t = r.createTrigger();
+      t.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 2 );
+      assertTrue( d.getError(0).getErrorId() == 21226 );
+      assertTrue( d.getError(1).getErrorId() == 21226 );
+      t.setPersistent(true);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21226 );
+      t.setInitialValue(false);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
+    public void test_internal_consistency_check_21231()
+    {
+      SBMLDocument d = new SBMLDocument(3,1);
+      long errors;
+      Model m = d.createModel();
+      Event r = m.createEvent();
+      r.setUseValuesFromTriggerTime(true);
+      ASTNode ast = libsbml.parseFormula("2*x");
+      Trigger t = r.createTrigger();
+      t.setMath(ast);
+      t.setPersistent(true);
+      t.setInitialValue(false);
+      EventAssignment ea = r.createEventAssignment();
+      ea.setVariable("ea");
+      ea.setMath(ast);
+      Priority prior = r.createPriority();
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21231 );
+      prior.setMath(ast);
+      d.getErrorLog().clearLog();
+      errors = d.checkInternalConsistency();
+      assertTrue( errors == 0 );
+      d = null;
+    }
+
     public void test_internal_consistency_check_99901()
     {
       SBMLDocument d = new SBMLDocument(2,4);
@@ -192,6 +907,8 @@
       c.setId("cc");
       Reaction r = m.createReaction();
       r.setId("r");
+      SpeciesReference sr = r.createReactant();
+      sr.setSpecies("s");
       KineticLaw kl = r.createKineticLaw();
       kl.setFormula("2");
       p.setId("p");
@@ -249,6 +966,8 @@
       c.setId("cc");
       Reaction r = m.createReaction();
       r.setId("r");
+      SpeciesReference sr = r.createReactant();
+      sr.setSpecies("s");
       kl.setFormula("2");
       kl.setMetaId("mmm");
       r.setKineticLaw(kl);
@@ -391,14 +1110,15 @@
       c.setId("c");
       Species s = m.createSpecies();
       s.setId("s");
+      s.setCompartment("c");
       Reaction r = m.createReaction();
       r.setId("r");
-      s.setCompartment("c");
       sr.setSpecies("s");
       sr.setMetaId("mmm");
       r.addProduct(sr);
       errors = d.checkInternalConsistency();
-      assertTrue( errors == 0 );
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21101 );
       d = null;
     }
 
@@ -676,12 +1396,17 @@
       c.setId("c");
       c.setConstant(false);
       Event e = m.createEvent();
+      ASTNode ast = libsbml.parseFormula("2*x");
+      Trigger t = e.createTrigger();
+      t.setMath(ast);
       EventAssignment ea = new EventAssignment(2,4);
       ea.setVariable("c");
       ea.setSBOTerm(2);
+      ea.setMath(ast);
       e.addEventAssignment(ea);
       errors = d.checkInternalConsistency();
-      assertTrue( errors == 0 );
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21203 );
       d = null;
     }
 
@@ -722,6 +1447,8 @@
       Model m = d.createModel();
       Reaction r = m.createReaction();
       r.setId("r");
+      SpeciesReference sr = r.createReactant();
+      sr.setSpecies("s");
       KineticLaw kl = new KineticLaw(2,4);
       kl.setSBOTerm(2);
       Parameter p = kl.createParameter();
@@ -844,7 +1571,8 @@
       sr.setSBOTerm(4);
       r.addReactant(sr);
       errors = d.checkInternalConsistency();
-      assertTrue( errors == 0 );
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21101 );
       d = null;
     }
 
@@ -1061,7 +1789,8 @@
       sr.setId("mmm");
       r.addProduct(sr);
       errors = d.checkInternalConsistency();
-      assertTrue( errors == 0 );
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21101 );
       d = null;
     }
 
@@ -1083,7 +1812,8 @@
       sr.setName("mmm");
       r.addReactant(sr);
       errors = d.checkInternalConsistency();
-      assertTrue( errors == 0 );
+      assertTrue( errors == 1 );
+      assertTrue( d.getError(0).getErrorId() == 21101 );
       d = null;
     }
 

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInternalConsistencyChecks.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInternalConsistencyChecks.java	2011-02-18 10:40:28 UTC (rev 12948)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInternalConsistencyChecks.java	2011-02-18 13:39:05 UTC (rev 12949)
@@ -1,9 +1,10 @@
 /*
  * @file    TestInternalConsistencyChecks.java
- * @brief   Tests the internal consistency validation.
+ * @brief   Tests the internal consistency validation.
  *
  * @author  Akiya Jouraku (Java conversion)
- * @author  Sarah Keating 
+ * @author  Sarah Keating
+ 
  *
  * $Id$
  * $HeadURL$
@@ -121,6 +122,720 @@
     throw new AssertionError();
   }
 
+  public void test_internal_consistency_check_20306()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    FunctionDefinition fd = m.createFunctionDefinition();
+    fd.setId("fd");
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20306 );
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    fd.setMath(ast);
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20307()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    FunctionDefinition fd = m.createFunctionDefinition();
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    fd.setMath(ast);
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20307 );
+    fd.setId("fd");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20419()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    UnitDefinition ud = m.createUnitDefinition();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20419 );
+    ud.setId("ud");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20421()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    UnitDefinition ud = m.createUnitDefinition();
+    ud.setId("ud");
+    Unit u = ud.createUnit();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 4 );
+    assertTrue( d.getError(0).getErrorId() == 20421 );
+    assertTrue( d.getError(1).getErrorId() == 20421 );
+    assertTrue( d.getError(2).getErrorId() == 20421 );
+    assertTrue( d.getError(3).getErrorId() == 20421 );
+    u.setKind(libsbml.UNIT_KIND_MOLE);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 3 );
+    assertTrue( d.getError(0).getErrorId() == 20421 );
+    assertTrue( d.getError(1).getErrorId() == 20421 );
+    assertTrue( d.getError(2).getErrorId() == 20421 );
+    u.setExponent(1.0);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 2 );
+    assertTrue( d.getError(0).getErrorId() == 20421 );
+    assertTrue( d.getError(1).getErrorId() == 20421 );
+    u.setScale(0);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20421 );
+    u.setMultiplier(1.0);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20517()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Compartment c = m.createCompartment();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 2 );
+    assertTrue( d.getError(0).getErrorId() == 20517 );
+    assertTrue( d.getError(1).getErrorId() == 20517 );
+    c.setId("c");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20517 );
+    c.setConstant(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20623()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Compartment c = m.createCompartment();
+    c.setId("c");
+    c.setConstant(true);
+    Species s = m.createSpecies();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 5 );
+    assertTrue( d.getError(0).getErrorId() == 20623 );
+    assertTrue( d.getError(1).getErrorId() == 20614 );
+    assertTrue( d.getError(2).getErrorId() == 20623 );
+    assertTrue( d.getError(3).getErrorId() == 20623 );
+    assertTrue( d.getError(4).getErrorId() == 20623 );
+    s.setId("s");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 4 );
+    assertTrue( d.getError(0).getErrorId() == 20614 );
+    assertTrue( d.getError(1).getErrorId() == 20623 );
+    assertTrue( d.getError(2).getErrorId() == 20623 );
+    assertTrue( d.getError(3).getErrorId() == 20623 );
+    s.setCompartment("c");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 3 );
+    assertTrue( d.getError(0).getErrorId() == 20623 );
+    assertTrue( d.getError(1).getErrorId() == 20623 );
+    assertTrue( d.getError(2).getErrorId() == 20623 );
+    s.setHasOnlySubstanceUnits(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 2 );
+    assertTrue( d.getError(0).getErrorId() == 20623 );
+    assertTrue( d.getError(1).getErrorId() == 20623 );
+    s.setBoundaryCondition(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20623 );
+    s.setConstant(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20706()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Parameter p = m.createParameter();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 2 );
+    assertTrue( d.getError(0).getErrorId() == 20706 );
+    assertTrue( d.getError(1).getErrorId() == 20706 );
+    p.setId("c");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20706 );
+    p.setConstant(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20804()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    InitialAssignment ia = m.createInitialAssignment();
+    ia.setSymbol("fd");
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20804 );
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    ia.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20805()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    InitialAssignment ia = m.createInitialAssignment();
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    ia.setMath(ast);
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20805 );
+    ia.setSymbol("fd");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20907_alg()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    AlgebraicRule r = m.createAlgebraicRule();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20907 );
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    r.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20907_assign()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    AssignmentRule r = m.createAssignmentRule();
+    r.setVariable("fd");
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20907 );
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    r.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20907_rate()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    RateRule r = m.createRateRule();
+    r.setVariable("fd");
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20907 );
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    r.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20908()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    AssignmentRule r = m.createAssignmentRule();
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    r.setMath(ast);
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20908 );
+    r.setVariable("fd");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_20909()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    RateRule r = m.createRateRule();
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    r.setMath(ast);
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 20909 );
+    r.setVariable("fd");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21007()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Constraint r = m.createConstraint();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21007 );
+    ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
+    r.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21101()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Reaction r = m.createReaction();
+    r.setId("r");
+    r.setReversible(true);
+    r.setFast(false);
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21101 );
+    SpeciesReference sr = r.createReactant();
+    sr.setSpecies("s");
+    sr.setConstant(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21110()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Reaction r = m.createReaction();
+    SpeciesReference sr = r.createProduct();
+    sr.setSpecies("s");
+    sr.setConstant(true);
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 3 );
+    assertTrue( d.getError(0).getErrorId() == 21110 );
+    assertTrue( d.getError(1).getErrorId() == 21110 );
+    assertTrue( d.getError(2).getErrorId() == 21110 );
+    r.setId("r");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 2 );
+    assertTrue( d.getError(0).getErrorId() == 21110 );
+    assertTrue( d.getError(1).getErrorId() == 21110 );
+    r.setReversible(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21110 );
+    r.setFast(false);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21116()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Reaction r = m.createReaction();
+    r.setId("r");
+    r.setReversible(true);
+    r.setFast(false);
+    SpeciesReference sr = r.createReactant();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 2 );
+    assertTrue( d.getError(0).getErrorId() == 21116 );
+    assertTrue( d.getError(1).getErrorId() == 21116 );
+    sr.setSpecies("s");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21116 );
+    sr.setConstant(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21117()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Reaction r = m.createReaction();
+    r.setId("r");
+    r.setReversible(true);
+    r.setFast(false);
+    SpeciesReference sr = r.createReactant();
+    sr.setSpecies("s");
+    sr.setConstant(true);
+    ModifierSpeciesReference msr = r.createModifier();
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21117 );
+    msr.setSpecies("s");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21130()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Reaction r = m.createReaction();
+    r.setId("r");
+    r.setReversible(true);
+    r.setFast(false);
+    SpeciesReference sr = r.createReactant();
+    sr.setSpecies("s");
+    sr.setConstant(true);
+    KineticLaw kl = r.createKineticLaw();
+    LocalParameter lp = kl.createLocalParameter();
+    lp.setId("s");
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21130 );
+    ASTNode ast = libsbml.parseFormula("2*x");
+    kl.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21172()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Reaction r = m.createReaction();
+    r.setId("r");
+    r.setReversible(true);
+    r.setFast(false);
+    SpeciesReference sr = r.createReactant();
+    sr.setSpecies("s");
+    sr.setConstant(true);
+    KineticLaw kl = r.createKineticLaw();
+    ASTNode ast = libsbml.parseFormula("2*x");
+    kl.setMath(ast);
+    LocalParameter lp = kl.createLocalParameter();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21172 );
+    lp.setId("pp");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21201()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("s");
+    ASTNode ast = libsbml.parseFormula("2*x");
+    ea.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21201 );
+    Trigger t = r.createTrigger();
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    t.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21203()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    ASTNode ast = libsbml.parseFormula("2*x");
+    Trigger t = r.createTrigger();
+    t.setMath(ast);
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21203 );
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("ea");
+    ea.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21209()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("s");
+    ASTNode ast = libsbml.parseFormula("2*x");
+    ea.setMath(ast);
+    Trigger t = r.createTrigger();
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21209 );
+    t.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21210()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    ASTNode ast = libsbml.parseFormula("2*x");
+    Trigger t = r.createTrigger();
+    t.setMath(ast);
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("ea");
+    ea.setMath(ast);
+    Delay delay = r.createDelay();
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21210 );
+    delay.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21213()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("s");
+    ASTNode ast = libsbml.parseFormula("2*x");
+    Trigger t = r.createTrigger();
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    t.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21213 );
+    ea.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21214()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    EventAssignment ea = r.createEventAssignment();
+    ASTNode ast = libsbml.parseFormula("2*x");
+    ea.setMath(ast);
+    Trigger t = r.createTrigger();
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    t.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21214 );
+    ea.setVariable("s");
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21225()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("s");
+    ASTNode ast = libsbml.parseFormula("2*x");
+    ea.setMath(ast);
+    Trigger t = r.createTrigger();
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    t.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21225 );
+    r.setUseValuesFromTriggerTime(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21226()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("s");
+    ASTNode ast = libsbml.parseFormula("2*x");
+    ea.setMath(ast);
+    Trigger t = r.createTrigger();
+    t.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 2 );
+    assertTrue( d.getError(0).getErrorId() == 21226 );
+    assertTrue( d.getError(1).getErrorId() == 21226 );
+    t.setPersistent(true);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21226 );
+    t.setInitialValue(false);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
+  public void test_internal_consistency_check_21231()
+  {
+    SBMLDocument d = new SBMLDocument(3,1);
+    long errors;
+    Model m = d.createModel();
+    Event r = m.createEvent();
+    r.setUseValuesFromTriggerTime(true);
+    ASTNode ast = libsbml.parseFormula("2*x");
+    Trigger t = r.createTrigger();
+    t.setMath(ast);
+    t.setPersistent(true);
+    t.setInitialValue(false);
+    EventAssignment ea = r.createEventAssignment();
+    ea.setVariable("ea");
+    ea.setMath(ast);
+    Priority prior = r.createPriority();
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21231 );
+    prior.setMath(ast);
+    d.getErrorLog().clearLog();
+    errors = d.checkInternalConsistency();
+    assertTrue( errors == 0 );
+    d = null;
+  }
+
   public void test_internal_consistency_check_99901()
   {
     SBMLDocument d = new SBMLDocument(2,4);
@@ -183,6 +898,8 @@
     c.setId("cc");
     Reaction r = m.createReaction();
     r.setId("r");
+    SpeciesReference sr = r.createReactant();
+    sr.setSpecies("s");
     KineticLaw kl = r.createKineticLaw();
     kl.setFormula("2");
     p.setId("p");
@@ -240,6 +957,8 @@
     c.setId("cc");
     Reaction r = m.createReaction();
     r.setId("r");
+    SpeciesReference sr = r.createReactant();
+    sr.setSpecies("s");
     kl.setFormula("2");
     kl.setMetaId("mmm");
     r.setKineticLaw(kl);
@@ -382,14 +1101,15 @@
     c.setId("c");
     Species s = m.createSpecies();
     s.setId("s");
+    s.setCompartment("c");
     Reaction r = m.createReaction();
     r.setId("r");
-    s.setCompartment("c");
     sr.setSpecies("s");
     sr.setMetaId("mmm");
     r.addProduct(sr);
     errors = d.checkInternalConsistency();
-    assertTrue( errors == 0 );
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21101 );
     d = null;
   }
 
@@ -667,12 +1387,17 @@
     c.setId("c");
     c.setConstant(false);
     Event e = m.createEvent();
+    ASTNode ast = libsbml.parseFormula("2*x");
+    Trigger t = e.createTrigger();
+    t.setMath(ast);
     EventAssignment ea = new EventAssignment(2,4);
     ea.setVariable("c");
     ea.setSBOTerm(2);
+    ea.setMath(ast);
     e.addEventAssignment(ea);
     errors = d.checkInternalConsistency();
-    assertTrue( errors == 0 );
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21203 );
     d = null;
   }
 
@@ -713,6 +1438,8 @@
     Model m = d.createModel();
     Reaction r = m.createReaction();
     r.setId("r");
+    SpeciesReference sr = r.createReactant();
+    sr.setSpecies("s");
     KineticLaw kl = new KineticLaw(2,4);
     kl.setSBOTerm(2);
     Parameter p = kl.createParameter();
@@ -835,7 +1562,8 @@
     sr.setSBOTerm(4);
     r.addReactant(sr);
     errors = d.checkInternalConsistency();
-    assertTrue( errors == 0 );
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21101 );
     d = null;
   }
 
@@ -1052,7 +1780,8 @@
     sr.setId("mmm");
     r.addProduct(sr);
     errors = d.checkInternalConsistency();
-    assertTrue( errors == 0 );
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21101 );
     d = null;
   }
 
@@ -1074,7 +1803,8 @@
     sr.setName("mmm");
     r.addReactant(sr);
     errors = d.checkInternalConsistency();
-    assertTrue( errors == 0 );
+    assertTrue( errors == 1 );
+    assertTrue( d.getError(0).getErrorId() == 21101 );
     d = null;
   }
 

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestInternalConsistencyChecks.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestInternalConsistencyChecks.py	2011-02-18 10:40:28 UTC (rev 12948)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestInternalConsistencyChecks.py	2011-02-18 13:39:05 UTC (rev 12949)
@@ -1,9 +1,10 @@
 #
 # @file    TestInternalConsistencyChecks.py
-# @brief   Tests the internal consistency validation.
+# @brief   Tests the internal consistency validation.
 #
 # @author  Akiya Jouraku (Python conversion)
-# @author  Sarah Keating 
+# @author  Sarah Keating
+ 
 #
 # $Id$
 # $HeadURL$
@@ -40,6 +41,660 @@
 class TestInternalConsistencyChecks(unittest.TestCase):
 
 
+  def test_internal_consistency_check_20306(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    fd = m.createFunctionDefinition()
+    fd.setId("fd")
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20306 )
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    fd.setMath(ast)
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20307(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    fd = m.createFunctionDefinition()
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    fd.setMath(ast)
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20307 )
+    fd.setId("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20419(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    ud = m.createUnitDefinition()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20419 )
+    ud.setId("ud")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20421(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    ud = m.createUnitDefinition()
+    ud.setId("ud")
+    u = ud.createUnit()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 4 )
+    self.assert_( d.getError(0).getErrorId() == 20421 )
+    self.assert_( d.getError(1).getErrorId() == 20421 )
+    self.assert_( d.getError(2).getErrorId() == 20421 )
+    self.assert_( d.getError(3).getErrorId() == 20421 )
+    u.setKind(libsbml.UNIT_KIND_MOLE)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 3 )
+    self.assert_( d.getError(0).getErrorId() == 20421 )
+    self.assert_( d.getError(1).getErrorId() == 20421 )
+    self.assert_( d.getError(2).getErrorId() == 20421 )
+    u.setExponent(1.0)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 2 )
+    self.assert_( d.getError(0).getErrorId() == 20421 )
+    self.assert_( d.getError(1).getErrorId() == 20421 )
+    u.setScale(0)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20421 )
+    u.setMultiplier(1.0)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20517(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    c = m.createCompartment()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 2 )
+    self.assert_( d.getError(0).getErrorId() == 20517 )
+    self.assert_( d.getError(1).getErrorId() == 20517 )
+    c.setId("c")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20517 )
+    c.setConstant(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20623(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    c = m.createCompartment()
+    c.setId("c")
+    c.setConstant(True)
+    s = m.createSpecies()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 5 )
+    self.assert_( d.getError(0).getErrorId() == 20623 )
+    self.assert_( d.getError(1).getErrorId() == 20614 )
+    self.assert_( d.getError(2).getErrorId() == 20623 )
+    self.assert_( d.getError(3).getErrorId() == 20623 )
+    self.assert_( d.getError(4).getErrorId() == 20623 )
+    s.setId("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 4 )
+    self.assert_( d.getError(0).getErrorId() == 20614 )
+    self.assert_( d.getError(1).getErrorId() == 20623 )
+    self.assert_( d.getError(2).getErrorId() == 20623 )
+    self.assert_( d.getError(3).getErrorId() == 20623 )
+    s.setCompartment("c")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 3 )
+    self.assert_( d.getError(0).getErrorId() == 20623 )
+    self.assert_( d.getError(1).getErrorId() == 20623 )
+    self.assert_( d.getError(2).getErrorId() == 20623 )
+    s.setHasOnlySubstanceUnits(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 2 )
+    self.assert_( d.getError(0).getErrorId() == 20623 )
+    self.assert_( d.getError(1).getErrorId() == 20623 )
+    s.setBoundaryCondition(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20623 )
+    s.setConstant(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20706(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    p = m.createParameter()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 2 )
+    self.assert_( d.getError(0).getErrorId() == 20706 )
+    self.assert_( d.getError(1).getErrorId() == 20706 )
+    p.setId("c")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20706 )
+    p.setConstant(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20804(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    ia = m.createInitialAssignment()
+    ia.setSymbol("fd")
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20804 )
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    ia.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20805(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    ia = m.createInitialAssignment()
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    ia.setMath(ast)
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20805 )
+    ia.setSymbol("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20907_alg(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createAlgebraicRule()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20907 )
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20907_assign(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createAssignmentRule()
+    r.setVariable("fd")
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20907 )
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20907_rate(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createRateRule()
+    r.setVariable("fd")
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20907 )
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20908(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createAssignmentRule()
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20908 )
+    r.setVariable("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_20909(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createRateRule()
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 20909 )
+    r.setVariable("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21007(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createConstraint()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21007 )
+    ast = libsbml.parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21101(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(True)
+    r.setFast(False)
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21101 )
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21110(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    sr = r.createProduct()
+    sr.setSpecies("s")
+    sr.setConstant(True)
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 3 )
+    self.assert_( d.getError(0).getErrorId() == 21110 )
+    self.assert_( d.getError(1).getErrorId() == 21110 )
+    self.assert_( d.getError(2).getErrorId() == 21110 )
+    r.setId("r")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 2 )
+    self.assert_( d.getError(0).getErrorId() == 21110 )
+    self.assert_( d.getError(1).getErrorId() == 21110 )
+    r.setReversible(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21110 )
+    r.setFast(False)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21116(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(True)
+    r.setFast(False)
+    sr = r.createReactant()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 2 )
+    self.assert_( d.getError(0).getErrorId() == 21116 )
+    self.assert_( d.getError(1).getErrorId() == 21116 )
+    sr.setSpecies("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21116 )
+    sr.setConstant(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21117(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(True)
+    r.setFast(False)
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(True)
+    msr = r.createModifier()
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21117 )
+    msr.setSpecies("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21130(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(True)
+    r.setFast(False)
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(True)
+    kl = r.createKineticLaw()
+    lp = kl.createLocalParameter()
+    lp.setId("s")
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21130 )
+    ast = libsbml.parseFormula("2*x")
+    kl.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21172(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(True)
+    r.setFast(False)
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(True)
+    kl = r.createKineticLaw()
+    ast = libsbml.parseFormula("2*x")
+    kl.setMath(ast)
+    lp = kl.createLocalParameter()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21172 )
+    lp.setId("pp")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21201(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = libsbml.parseFormula("2*x")
+    ea.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21201 )
+    t = r.createTrigger()
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21203(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ast = libsbml.parseFormula("2*x")
+    t = r.createTrigger()
+    t.setMath(ast)
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21203 )
+    ea = r.createEventAssignment()
+    ea.setVariable("ea")
+    ea.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21209(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = libsbml.parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21209 )
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21210(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ast = libsbml.parseFormula("2*x")
+    t = r.createTrigger()
+    t.setMath(ast)
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    ea = r.createEventAssignment()
+    ea.setVariable("ea")
+    ea.setMath(ast)
+    delay = r.createDelay()
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21210 )
+    delay.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21213(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = libsbml.parseFormula("2*x")
+    t = r.createTrigger()
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21213 )
+    ea.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21214(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ea = r.createEventAssignment()
+    ast = libsbml.parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21214 )
+    ea.setVariable("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21225(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = libsbml.parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21225 )
+    r.setUseValuesFromTriggerTime(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21226(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = libsbml.parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 2 )
+    self.assert_( d.getError(0).getErrorId() == 21226 )
+    self.assert_( d.getError(1).getErrorId() == 21226 )
+    t.setPersistent(True)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21226 )
+    t.setInitialValue(False)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
+  def test_internal_consistency_check_21231(self):
+    d = libsbml.SBMLDocument(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(True)
+    ast = libsbml.parseFormula("2*x")
+    t = r.createTrigger()
+    t.setMath(ast)
+    t.setPersistent(True)
+    t.setInitialValue(False)
+    ea = r.createEventAssignment()
+    ea.setVariable("ea")
+    ea.setMath(ast)
+    prior = r.createPriority()
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21231 )
+    prior.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    self.assert_( errors == 0 )
+    d = None
+    pass  
+
   def test_internal_consistency_check_99901(self):
     d = libsbml.SBMLDocument(2,4)
     c = libsbml.Compartment(2,4)
@@ -94,6 +749,8 @@
     c.setId("cc")
     r = m.createReaction()
     r.setId("r")
+    sr = r.createReactant()
+    sr.setSpecies("s")
     kl = r.createKineticLaw()
     kl.setFormula("2")
     p.setId("p")
@@ -145,6 +802,8 @@
     c.setId("cc")
     r = m.createReaction()
     r.setId("r")
+    sr = r.createReactant()
+    sr.setSpecies("s")
     kl.setFormula("2")
     kl.setMetaId("mmm")
     r.setKineticLaw(kl)
@@ -271,14 +930,15 @@
     c.setId("c")
     s = m.createSpecies()
     s.setId("s")
+    s.setCompartment("c")
     r = m.createReaction()
     r.setId("r")
-    s.setCompartment("c")
     sr.setSpecies("s")
     sr.setMetaId("mmm")
     r.addProduct(sr)
     errors = d.checkInternalConsistency()
-    self.assert_( errors == 0 )
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21101 )
     d = None
     pass  
 
@@ -522,12 +1182,17 @@
     c.setId("c")
     c.setConstant(False)
     e = m.createEvent()
+    ast = libsbml.parseFormula("2*x")
+    t = e.createTrigger()
+    t.setMath(ast)
     ea = libsbml.EventAssignment(2,4)
     ea.setVariable("c")
     ea.setSBOTerm(2)
+    ea.setMath(ast)
     e.addEventAssignment(ea)
     errors = d.checkInternalConsistency()
-    self.assert_( errors == 0 )
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21203 )
     d = None
     pass  
 
@@ -562,6 +1227,8 @@
     m = d.createModel()
     r = m.createReaction()
     r.setId("r")
+    sr = r.createReactant()
+    sr.setSpecies("s")
     kl = libsbml.KineticLaw(2,4)
     kl.setSBOTerm(2)
     p = kl.createParameter()
@@ -670,7 +1337,8 @@
     sr.setSBOTerm(4)
     r.addReactant(sr)
     errors = d.checkInternalConsistency()
-    self.assert_( errors == 0 )
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21101 )
     d = None
     pass  
 
@@ -863,7 +1531,8 @@
     sr.setId("mmm")
     r.addProduct(sr)
     errors = d.checkInternalConsistency()
-    self.assert_( errors == 0 )
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21101 )
     d = None
     pass  
 
@@ -883,7 +1552,8 @@
     sr.setName("mmm")
     r.addReactant(sr)
     errors = d.checkInternalConsistency()
-    self.assert_( errors == 0 )
+    self.assert_( errors == 1 )
+    self.assert_( d.getError(0).getErrorId() == 21101 )
     d = None
     pass  
 

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestInternalConsistencyChecks.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestInternalConsistencyChecks.rb	2011-02-18 10:40:28 UTC (rev 12948)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestInternalConsistencyChecks.rb	2011-02-18 13:39:05 UTC (rev 12949)
@@ -1,8 +1,9 @@
 # @file    TestInternalConsistencyChecks.rb
-# @brief   Tests the internal consistency validation.
+# @brief   Tests the internal consistency validation.
 #
 # @author  Akiya Jouraku (Ruby conversion)
-# @author  Sarah Keating 
+# @author  Sarah Keating
+ 
 #
 # $Id$
 # $HeadURL$
@@ -35,6 +36,660 @@
 
 class TestInternalConsistencyChecks < Test::Unit::TestCase
 
+  def test_internal_consistency_check_20306
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    fd = m.createFunctionDefinition()
+    fd.setId("fd")
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20306 )
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    fd.setMath(ast)
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20307
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    fd = m.createFunctionDefinition()
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    fd.setMath(ast)
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20307 )
+    fd.setId("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20419
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    ud = m.createUnitDefinition()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20419 )
+    ud.setId("ud")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20421
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    ud = m.createUnitDefinition()
+    ud.setId("ud")
+    u = ud.createUnit()
+    errors = d.checkInternalConsistency()
+    assert( errors == 4 )
+    assert( d.getError(0).getErrorId() == 20421 )
+    assert( d.getError(1).getErrorId() == 20421 )
+    assert( d.getError(2).getErrorId() == 20421 )
+    assert( d.getError(3).getErrorId() == 20421 )
+    u.setKind(LibSBML::UNIT_KIND_MOLE)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 3 )
+    assert( d.getError(0).getErrorId() == 20421 )
+    assert( d.getError(1).getErrorId() == 20421 )
+    assert( d.getError(2).getErrorId() == 20421 )
+    u.setExponent(1.0)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 2 )
+    assert( d.getError(0).getErrorId() == 20421 )
+    assert( d.getError(1).getErrorId() == 20421 )
+    u.setScale(0)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20421 )
+    u.setMultiplier(1.0)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20517
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    c = m.createCompartment()
+    errors = d.checkInternalConsistency()
+    assert( errors == 2 )
+    assert( d.getError(0).getErrorId() == 20517 )
+    assert( d.getError(1).getErrorId() == 20517 )
+    c.setId("c")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20517 )
+    c.setConstant(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20623
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    c = m.createCompartment()
+    c.setId("c")
+    c.setConstant(true)
+    s = m.createSpecies()
+    errors = d.checkInternalConsistency()
+    assert( errors == 5 )
+    assert( d.getError(0).getErrorId() == 20623 )
+    assert( d.getError(1).getErrorId() == 20614 )
+    assert( d.getError(2).getErrorId() == 20623 )
+    assert( d.getError(3).getErrorId() == 20623 )
+    assert( d.getError(4).getErrorId() == 20623 )
+    s.setId("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 4 )
+    assert( d.getError(0).getErrorId() == 20614 )
+    assert( d.getError(1).getErrorId() == 20623 )
+    assert( d.getError(2).getErrorId() == 20623 )
+    assert( d.getError(3).getErrorId() == 20623 )
+    s.setCompartment("c")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 3 )
+    assert( d.getError(0).getErrorId() == 20623 )
+    assert( d.getError(1).getErrorId() == 20623 )
+    assert( d.getError(2).getErrorId() == 20623 )
+    s.setHasOnlySubstanceUnits(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 2 )
+    assert( d.getError(0).getErrorId() == 20623 )
+    assert( d.getError(1).getErrorId() == 20623 )
+    s.setBoundaryCondition(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20623 )
+    s.setConstant(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20706
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    p = m.createParameter()
+    errors = d.checkInternalConsistency()
+    assert( errors == 2 )
+    assert( d.getError(0).getErrorId() == 20706 )
+    assert( d.getError(1).getErrorId() == 20706 )
+    p.setId("c")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20706 )
+    p.setConstant(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20804
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    ia = m.createInitialAssignment()
+    ia.setSymbol("fd")
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20804 )
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    ia.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20805
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    ia = m.createInitialAssignment()
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    ia.setMath(ast)
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20805 )
+    ia.setSymbol("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20907_alg
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createAlgebraicRule()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20907 )
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20907_assign
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createAssignmentRule()
+    r.setVariable("fd")
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20907 )
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20907_rate
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createRateRule()
+    r.setVariable("fd")
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20907 )
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20908
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createAssignmentRule()
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20908 )
+    r.setVariable("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_20909
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createRateRule()
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 20909 )
+    r.setVariable("fd")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21007
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createConstraint()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21007 )
+    ast = LibSBML::parseFormula("lambda(x, 2*x)")
+    r.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21101
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(true)
+    r.setFast(false)
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21101 )
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21110
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    sr = r.createProduct()
+    sr.setSpecies("s")
+    sr.setConstant(true)
+    errors = d.checkInternalConsistency()
+    assert( errors == 3 )
+    assert( d.getError(0).getErrorId() == 21110 )
+    assert( d.getError(1).getErrorId() == 21110 )
+    assert( d.getError(2).getErrorId() == 21110 )
+    r.setId("r")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 2 )
+    assert( d.getError(0).getErrorId() == 21110 )
+    assert( d.getError(1).getErrorId() == 21110 )
+    r.setReversible(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21110 )
+    r.setFast(false)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21116
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(true)
+    r.setFast(false)
+    sr = r.createReactant()
+    errors = d.checkInternalConsistency()
+    assert( errors == 2 )
+    assert( d.getError(0).getErrorId() == 21116 )
+    assert( d.getError(1).getErrorId() == 21116 )
+    sr.setSpecies("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21116 )
+    sr.setConstant(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21117
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(true)
+    r.setFast(false)
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(true)
+    msr = r.createModifier()
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21117 )
+    msr.setSpecies("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21130
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(true)
+    r.setFast(false)
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(true)
+    kl = r.createKineticLaw()
+    lp = kl.createLocalParameter()
+    lp.setId("s")
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21130 )
+    ast = LibSBML::parseFormula("2*x")
+    kl.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21172
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createReaction()
+    r.setId("r")
+    r.setReversible(true)
+    r.setFast(false)
+    sr = r.createReactant()
+    sr.setSpecies("s")
+    sr.setConstant(true)
+    kl = r.createKineticLaw()
+    ast = LibSBML::parseFormula("2*x")
+    kl.setMath(ast)
+    lp = kl.createLocalParameter()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21172 )
+    lp.setId("pp")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21201
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = LibSBML::parseFormula("2*x")
+    ea.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21201 )
+    t = r.createTrigger()
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21203
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ast = LibSBML::parseFormula("2*x")
+    t = r.createTrigger()
+    t.setMath(ast)
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21203 )
+    ea = r.createEventAssignment()
+    ea.setVariable("ea")
+    ea.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21209
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = LibSBML::parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21209 )
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21210
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ast = LibSBML::parseFormula("2*x")
+    t = r.createTrigger()
+    t.setMath(ast)
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    ea = r.createEventAssignment()
+    ea.setVariable("ea")
+    ea.setMath(ast)
+    delay = r.createDelay()
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21210 )
+    delay.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21213
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = LibSBML::parseFormula("2*x")
+    t = r.createTrigger()
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21213 )
+    ea.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21214
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ea = r.createEventAssignment()
+    ast = LibSBML::parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21214 )
+    ea.setVariable("s")
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21225
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = LibSBML::parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21225 )
+    r.setUseValuesFromTriggerTime(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21226
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ea = r.createEventAssignment()
+    ea.setVariable("s")
+    ast = LibSBML::parseFormula("2*x")
+    ea.setMath(ast)
+    t = r.createTrigger()
+    t.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 2 )
+    assert( d.getError(0).getErrorId() == 21226 )
+    assert( d.getError(1).getErrorId() == 21226 )
+    t.setPersistent(true)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21226 )
+    t.setInitialValue(false)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
+  def test_internal_consistency_check_21231
+    d = LibSBML::SBMLDocument.new(3,1)
+    m = d.createModel()
+    r = m.createEvent()
+    r.setUseValuesFromTriggerTime(true)
+    ast = LibSBML::parseFormula("2*x")
+    t = r.createTrigger()
+    t.setMath(ast)
+    t.setPersistent(true)
+    t.setInitialValue(false)
+    ea = r.createEventAssignment()
+    ea.setVariable("ea")
+    ea.setMath(ast)
+    prior = r.createPriority()
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21231 )
+    prior.setMath(ast)
+    d.getErrorLog().clearLog()
+    errors = d.checkInternalConsistency()
+    assert( errors == 0 )
+    d = nil
+  end
+
   def test_internal_consistency_check_99901
     d = LibSBML::SBMLDocument.new(2,4)
     c = LibSBML::Compartment.new(2,4)
@@ -89,6 +744,8 @@
     c.setId("cc")
     r = m.createReaction()
     r.setId("r")
+    sr = r.createReactant()
+    sr.setSpecies("s")
     kl = r.createKineticLaw()
     kl.setFormula("2")
     p.setId("p")
@@ -140,6 +797,8 @@
     c.setId("cc")
     r = m.createReaction()
     r.setId("r")
+    sr = r.createReactant()
+    sr.setSpecies("s")
     kl.setFormula("2")
     kl.setMetaId("mmm")
     r.setKineticLaw(kl)
@@ -266,14 +925,15 @@
     c.setId("c")
     s = m.createSpecies()
     s.setId("s")
+    s.setCompartment("c")
     r = m.createReaction()
     r.setId("r")
-    s.setCompartment("c")
     sr.setSpecies("s")
     sr.setMetaId("mmm")
     r.addProduct(sr)
     errors = d.checkInternalConsistency()
-    assert( errors == 0 )
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21101 )
     d = nil
   end
 
@@ -517,12 +1177,17 @@
     c.setId("c")
     c.setConstant(false)
     e = m.createEvent()
+    ast = LibSBML::parseFormula("2*x")
+    t = e.createTrigger()
+    t.setMath(ast)
     ea = LibSBML::EventAssignment.new(2,4)
     ea.setVariable("c")
     ea.setSBOTerm(2)
+    ea.setMath(ast)
     e.addEventAssignment(ea)
     errors = d.checkInternalConsistency()
-    assert( errors == 0 )
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21203 )
     d = nil
   end
 
@@ -557,6 +1222,8 @@
     m = d.createModel()
     r = m.createReaction()
     r.setId("r")
+    sr = r.createReactant()
+    sr.setSpecies("s")
     kl = LibSBML::KineticLaw.new(2,4)
     kl.setSBOTerm(2)
     p = kl.createParameter()
@@ -665,7 +1332,8 @@
     sr.setSBOTerm(4)
     r.addReactant(sr)
     errors = d.checkInternalConsistency()
-    assert( errors == 0 )
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21101 )
     d = nil
   end
 
@@ -858,7 +1526,8 @@
     sr.setId("mmm")
     r.addProduct(sr)
     errors = d.checkInternalConsistency()
-    assert( errors == 0 )
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21101 )
     d = nil
   end
 
@@ -878,7 +1547,8 @@
     sr.setName("mmm")
     r.addReactant(sr)
     errors = d.checkInternalConsistency()
-    assert( errors == 0 )
+    assert( errors == 1 )
+    assert( d.getError(0).getErrorId() == 21101 )
     d = nil
   end
 

Modified: trunk/libsbml/src/sbml/test/TestInternalConsistencyChecks.cpp
===================================================================

@@ Diff output truncated at 100000 characters. @@

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12968
          http://sbml.svn.sourceforge.net/sbml/?rev=12968&view=rev
Author:   sarahkeating
Date:     2011-02-19 14:34:22 +0000 (Sat, 19 Feb 2011)

Log Message:
-----------
even further improvement to conversion of l3 to L2 relating to stoichiometry

Modified Paths:
--------------
    trunk/libsbml/src/sbml/SBMLConvert.cpp
    trunk/libsbml/src/sbml/SBMLErrorTable.h

Removed Paths:
-------------
    trunk/libsbml/src/validator/test/test-data-conversion/92010-fail-01-01.xml

Modified: trunk/libsbml/src/sbml/SBMLConvert.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLConvert.cpp	2011-02-19 13:01:21 UTC (rev 12967)
+++ trunk/libsbml/src/sbml/SBMLConvert.cpp	2011-02-19 14:34:22 UTC (rev 12968)
@@ -1136,12 +1136,6 @@
   unsigned int idCount = 0;
   char newid[15];
   std::string id;
-   /* at moment constant is true - since we are not converting if false
-    * so we are just considering three cases (no stoichiometry declared)
-    * 1) where the id is used by an initialAssignment to set stoichiometry
-    * 2) where the stoichiometry is just not declared no id set
-    * 3) no stoichiometry declared id set but not used
-    */
   for (unsigned int i = 0; i < getNumReactions(); i++)
   {
     Reaction *r = getReaction(i);
@@ -1153,7 +1147,8 @@
       {
         if (!(sr->isSetId()))
         {
-          // definitely case 2
+          // no stoichiometry and no id to set the stoichiometry
+          // replace with stoichiometryMath using a parameter with no value
           sprintf(newid, "parameterId_%u", idCount);
           id.assign(newid);
           idCount++;
@@ -1170,10 +1165,43 @@
         }
         else
         {
-          // id is set
-          if (getInitialAssignment(sr->getId()) == NULL)
+          // id is set it could be used by initialAssignment
+          // used by rule
+          // not used
+          if (getInitialAssignment(sr->getId()) != NULL)
           {
-            // case 3
+            // use stoichiometryMath instead
+            StoichiometryMath *sm = sr->createStoichiometryMath();
+            if (sm != NULL)
+            {
+              sm->setMath(getInitialAssignment(sr->getId())->getMath());
+              removeInitialAssignment(sr->getId());
+            }
+          }
+          else if (getRule(sr->getId()) != NULL)
+          {
+            // use stoichiometryMath instead
+            StoichiometryMath *sm = sr->createStoichiometryMath();
+            if (sm != NULL)
+            {
+              sm->setMath(getRule(sr->getId())->getMath());
+              removeRule(sr->getId());
+            }
+          }
+          //else if (getRateRule(sr->getId()) != NULL)
+          //{
+          //  // use stoichiometryMath instead
+          //  StoichiometryMath *sm = sr->createStoichiometryMath();
+          //  if (sm != NULL)
+          //  {
+          //    sm->setMath(getRateRule(sr->getId())->getMath());
+          //    removeRateRule(sr->getId());
+          //  }
+          //}
+          else
+          {
+            // is set but not used 
+            // use StoichiometryMath with parameter with no value
             sprintf(newid, "parameterId_%u", idCount);
             id.assign(newid);
             idCount++;
@@ -1188,10 +1216,18 @@
               sm->setMath(ast);
             }
           }
-          else
+        }
+      }
+      else
+      {
+        // stoichiometry is set
+        if (sr->isSetId())
+        {
+          // id is set it could be used by initialAssignment
+          // used by rule
+          // not used
+          if (getInitialAssignment(sr->getId()) != NULL)
           {
-            // id used by initialAssignment
-            // case 1
             // use stoichiometryMath instead
             StoichiometryMath *sm = sr->createStoichiometryMath();
             if (sm != NULL)
@@ -1200,21 +1236,28 @@
               removeInitialAssignment(sr->getId());
             }
           }
-        }
-      }
-      else
-      {
-        // need to deal with the case where stoichiometry is set 
-        // but there is also an initialAssignment
-        if (sr->isSetId() && getInitialAssignment(sr->getId()) != NULL)
-        {
+          else if (getRule(sr->getId()) != NULL)
+          {
+            // use stoichiometryMath instead
             StoichiometryMath *sm = sr->createStoichiometryMath();
             if (sm != NULL)
             {
-              sm->setMath(getInitialAssignment(sr->getId())->getMath());
-              removeInitialAssignment(sr->getId());
+              sm->setMath(getRule(sr->getId())->getMath());
+              removeRule(sr->getId());
             }
+          }
+          //else if (getRateRule(sr->getId()) != NULL)
+          //{
+          //  // use stoichiometryMath instead
+          //  StoichiometryMath *sm = sr->createStoichiometryMath();
+          //  if (sm != NULL)
+          //  {
+          //    sm->setMath(getRateRule(sr->getId())->getMath());
+          //    removeRateRule(sr->getId());
+          //  }
+          //}
         }
+        // no id set - do not need to do anything
       }
     }
     for (j = 0; j < r->getNumProducts(); j++)
@@ -1224,7 +1267,8 @@
       {
         if (!(sr->isSetId()))
         {
-          // definitely case 2
+          // no stoichiometry and no id to set the stoichiometry
+          // replace with stoichiometryMath using a parameter with no value
           sprintf(newid, "parameterId_%u", idCount);
           id.assign(newid);
           idCount++;
@@ -1241,10 +1285,43 @@
         }
         else
         {
-          // id is set
-          if (getInitialAssignment(sr->getId()) == NULL)
+          // id is set it could be used by initialAssignment
+          // used by rule
+          // not used
+          if (getInitialAssignment(sr->getId()) != NULL)
           {
-            // case 3
+            // use stoichiometryMath instead
+            StoichiometryMath *sm = sr->createStoichiometryMath();
+            if (sm != NULL)
+            {
+              sm->setMath(getInitialAssignment(sr->getId())->getMath());
+              removeInitialAssignment(sr->getId());
+            }
+          }
+          else if (getRule(sr->getId()) != NULL)
+          {
+            // use stoichiometryMath instead
+            StoichiometryMath *sm = sr->createStoichiometryMath();
+            if (sm != NULL)
+            {
+              sm->setMath(getRule(sr->getId())->getMath());
+              removeRule(sr->getId());
+            }
+          }
+          //else if (getRateRule(sr->getId()) != NULL)
+          //{
+          //  // use stoichiometryMath instead
+          //  StoichiometryMath *sm = sr->createStoichiometryMath();
+          //  if (sm != NULL)
+          //  {
+          //    sm->setMath(getRateRule(sr->getId())->getMath());
+          //    removeRateRule(sr->getId());
+          //  }
+          //}
+          else
+          {
+            // is set but not used 
+            // use StoichiometryMath with parameter with no value
             sprintf(newid, "parameterId_%u", idCount);
             id.assign(newid);
             idCount++;
@@ -1259,9 +1336,18 @@
               sm->setMath(ast);
             }
           }
-          else
+        }
+      }
+      else
+      {
+        // stoichiometry is set
+        if (sr->isSetId())
+        {
+          // id is set it could be used by initialAssignment
+          // used by rule
+          // not used
+          if (getInitialAssignment(sr->getId()) != NULL)
           {
-            // id used by initialAssignment
             // use stoichiometryMath instead
             StoichiometryMath *sm = sr->createStoichiometryMath();
             if (sm != NULL)
@@ -1270,21 +1356,28 @@
               removeInitialAssignment(sr->getId());
             }
           }
-        }        
-      }
-      else
-      {
-        // need to deal with the case where stoichiometry is set 
-        // but there is also an initialAssignment
-        if (sr->isSetId() && getInitialAssignment(sr->getId()) != NULL)
-        {
+          else if (getRule(sr->getId()) != NULL)
+          {
+            // use stoichiometryMath instead
             StoichiometryMath *sm = sr->createStoichiometryMath();
             if (sm != NULL)
             {
-              sm->setMath(getInitialAssignment(sr->getId())->getMath());
-              removeInitialAssignment(sr->getId());
+              sm->setMath(getRule(sr->getId())->getMath());
+              removeRule(sr->getId());
             }
+          }
+          //else if (getRateRule(sr->getId()) != NULL)
+          //{
+          //  // use stoichiometryMath instead
+          //  StoichiometryMath *sm = sr->createStoichiometryMath();
+          //  if (sm != NULL)
+          //  {
+          //    sm->setMath(getRateRule(sr->getId())->getMath());
+          //    removeRateRule(sr->getId());
+          //  }
+          //}
         }
+        // no id set - do not need to do anything
       }
     }
   }

Modified: trunk/libsbml/src/sbml/SBMLErrorTable.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorTable.h	2011-02-19 13:01:21 UTC (rev 12967)
+++ trunk/libsbml/src/sbml/SBMLErrorTable.h	2011-02-19 14:34:22 UTC (rev 12968)
@@ -7023,7 +7023,7 @@
     LIBSBML_SEV_NOT_APPLICABLE,
     LIBSBML_SEV_NOT_APPLICABLE,
     LIBSBML_SEV_NOT_APPLICABLE,
-    LIBSBML_SEV_ERROR,
+    LIBSBML_SEV_NOT_APPLICABLE,
     "Conversion of a varying stoichiometry to an SBML L2 StoichiometryMath "
     "element is not yet supported."
   },

Deleted: trunk/libsbml/src/validator/test/test-data-conversion/92010-fail-01-01.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data-conversion/92010-fail-01-01.xml	2011-02-19 13:01:21 UTC (rev 12967)
+++ trunk/libsbml/src/validator/test/test-data-conversion/92010-fail-01-01.xml	2011-02-19 14:34:22 UTC (rev 12968)
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1">
-  <model>
-    <listOfCompartments>
-      <compartment id="c" constant="true" spatialDimensions="3"/>
-    </listOfCompartments>
-    <listOfParameters>
-      <parameter id="p" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="l" fast="false" reversible="false">
-        <listOfReactants>
-          <speciesReference species="s" constant="false" stoichiometry="1"/>
-        </listOfReactants>
-      </reaction>
-    </listOfReactions>
-    <listOfSpecies>
-      <species id="s" compartment="c" boundaryCondition="false" hasOnlySubstanceUnits="false" constant="false"/>
-    </listOfSpecies>
-  </model>
-</sbml>


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 12995
          http://sbml.svn.sourceforge.net/sbml/?rev=12995&view=rev
Author:   fbergmann
Date:     2011-02-21 18:13:54 +0000 (Mon, 21 Feb 2011)

Log Message:
-----------
- BugFix: for recent validator crashes. When invalid MathML is read and no SBMLNamespaces are set on the stream  libsbml will crash

Modified Paths:
--------------
    trunk/libsbml/src/math/MathML.cpp
    trunk/libsbml/src/sbml/KineticLaw.cpp

Modified: trunk/libsbml/src/math/MathML.cpp
===================================================================
--- trunk/libsbml/src/math/MathML.cpp	2011-02-21 17:35:39 UTC (rev 12994)
+++ trunk/libsbml/src/math/MathML.cpp	2011-02-21 18:13:54 UTC (rev 12995)
@@ -337,7 +337,7 @@
  * Errors will be logged in the stream's SBMLErrorLog object.
  */
 static void
-setTypeCI (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
+  setTypeCI (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
 {
   if (&node == NULL || &element == NULL || &stream == NULL) return;
 
@@ -351,10 +351,20 @@
     else if ( url == URL_AVOGADRO  ) node.setType(AST_NAME_AVOGADRO);
     else 
     {
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
       static_cast <SBMLErrorLog*>
-	        (stream.getErrorLog())->logError(BadCsymbolDefinitionURLValue,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+        (stream.getErrorLog())->logError(BadCsymbolDefinitionURLValue,
+        ns->getLevel(), 
+        ns->getVersion());
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(BadCsymbolDefinitionURLValue);
+      
+      }
     }
   }
   else if (element.getName() == "ci")
@@ -372,7 +382,7 @@
  * Errors will be logged in the stream's SBMLErrorLog object.
  */
 static void
-setTypeCN (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
+  setTypeCN (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
 {
   if (&node == NULL || &element == NULL || &stream == NULL) return;
 
@@ -397,10 +407,19 @@
       || node.isNegInfinity()
       )
     {
-      static_cast <SBMLErrorLog*>
-        (stream.getErrorLog())->logError(FailedMathMLReadOfDouble,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfDouble,
+          ns->getLevel(), 
+          ns->getVersion());
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfDouble);      
+      }
     }
 
   }
@@ -414,17 +433,36 @@
 
     if (isint.fail())
     {
-      static_cast <SBMLErrorLog*>
-        (stream.getErrorLog())->logError(FailedMathMLReadOfInteger,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfInteger,
+          ns->getLevel(), 
+          ns->getVersion());
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfInteger);
+
+      }
     }
     else if ( sizeof(int) > 4 && ( (value > SBML_INT_MAX) || (value < SBML_INT_MIN) ) )
     {
-      static_cast <SBMLErrorLog*>
-        (stream.getErrorLog())->logError(FailedMathMLReadOfInteger,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfInteger,
+          ns->getLevel(), 
+          ns->getVersion());
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfInteger);
+      }
     }
 
     node.setValue(value);
@@ -453,12 +491,21 @@
       || node.isInfinity()
       || node.isNegInfinity())
     {
-      static_cast <SBMLErrorLog*>
-        (stream.getErrorLog())->logError(FailedMathMLReadOfExponential,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfExponential,
+          ns->getLevel(), 
+          ns->getVersion());
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfExponential);        
+      }
     }
-    
+
   }
 
   else if (type == "rational")
@@ -480,31 +527,59 @@
 
     if (isnumerator.fail() || isdenominator.fail())
     {
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
       static_cast <SBMLErrorLog*>
         (stream.getErrorLog())->logError(FailedMathMLReadOfRational,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+        ns->getLevel(), 
+        ns->getVersion());
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(FailedMathMLReadOfRational);
+      
+      }
     }
     else if ( sizeof(int) > 4 && 
-        ( ( (numerator > SBML_INT_MAX) || (numerator < SBML_INT_MIN) ) 
-          ||
-          ( (denominator > SBML_INT_MAX) || (denominator < SBML_INT_MIN) ) 
-        ))
+      ( ( (numerator > SBML_INT_MAX) || (numerator < SBML_INT_MIN) ) 
+      ||
+      ( (denominator > SBML_INT_MAX) || (denominator < SBML_INT_MIN) ) 
+      ))
     {
-      static_cast <SBMLErrorLog*>
-        (stream.getErrorLog())->logError(FailedMathMLReadOfRational,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfRational,
+          ns->getLevel(), 
+          ns->getVersion());
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(FailedMathMLReadOfRational);      
+      }
     }
 
     node.setValue(static_cast<long>(numerator), static_cast<long>(denominator));
   }
   else
   {
-    static_cast <SBMLErrorLog*>
-      (stream.getErrorLog())->logError(DisallowedMathTypeAttributeValue,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion());
+    SBMLNamespaces* ns = stream.getSBMLNamespaces();
+    if (ns != NULL)
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathTypeAttributeValue,
+        ns->getLevel(), 
+        ns->getVersion());
+    }
+    else
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathTypeAttributeValue);    
+    }
   }
 
   // set the units
@@ -604,7 +679,7 @@
  * Errors will be logged in the stream's SBMLErrorLog object.
  */
 static void
-readMathML (ASTNode& node, XMLInputStream& stream, std::string reqd_prefix)
+  readMathML (ASTNode& node, XMLInputStream& stream, std::string reqd_prefix)
 {
   if (&node == NULL || &stream == NULL) return;
 
@@ -627,17 +702,28 @@
       if (prefix != reqd_prefix)
       {
         const string message = "Element <" + stream.peek().getName() + "> should have prefix \"" + reqd_prefix + "\".";
-        static_cast <SBMLErrorLog*>
-          (stream.getErrorLog())->logError(InvalidMathElement, 
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion(),
-          message);
+        SBMLNamespaces* ns = stream.getSBMLNamespaces();
+        if (ns != NULL)
+        {
+          static_cast <SBMLErrorLog*>
+            (stream.getErrorLog())->logError(InvalidMathElement, 
+            ns->getLevel(), 
+            ns->getVersion(),
+            message);
+        }
+        else
+        {
+          static_cast <SBMLErrorLog*>
+            (stream.getErrorLog())->logError(InvalidMathElement, 
+            SBML_DEFAULT_LEVEL, SBML_DEFAULT_VERSION, message);        
+        }
+
       }
     }
     stream.skipPastEnd(stream.peek());
     return;
   }
- 
+
   const XMLToken elem = stream.next ();
   const string&  name = elem.getName();
 
@@ -648,10 +734,19 @@
 
   if (!found)
   {
-    static_cast <SBMLErrorLog*>
-      (stream.getErrorLog())->logError(DisallowedMathMLSymbol, 
-      stream.getSBMLNamespaces()->getLevel(), 
-      stream.getSBMLNamespaces()->getVersion());
+    SBMLNamespaces* ns = stream.getSBMLNamespaces();
+    if (ns != NULL)
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathMLSymbol, 
+        ns->getLevel(), 
+        ns->getVersion());
+    }
+    else
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathMLSymbol);
+    }
   }
 
   // check any reqd prefix is correct
@@ -661,11 +756,23 @@
     if (prefix != reqd_prefix)
     {
       const string message = "Element <" + name + "> should have prefix \"" + reqd_prefix + "\".";
-      static_cast <SBMLErrorLog*>
-        (stream.getErrorLog())->logError(InvalidMathElement, 
-        stream.getSBMLNamespaces()->getLevel(), 
-        stream.getSBMLNamespaces()->getVersion(),
-        message);
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(InvalidMathElement, 
+          ns->getLevel(), 
+          ns->getVersion(),
+          message);
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(InvalidMathElement, 
+          SBML_DEFAULT_LEVEL, 
+          SBML_DEFAULT_VERSION,
+          message);
+      }
     }
   }
 
@@ -681,42 +788,69 @@
 
   if ( !type.empty() && name != "cn")
   {
-    static_cast <SBMLErrorLog*>
-      (stream.getErrorLog())->logError(DisallowedMathTypeAttributeUse, 
-      stream.getSBMLNamespaces()->getLevel(), 
-      stream.getSBMLNamespaces()->getVersion());
+    SBMLNamespaces* ns = stream.getSBMLNamespaces();
+    if (ns != NULL)
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathTypeAttributeUse, 
+        ns->getLevel(), 
+        ns->getVersion());
+    }
+    else
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathTypeAttributeUse);    
+    }
   }
 
   if ( !encoding.empty() && name != "csymbol")
   {
-    static_cast <SBMLErrorLog*>
-      (stream.getErrorLog())->logError(DisallowedMathMLEncodingUse, 
-      stream.getSBMLNamespaces()->getLevel(), 
-      stream.getSBMLNamespaces()->getVersion());
+    SBMLNamespaces* ns = stream.getSBMLNamespaces();
+    if (ns != NULL)
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathMLEncodingUse, 
+        ns->getLevel(), 
+        ns->getVersion());
+    }
+    else
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathMLEncodingUse);    
+    }
   }
 
   // allow definition url on csymbol/semantics and bvar
   // and on ci in L3
   if ( !url.empty())
   {  
-    if (stream.getSBMLNamespaces()->getLevel() > 2)
+    SBMLNamespaces* ns = stream.getSBMLNamespaces();
+    if (ns != NULL && ns->getLevel() > 2)
     {
       if (name != "csymbol" && name != "semantics" && name != "ci")
       {
         static_cast <SBMLErrorLog*>
           (stream.getErrorLog())->logError(DisallowedDefinitionURLUse, 
-      stream.getSBMLNamespaces()->getLevel(), 
-      stream.getSBMLNamespaces()->getVersion());
+          ns->getLevel(), 
+          ns->getVersion());
       }
     }
     else
     {
       if (name != "csymbol" && name != "semantics")
       {
-        static_cast <SBMLErrorLog*>
-          (stream.getErrorLog())->logError(DisallowedDefinitionURLUse, 
-      stream.getSBMLNamespaces()->getLevel(), 
-      stream.getSBMLNamespaces()->getVersion());
+        if (ns != NULL)
+        {
+          static_cast <SBMLErrorLog*>
+            (stream.getErrorLog())->logError(DisallowedDefinitionURLUse, 
+            ns->getLevel(), 
+            ns->getVersion());
+        }
+        else
+        {
+          static_cast <SBMLErrorLog*>
+            (stream.getErrorLog())->logError(DisallowedDefinitionURLUse);
+        }
       }
     }
 
@@ -725,10 +859,20 @@
 
   if ( !units.empty() && name != "cn")
   {
-    static_cast <SBMLErrorLog*>
-      (stream.getErrorLog())->logError(DisallowedMathUnitsUse, 
-                                      stream.getSBMLNamespaces()->getLevel(), 
-                                      stream.getSBMLNamespaces()->getVersion());
+    SBMLNamespaces* ns = stream.getSBMLNamespaces();
+    if (ns != NULL)
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathUnitsUse, 
+        ns->getLevel(), 
+        ns->getVersion());
+    }
+    else
+    {
+      static_cast <SBMLErrorLog*>
+        (stream.getErrorLog())->logError(DisallowedMathUnitsUse);
+
+    }
   }
 
   if (name == "apply" || name == "lambda" || name == "piecewise")
@@ -739,8 +883,8 @@
       if (elem.isStart() && elem.isEnd()) return;
 
       /* catch case where user has applied a function that
-       * has no arguments 
-       */
+      * has no arguments 
+      */
       if (elem.isEnd()) return;
 
       readMathML(node, stream, reqd_prefix);
@@ -748,21 +892,31 @@
       if (node.isName()) node.setType(AST_FUNCTION);
 
       /* there are several <apply> <...> constructs that are invalid
-       * these need to caught here as they will mess up validation later
-       * These are
-       * <apply> <cn>
-       * <apply> <true> OR <false>
-       * <apply> <pi> OR <exponentiale>
-       * <apply
-       */
+      * these need to caught here as they will mess up validation later
+      * These are
+      * <apply> <cn>
+      * <apply> <true> OR <false>
+      * <apply> <pi> OR <exponentiale>
+      * <apply
+      */
       if (node.isNumber())   
       {
         std::string message = "A number is not an operator and cannot be used ";
         message += "directly following an <apply> tag.";
 
-        static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathML,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion(), message);
+        SBMLNamespaces* ns = stream.getSBMLNamespaces();
+        if (ns != NULL)
+        {
+          static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathML,
+            ns->getLevel(), 
+            ns->getVersion(), message);
+        }
+        else
+        {
+          static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathML,
+            SBML_DEFAULT_LEVEL, 
+            SBML_DEFAULT_VERSION, message);
+        }
         return;
 
       }
@@ -777,9 +931,19 @@
         message += "> is not an operator and cannot be used directly following an";
         message += " <apply> tag.";
 
-        static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathML,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion(), message);
+        SBMLNamespaces* ns = stream.getSBMLNamespaces();
+        if (ns != NULL)
+        {
+          static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathML,
+            ns->getLevel(), 
+            ns->getVersion(), message);
+        }
+        else
+        {
+          static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathML,
+            SBML_DEFAULT_LEVEL, 
+            SBML_DEFAULT_VERSION, message);
+        }
         return;
 
       }
@@ -791,7 +955,7 @@
     else
     {
       /* catch case where there is no otherwise
-       */
+      */
       if (elem.isEnd()) 
       {
         //node = NULL;
@@ -803,8 +967,8 @@
     while (stream.isGood() && stream.peek().isEndFor(elem) == false)
     {
       /* it is possible to have a piecewise with no otherwise
-       * OR a function with no arguments
-       */
+      * OR a function with no arguments
+      */
       stream.skipText();
       if (elem.getName() == "piecewise" 
         && stream.peek().getName() == "piecewise") continue;
@@ -818,9 +982,9 @@
       readMathML(*child, stream, reqd_prefix);
 
       stream.skipText();
-       /* look to see whether a lambda is followed by an
-       * appropriate tag
-       */
+      /* look to see whether a lambda is followed by an
+      * appropriate tag
+      */
       if (elem.getName() == "lambda" 
         && stream.peek().getName() != "lambda"
         && stream.peek().getName() != "bvar")
@@ -832,17 +996,27 @@
           message += "> cannot be used directly following a";
           message += " <bvar> element.";
 
-        static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathMLNodeType,
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion(), message);
+          SBMLNamespaces* ns = stream.getSBMLNamespaces();
+          if (ns != NULL)
+          {
+          static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathMLNodeType,
+            ns->getLevel(), 
+            ns->getVersion(), message);
+          }
+          else
+          {
+            static_cast <SBMLErrorLog*> (stream.getErrorLog())->logError(BadMathMLNodeType,
+              SBML_DEFAULT_LEVEL, 
+              SBML_DEFAULT_VERSION, message);
+          }
         }
       }
 
       /* it is possible to have a function that has no children
-       * ie a lambda with no bvars
-       * dont want to add the child since this makes it look like
-       * it has a bvar
-       */
+      * ie a lambda with no bvars
+      * dont want to add the child since this makes it look like
+      * it has a bvar
+      */
       if (stream.peek().getName() == "math") 
       {
         delete child;
@@ -862,7 +1036,7 @@
   }
 
   else if (name == "degree" || name == "logbase" ||
-           name == "piece" || name == "otherwise" )
+    name == "piece" || name == "otherwise" )
   {
     readMathML(node, stream, reqd_prefix);
     if (name == "piece") return;
@@ -1450,8 +1624,8 @@
  * abstract syntax tree and returns a pointer to the root of the tree.
  */
 LIBSBML_EXTERN
-ASTNode*
-readMathML (XMLInputStream& stream, std::string reqd_prefix)
+  ASTNode*
+  readMathML (XMLInputStream& stream, std::string reqd_prefix)
 {
   if (&stream == NULL) return NULL;
 
@@ -1474,28 +1648,40 @@
     if (prefix != reqd_prefix)
     {
       const string message = "Element <" + name + "> should have prefix \"" + reqd_prefix + "\".";
-      static_cast <SBMLErrorLog*>
-        (stream.getErrorLog())->logError(InvalidMathElement, 
-        stream.getSBMLNamespaces()->getLevel(), 
-        stream.getSBMLNamespaces()->getVersion(),
-        message);
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(InvalidMathElement, 
+          ns->getLevel(), 
+          ns->getVersion(),
+          message);
+      }
+      else
+      {
+        static_cast <SBMLErrorLog*>
+          (stream.getErrorLog())->logError(InvalidMathElement, 
+          SBML_DEFAULT_LEVEL, 
+          SBML_DEFAULT_VERSION,
+          message);
+      }
     }
   }
 
 
   /* this code is slightly redundant as you will only
-   * get here if the name is "math"
-   * but does serve as a catch
-   */
+  * get here if the name is "math"
+  * but does serve as a catch
+  */
   if (name == "math")
   {
     const XMLToken elem = stream.next();
-      
+
     if (elem.isStart() && elem.isEnd()) return node;
 
     /* check that math tag is followed by an appropriate
-     * tag
-     */
+    * tag
+    */
     stream.skipText();
     const string& name1 = stream.peek().getName();
 
@@ -1506,11 +1692,23 @@
       if (prefix != reqd_prefix)
       {
         const string message = "Element <" + name1 + "> should have prefix \"" + reqd_prefix + "\".";
-        static_cast <SBMLErrorLog*>
-          (stream.getErrorLog())->logError(InvalidMathElement, 
-          stream.getSBMLNamespaces()->getLevel(), 
-          stream.getSBMLNamespaces()->getVersion(),
-          message);
+        SBMLNamespaces* ns = stream.getSBMLNamespaces();
+        if (ns != NULL)
+        {
+          static_cast <SBMLErrorLog*>
+            (stream.getErrorLog())->logError(InvalidMathElement, 
+            ns->getLevel(), 
+            ns->getVersion(),
+            message);
+        }
+        else
+        {
+          static_cast <SBMLErrorLog*>
+            (stream.getErrorLog())->logError(InvalidMathElement, 
+            SBML_DEFAULT_LEVEL, 
+            SBML_DEFAULT_VERSION,
+            message);
+        }
       }
     }
     if ( isMathMLNodeTag(name1) || name1 == "lambda")
@@ -1519,14 +1717,24 @@
     }
     else
     {
-        std::string message = "<";
-        message += name1;
-        message += "> cannot be used directly following a";
-        message += " <math> tag.";
+      std::string message = "<";
+      message += name1;
+      message += "> cannot be used directly following a";
+      message += " <math> tag.";
 
+      SBMLNamespaces* ns = stream.getSBMLNamespaces();
+      if (ns != NULL)
+      {
+      static_cast <SBMLErrorLog*> (stream.getErrorLog())
+        ->logError(BadMathMLNodeType, ns->getLevel(),
+        ns->getVersion(), message);
+      }
+      else
+      {
         static_cast <SBMLErrorLog*> (stream.getErrorLog())
-          ->logError(BadMathMLNodeType, stream.getSBMLNamespaces()->getLevel(),
-          stream.getSBMLNamespaces()->getVersion(), message);
+          ->logError(BadMathMLNodeType, SBML_DEFAULT_LEVEL,
+          SBML_DEFAULT_VERSION, message);
+      }
     }
 
     stream.skipPastEnd(elem);
@@ -1534,7 +1742,7 @@
   else if (name == "apply" )
   {
     const XMLToken elem = stream.next();
-      
+
     if (elem.isStart() && elem.isEnd()) return node;
 
     readMathML(*node, stream, reqd_prefix);

Modified: trunk/libsbml/src/sbml/KineticLaw.cpp
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.cpp	2011-02-21 17:35:39 UTC (rev 12994)
+++ trunk/libsbml/src/sbml/KineticLaw.cpp	2011-02-21 18:13:54 UTC (rev 12995)
@@ -1216,6 +1216,12 @@
     const XMLToken elem = stream.peek();
     const std::string prefix = checkMathMLNamespace(elem);
 
+    // the following assumes that the SBML Namespaces object is valid
+    if (stream.getSBMLNamespaces() == NULL)
+    {
+      stream.setSBMLNamespaces(new SBMLNamespaces(getLevel(), getVersion()));
+    }
+
     delete mMath;
     mMath = readMathML(stream, prefix);
     if (mMath != NULL) mMath->setParentSBMLObject(this);


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 13063
          http://sbml.svn.sourceforge.net/sbml/?rev=13063&view=rev
Author:   mhucka
Date:     2011-02-27 05:16:27 +0000 (Sun, 27 Feb 2011)

Log Message:
-----------
Improved handling of conditional documentation sections
for different languages.  Now using @else inside @if...@..., after having
modified swigdoc.py to make it work.

Modified Paths:
--------------
    trunk/libsbml/src/annotation/CVTerm.h
    trunk/libsbml/src/annotation/RDFAnnotation.h
    trunk/libsbml/src/math/ASTNode.h
    trunk/libsbml/src/math/FormulaFormatter.h
    trunk/libsbml/src/math/FormulaParser.h
    trunk/libsbml/src/sbml/Compartment.h
    trunk/libsbml/src/sbml/CompartmentType.h
    trunk/libsbml/src/sbml/InitialAssignment.h
    trunk/libsbml/src/sbml/KineticLaw.h
    trunk/libsbml/src/sbml/LocalParameter.h
    trunk/libsbml/src/sbml/Model.h
    trunk/libsbml/src/sbml/Parameter.h
    trunk/libsbml/src/sbml/Rule.h
    trunk/libsbml/src/sbml/SBMLDocument.h
    trunk/libsbml/src/sbml/SBMLError.h
    trunk/libsbml/src/sbml/SBMLErrorLog.h
    trunk/libsbml/src/sbml/SBMLNamespaces.h
    trunk/libsbml/src/sbml/SBMLReader.h
    trunk/libsbml/src/sbml/SBMLWriter.h
    trunk/libsbml/src/sbml/SBase.h
    trunk/libsbml/src/sbml/Species.h
    trunk/libsbml/src/sbml/SpeciesReference.h
    trunk/libsbml/src/sbml/SpeciesType.h
    trunk/libsbml/src/sbml/Unit.h
    trunk/libsbml/src/sbml/UnitDefinition.h
    trunk/libsbml/src/xml/XMLError.h
    trunk/libsbml/src/xml/XMLErrorLog.h
    trunk/libsbml/src/xml/XMLNamespaces.h
    trunk/libsbml/src/xml/XMLNode.h
    trunk/libsbml/src/xml/XMLToken.h

Modified: trunk/libsbml/src/annotation/CVTerm.h
===================================================================
--- trunk/libsbml/src/annotation/CVTerm.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/annotation/CVTerm.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -55,34 +55,34 @@
  * such as Species, Compartment, etc.  The following template illustrates
  * the different parts of SBML annotations in XML form:
  * 
-<div class="fragment">
-&lt;<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid=&quot;<span style="border-bottom: 1px solid black">meta id</span>&quot; <span style="background-color: #d0eed0">+++</span>&gt;<br>
-&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
-&nbsp;&nbsp;&lt;annotation&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
-&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:dc="http://purl.org/dc/elements/1.1/"<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:dcterm="http://purl.org/dc/terms/"<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:bqmodel="http://biomodels.net/model-qualifiers/" &gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Description rdf:about=&quot;#<span style="border-bottom: 1px solid black">meta id</span>&quot;&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span><br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Bag&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:li rdf:resource=&quot;<span style="background-color: #d0d0ee">URI</span>&quot; /&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Bag&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Description&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
-&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:RDF&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
-&nbsp;&nbsp;&lt;/annotation&gt;<br>
-&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
-&lt;/<span style="background-color: #bbb">SBML_ELEMENT</span>&gt;<br>
-</div>
+ <div class="fragment">
+ &lt;<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid=&quot;<span style="border-bottom: 1px solid black">meta id</span>&quot; <span style="background-color: #d0eed0">+++</span>&gt;<br>
+ &nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+ &nbsp;&nbsp;&lt;annotation&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:dc="http://purl.org/dc/elements/1.1/"<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:dcterm="http://purl.org/dc/terms/"<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xmlns:bqmodel="http://biomodels.net/model-qualifiers/" &gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Description rdf:about=&quot;#<span style="border-bottom: 1px solid black">meta id</span>&quot;&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span><br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Bag&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:li rdf:resource=&quot;<span style="background-color: #d0d0ee">URI</span>&quot; /&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Bag&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Description&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+ &nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:RDF&gt;<br>
+ &nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+ &nbsp;&nbsp;&lt;/annotation&gt;<br>
+ &nbsp;&nbsp;<span style="background-color: #d0eed0">+++</span><br>
+ &lt;/<span style="background-color: #bbb">SBML_ELEMENT</span>&gt;<br>
+ </div>
  * 
  * In the template above, the placeholder
  * <span class="code" style="background-color: #bbb">SBML_ELEMENT</span> stands for
@@ -99,7 +99,7 @@
  * <span class="code" style="background-color: #edd">...</span>
  * are placeholders for zero or more elements of the same form as the
  * immediately preceding element.  The optional content
- * <span class="code" style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span>
+ * <span class="code" style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span>
  * is a creation and modification history; in libSBML, this is stored
  * using ModelHistory objects.
  *
@@ -226,8 +226,7 @@
 
   /**
    * Creates an empty CVTerm, optionally with the given
-   * @if clike #QualifierType_t@... java qualifier type code@... value
-   * @p type.
+   * @if clike #QualifierType_t value@... qualifier@... @p type.
    *
    * The SBML Level&nbsp;2 and Level&nbsp;3 specifications define a simple
    * format for annotating models when (a) referring to controlled
@@ -253,8 +252,8 @@
    * an explicit value for @p type is not given, this method defaults to
    * using @link QualifierType_t#UNKNOWN_QUALIFIER
    * UNKNOWN_QUALIFIER@....  The
-   * @if clike #QualifierType_t@... java qualifier type code@... 
-   * type value can be set later using the
+   * @if clike #QualifierType_t value@... qualifier type@... 
+   * can be set later using the
    * CVTerm::setQualifierType(@if java int type@...) method.
    *
    * Different BioModels.net qualifier elements encode different types of
@@ -263,7 +262,7 @@
    * qualifiers web page</a> for an explanation of the meaning of these
    * different qualifiers.
    *
-   * @param type a @if clike #QualifierType_t@... java qualifier type code@... value
+   * @param type a @if clike #QualifierType_t value@... qualifier type@...
    *
    * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
    */
@@ -337,7 +336,7 @@
 
 
   /**
-   * Returns the qualifier type code for this CVTerm object.
+   * Returns the qualifier type of this CVTerm object.
    *
    * @htmlinclude cvterm-common-description-text.html
    *
@@ -363,8 +362,8 @@
    * the @em other two methods to call to find out the specific
    * relationship.
    *
-   * @return the @if clike #QualifierType_t@... java qualifier type code@... value of this object or
-   * @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@...
+   * @return the @if clike #QualifierType_t value@... qualifier type@...
+   * of this object or @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@...
    * (the default).
    *
    * @see getResources()
@@ -375,7 +374,7 @@
 
 
   /**
-   * Returns the model qualifier type code for this CVTerm object.
+   * Returns the model qualifier type of this CVTerm object.
    * 
    * @htmlinclude cvterm-common-description-text.html
    *
@@ -399,15 +398,15 @@
    * unknown by libSBML and reported as
    * @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@....
    *
-   * @return the @if clike #ModelQualifierType_t@... java model qualifier type code@... value of this object or
-   * @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@...
+   * @return the @if clike #ModelQualifierType_t value@... model qualifier type@...
+   * of this object or @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@...
    * (the default).
    */
   ModelQualifierType_t getModelQualifierType();
 
 
   /**
-   * Returns the biological qualifier type code for this CVTerm object.
+   * Returns the biological qualifier type of this CVTerm object.
    * 
    * @htmlinclude cvterm-common-description-text.html
    *
@@ -440,8 +439,8 @@
    * unknown by libSBML and reported as
    * @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@....
    *
-   * @return the @if clike #BiolQualifierType_t@... java biology qualifier type code@... value of this object or
-   * @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@...
+   * @return the @if clike #BiolQualifierType_t value@... biology qualifier type@...
+   * of this object or @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@...
    * (the default).
    */
   BiolQualifierType_t getBiologicalQualifierType();
@@ -545,11 +544,11 @@
 
   
   /**
-   * Sets the @if clike #QualifierType_t@... java qualifier type code@... value of this CVTerm object.
+   * Sets the @if clike #QualifierType_t@... qualifier code@... of this
+   * CVTerm object.
    *
-   * @param type the @if clike #QualifierType_t@... java qualifier type code@... type value 
-   * function. The possible values
-   * returned by this function are:
+   * @param type the @if clike #QualifierType_t value@... qualifier type@....
+   * The possible values returned by this function are:
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@...
    *
    * @see getQualifierType()
@@ -558,13 +557,13 @@
 
 
   /**
-   * Sets the @if clike #ModelQualifierType_t@... java model qualifier type code@... value of this CVTerm object.
+   * Sets the @if clike #ModelQualifierType_t value@... model qualifier type@...
+   * of this CVTerm object.
    *
-   * @param type the @if clike #ModelQualifierType_t@... java model qualifier type code@... value
+   * @param type the @if clike #ModelQualifierType_t value@... model qualifier type@...
    *
    * @return integer value indicating success/failure of the
-   * function. The possible values
-   * returned by this function are:
+   * function. The possible values returned by this function are:
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@...
    * @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@...
    *
@@ -580,19 +579,19 @@
 
 
   /**
-   * Sets the @if clike #BiolQualifierType_t@... java biology qualifier type code@... of this CVTerm object.
+   * Sets the @if clike #BiolQualifierType_t value@... biology qualifier type@...
+   * of this CVTerm object.
    *
-   * @param type the @if clike #BiolQualifierType_t@... java biology qualifier type code@... value
+   * @param type the @if clike #BiolQualifierType_t value@... biology qualifier type@....
    *
    * @return integer value indicating success/failure of the
-   * function. The possible values
-   * returned by this function are:
+   * function. The possible values returned by this function are:
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@...
    * @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@...
    *
    * @note If the Qualifier Type of this object is not
    * @link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@...,
-   * then the @if clike #BiolQualifierType_t@... java biology qualifier type code@... value will default
+   * then the @if clike #BiolQualifierType_t value@... biology qualifier type@... will default
    * to @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@....
    *
    * @see getQualifierType()
@@ -620,18 +619,18 @@
    * together identified uniquely using a URI.  The following template
    * illustrates the structure:
    *
-<DIV class="fragment">
-&lt;rdf:Description rdf:about=&quot;#<span style="border-bottom: 1px solid black">meta id</span>&quot;&gt;<br>
-&nbsp;&nbsp;<span style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span><br>
-&nbsp;&nbsp;&lt;<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Bag&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:li rdf:resource=&quot;<span style="background-color: #d0d0ee">resource URI</span>&quot; /&gt;<br>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
-&nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Bag&gt;<br>
-&nbsp;&nbsp;&lt;/<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
-&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
-&lt;/rdf:Description&gt;<br>
-</div>
+   <DIV class="fragment">
+   &lt;rdf:Description rdf:about=&quot;#<span style="border-bottom: 1px solid black">meta id</span>&quot;&gt;<br>
+   &nbsp;&nbsp;<span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span><br>
+   &nbsp;&nbsp;&lt;<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+   &nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:Bag&gt;<br>
+   &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&lt;rdf:li rdf:resource=&quot;<span style="background-color: #d0d0ee">resource URI</span>&quot; /&gt;<br>
+   &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+   &nbsp;&nbsp;&nbsp;&nbsp;&lt;/rdf:Bag&gt;<br>
+   &nbsp;&nbsp;&lt;/<span style="background-color: #bbb">RELATION_ELEMENT</span>&gt;<br>
+   &nbsp;&nbsp;<span style="background-color: #edd">...</span><br>
+   &lt;/rdf:Description&gt;<br>
+   </div>
    *
    * In the template above, the placeholder <span class="code"
    * style="border-bottom: 1px solid black">meta id</span> stands for the

Modified: trunk/libsbml/src/annotation/RDFAnnotation.h
===================================================================
--- trunk/libsbml/src/annotation/RDFAnnotation.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/annotation/RDFAnnotation.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -44,7 +44,7 @@
  * RDF-based annotations attached to a given SBML
  * <code>&lt;annotation&gt;</code> element are read by RDFAnnotationParser
  * and converted into a list of CVTerm objects.  There
- * are different versions of the main method, @if clike RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, %List *CVTerms) @endif@... java RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, CVTermList *CVTerms) @endif
+ * are different versions of the main method, @if clike RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, %List *CVTerms) @else RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, CVTermList *CVTerms) @endif
  * and RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation), 
  * used depending on whether the annotation in question concerns the MIRIAM
  * model history or other MIRIAM resource annotations.  A special object
@@ -128,7 +128,7 @@
 int success;                              // Status code variable, used below.
 
 XMLNode *RDF = createRDFAnnotation();     // Create RDF annotation XML structure.
-success = RDF->addChild(content);         // Put some content into it.
+success = RDF->addChild(...content...);   // Put some content into it.
 ...                                       // Check "success" return code value.
 
 XMLNode *ann = createAnnotation();        // Create <annotation> container.
@@ -138,12 +138,12 @@
 success = sbmlObject->setAnnotation(ann); // Set object's annotation to what we built.
 ...                                       // Check "success" return code value.
 @endverbatim
-@... java
+   * @endif@... java
 @verbatim
 int success;                                   // Status code variable, used below.
 
 XMLNode RDF = createRDFAnnotation();          // Create RDF annotation XML structure.
-success      = RDF.addChild(content);          // Put some content into it.
+success      = RDF.addChild(...content...);    // Put some content into it.
 ...                                            // Check "success" return code value.
 
 XMLNode ann = createAnnotation();             // Create <annotation> container.
@@ -153,7 +153,20 @@
 success      = sbmlObject.setAnnotation(ann); // Set object's annotation to what we built.
 ...                                            // Check "success" return code value.
 @endverbatim
-@...
+   * @endif@... python
+@verbatim
+RDF     = RDFAnnotationParser.createRDFAnnotation() # Create RDF annotation XML structure.
+success = RDF.addChild(...content...)               # Put some content into it.
+...                                                 # Check "success" return code value.
+
+annot   = RDFAnnotationParser.createAnnotation()    # Create <annotation> container.
+success = annot.addChild(RDF)                       # Put the RDF annotation into it.
+...                                                 # Check "success" return code value.
+
+success = sbmlObject.setAnnotation(annot)           # Set object's annotation to what we built.
+...                                                 # Check "success" return code value.
+@endverbatim
+   * @endif
    * The SBML specification contains more information about the format of
    * annotations.  We urge readers to consult Section&nbsp;6 of the SBML
    * Level&nbsp;2 (Versions 2&ndash;4) and SBML Level&nbsp;3 specification
@@ -185,7 +198,7 @@
    *
    * Note that this does not create the containing SBML
    * <code>&lt;annotation&gt;</code> element; the method
-   * @if clike createAnnotation()@endif@... java RDFAnnotationParser::createAnnotation()@endif
+   * @if clike createAnnotation()@else RDFAnnotationParser::createAnnotation()@endif
    * is available for creating the container.
    *
    * @return a pointer to an XMLNode
@@ -233,7 +246,7 @@
    * Note that this method does @em not create a complete annotation or
    * even an RDF element; it only creates the "Description" portion.  Callers
    * will need to use other methods such as
-   * @if clike createRDFAnnotation()@endif@... java RDFAnnotationParser::createRDFAnnotation()@endif
+   * @if clike createRDFAnnotation()@else RDFAnnotationParser::createRDFAnnotation()@endif
    * to create the rest of the structure for an annotation.
    *
    * @param object the object to which the "Description" refers
@@ -252,7 +265,7 @@
    *
    * This essentially takes the given SBML object, reads out the CVTerm objects
    * attached to it, calls
-   * @if clike createRDFDescription()@endif@... java RDFAnnotationParser::createRDFDescription(SBase object)@endif
+   * @if clike createRDFDescription()@else RDFAnnotationParser::createRDFDescription(SBase object)@endif
    * to create an RDF "Description" element to hold the terms and adds
    * each term with appropriate qualifiers.
    *
@@ -269,13 +282,13 @@
    * around it.
    *
    * This essentially takes the given SBML object, calls
-   * @if clike RDFAnnotationParser::createCVTerms()@endif@... java RDFAnnotationParser::createCVTerms(SBase object)@endif
+   * @if clike RDFAnnotationParser::createCVTerms()@else RDFAnnotationParser::createCVTerms(SBase object)@endif
    * to read out the CVTerm objects
    * attached to it, calls
-   * @if clike createRDFAnnotation()@endif@... java RDFAnnotationParser::createRDFAnnotation()@endif
+   * @if clike createRDFAnnotation()@else RDFAnnotationParser::createRDFAnnotation()@endif
    * to create an RDF
    * annotation to hold the terms, and finally calls
-   * @if clike createAnnotation()@endif@... java RDFAnnotationParser::createAnnotation()@endif
+   * @if clike createAnnotation()@else RDFAnnotationParser::createAnnotation()@endif
    * to wrap the result as an SBML <code>&lt;annotation&gt;</code> element.
    *
    * @param object the SBML object to start from

Modified: trunk/libsbml/src/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/math/ASTNode.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/math/ASTNode.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -80,7 +80,7 @@
  *
  *
  * @if clike <h3><a class="anchor" name="ASTNodeType_t">
- * ASTNodeType_t</a></h3> @endif@... java <h3><a class="anchor"
+ * ASTNodeType_t</a></h3> @else <h3><a class="anchor"
  * name="ASTNodeType_t">The set of possible %ASTNode types</a></h3> @endif
  *
  * @if clike Every ASTNode has an associated type code to indicate,
@@ -89,7 +89,7 @@
  * @link ASTNode.h::ASTNodeType_t ASTNodeType_t@....  The list of
  * possible types is quite long, because it covers all the mathematical
  * functions that are permitted in SBML.  The values are shown in the
- * following table: @endif@... java Every ASTNode has an associated
+ * following table: @else Every ASTNode has an associated
  * type code to indicate, for example, whether it holds a number or stands for
  * an arithmetic operator.  The type is recorded as a value drawn from a
  * set of static integer constants defined in the class {@link
@@ -142,8 +142,8 @@
  * 
  * <h3><a class="anchor" name="math-convert">Converting between ASTs and text strings</a></h3>
  * 
- * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
- * read by @if clike SBML_parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
+ * read by @if clike SBML_parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
  * are simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
  * formula in this text-string form can be handed to a program that
  * understands SBML Level&nbsp;1 mathematical expressions, or used as part
@@ -386,10 +386,10 @@
    * AST_UNKNOWN@....  If the type isn't supplied when caling this
    * constructor, the caller should set the node type to something else as
    * soon as possible using
-   * @if clike setType()@endif@... java ASTNode::setType(int)@endif.
+   * @if clike setType()@else ASTNode::setType(int)@endif.
    *
    * @param type an optional
-   * @if clike @link #ASTNodeType_t ASTNodeType_t@... java type@...
+   * @if clike @link #ASTNodeType_t ASTNodeType_t@... type@...
    * code indicating the type of node to create.
    *
    * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
@@ -503,7 +503,7 @@
    * render the representation invalid.  Callers need to be careful to use
    * this method in the context of other operations to create complete and
    * correct formulas.  The method
-   * @if clike isWellFormedASTNode()@endif@... java ASTNode::isWellFormedASTNode()@endif
+   * @if clike isWellFormedASTNode()@else ASTNode::isWellFormedASTNode()@endif
    * may also be useful for checking the results of node modifications.
    *
    * @see prependChild(ASTNode* child)
@@ -631,7 +631,7 @@
    * 
    * @return the nth child of this ASTNode or @c NULL if this node has no nth
    * child (<code>n &gt; </code>
-   * @if clike getNumChildren()@endif@... java ASTNode::getNumChildren()@endif
+   * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
    * <code>- 1</code>).
    */
   LIBSBML_EXTERN
@@ -642,7 +642,7 @@
    * Get the left child of this node.
    * 
    * @return the left child of this ASTNode.  This is equivalent to calling
-   * @if clike getChild()@endif@... java ASTNode::getChild(unsigned int)@endif
+   * @if clike getChild()@else ASTNode::getChild(unsigned int)@endif
    * with an argument of @c 0.
    */
   LIBSBML_EXTERN
@@ -654,7 +654,7 @@
    *
    * @return the right child of this ASTNode, or @c NULL if this node has no
    * right child.  If
-   * @if clike getNumChildren()@endif@... java ASTNode::getNumChildren()@endif
+   * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
    * <code>&gt; 1</code>, then this is equivalent to:
    * @code
    * getChild( getNumChildren() - 1 );
@@ -721,7 +721,7 @@
    * 
    * @return the nth annotation of this ASTNode, or @c NULL if this node has
    * no nth annotation (<code>n &gt;</code>
-   * @if clike getNumChildren()@endif@... java ASTNode::getNumChildren()@endif
+   * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
    * <code>- 1</code>).
    *
    * @see ASTNode::addSemanticsAnnotation(XMLNode* sAnnotation)
@@ -789,7 +789,7 @@
   /**
    * Get the value of this node as a single character.  This function
    * should be called only when
-   * @if clike getType()@endif@... java ASTNode::getType()@endif returns
+   * @if clike getType()@else ASTNode::getType()@endif returns
    * @link ASTNodeType_t#AST_PLUS AST_PLUS@...,
    * @link ASTNodeType_t#AST_MINUS AST_MINUS@...,
    * @link ASTNodeType_t#AST_TIMES AST_TIMES@...,
@@ -805,7 +805,7 @@
   /**
    * Get the value of this node as an integer. This function should be
    * called only when
-   * @if clike getType()@endif@... java ASTNode::getType()@endif
+   * @if clike getType()@else ASTNode::getType()@endif
    * <code>== @link ASTNodeType_t#AST_INTEGER AST_INTEGER@...>.
    * 
    * @return the value of this ASTNode as a (<code>long</code>) integer. 
@@ -817,9 +817,9 @@
   /**
    * Get the value of this node as a string.  This function may be called
    * on nodes that (1) are not operators, i.e., nodes for which
-   * @if clike isOperator()@endif@... java ASTNode::isOperator()@endif
+   * @if clike isOperator()@else ASTNode::isOperator()@endif
    * returns @c false, and (2) are not numbers, i.e.,
-   * @if clike isNumber()@endif@... java ASTNode::isNumber()@endif returns @c false.
+   * @if clike isNumber()@else ASTNode::isNumber()@endif returns @c false.
    * 
    * @return the value of this ASTNode as a string.
    */
@@ -830,7 +830,7 @@
   /**
    * Get the value of the numerator of this node.  This function should be
    * called only when
-   * @if clike getType()@endif@... java ASTNode::getType()@endif
+   * @if clike getType()@else ASTNode::getType()@endif
    * <code>== @link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@...>.
    * 
    * @return the value of the numerator of this ASTNode.  
@@ -842,7 +842,7 @@
   /**
    * Get the value of the denominator of this node.  This function should
    * be called only when
-   * @if clike getType()@endif@... java ASTNode::getType()@endif
+   * @if clike getType()@else ASTNode::getType()@endif
    * <code>== @link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@...>.
    * 
    * @return the value of the denominator of this ASTNode.
@@ -854,7 +854,7 @@
   /**
    * Get the real-numbered value of this node.  This function
    * should be called only when
-   * @if clike isReal()@endif@... java ASTNode::isReal()@endif
+   * @if clike isReal()@else ASTNode::isReal()@endif
    * <code>== true</code>.
    *
    * This function performs the necessary arithmetic if the node type is
@@ -870,13 +870,13 @@
 
   /**
    * Get the mantissa value of this node.  This function should be called
-   * only when @if clike getType()@endif@... java ASTNode::getType()@endif
+   * only when @if clike getType()@else ASTNode::getType()@endif
    * returns @link ASTNodeType_t#AST_REAL_E AST_REAL_E@...
    * or @link ASTNodeType_t#AST_REAL AST_REAL@....
-   * If @if clike getType()@endif@... java ASTNode::getType()@endif
+   * If @if clike getType()@else ASTNode::getType()@endif
    * returns @link ASTNodeType_t#AST_REAL AST_REAL@...,
    * this method is identical to
-   * @if clike getReal()@endif@... java ASTNode::getReal()@endif.
+   * @if clike getReal()@else ASTNode::getReal()@endif.
    * 
    * @return the value of the mantissa of this ASTNode. 
    */
@@ -887,7 +887,7 @@
   /**
    * Get the exponent value of this ASTNode.  This function should be
    * called only when
-   * @if clike getType()@endif@... java ASTNode::getType()@endif
+   * @if clike getType()@else ASTNode::getType()@endif
    * returns @link ASTNodeType_t#AST_REAL_E AST_REAL_E@...
    * or @link ASTNodeType_t#AST_REAL AST_REAL@....
    * 
@@ -1158,7 +1158,7 @@
    * 
    * For numbers, unary minus nodes can be "collapsed" by negating the
    * number.  In fact, 
-   * @if clike SBML_parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif does this during its parsing process.
+   * @if clike SBML_parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif does this during its parsing process.
    * However, unary minus nodes for symbols
    * (@link ASTNodeType_t#AST_NAME AST_NAME@...) cannot
    * be "collapsed", so this predicate function is necessary.
@@ -1242,9 +1242,9 @@
    * As a side-effect, this ASTNode object's type will be reset to
    * @link ASTNodeType_t#AST_NAME AST_NAME@... if (and <em>only
    * if</em>) the ASTNode was previously an operator (
-   * @if clike isOperator()@endif@... java ASTNode::isOperator()@endif
+   * @if clike isOperator()@else ASTNode::isOperator()@endif
    * <code>== true</code>), number (
-   * @if clike isNumber()@endif@... java ASTNode::isNumber()@endif
+   * @if clike isNumber()@else ASTNode::isNumber()@endif
    * <code>== true</code>), or unknown.
    * This allows names to be set for @link ASTNodeType_t#AST_FUNCTION
    * AST_FUNCTION@... nodes and the like.
@@ -1363,7 +1363,7 @@
    * The units will be set @em only if this ASTNode object represents a
    * MathML <code>&lt;cn&gt;</code> element, i.e., represents a number.
    * Callers may use
-   * @if clike isNumber()@endif@... java ASTNode::isNumber()@endif
+   * @if clike isNumber()@else ASTNode::isNumber()@endif
    * to inquire whether the node is of that type.
    *
    * @htmlinclude about-sbml-units-attrib.html

Modified: trunk/libsbml/src/math/FormulaFormatter.h
===================================================================
--- trunk/libsbml/src/math/FormulaFormatter.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/math/FormulaFormatter.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -51,7 +51,7 @@
  * this text-string form therefore can be handed to a program that
  * understands SBML Level&nbsp;1 mathematical expressions, or used as part
  * of a formula translation system.  The syntax is described in detail in
- * the documentation for ASTNode. @endif@... java The text-string form of
+ * the documentation for ASTNode. @else The text-string form of
  * mathematical formulas produced by <code><a
  * href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">
  * libsbml.formulaToString()</a></code> and read by

Modified: trunk/libsbml/src/math/FormulaParser.h
===================================================================
--- trunk/libsbml/src/math/FormulaParser.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/math/FormulaParser.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -52,7 +52,7 @@
  * this text-string form therefore can be handed to a program that
  * understands SBML Level&nbsp;1 mathematical expressions, or used as part
  * of a formula translation system.  The syntax is described in detail in
- * the documentation for ASTNode. @endif@... java The text-string form of
+ * the documentation for ASTNode. @else The text-string form of
  * mathematical formulas produced by <code><a
  * href="libsbml.html">libsbml.formulaToString()</a></code> and read by
  * <code><a href="libsbml.html">libsbml.parseFormula()</a></code> are

Modified: trunk/libsbml/src/sbml/Compartment.h
===================================================================
--- trunk/libsbml/src/sbml/Compartment.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Compartment.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -376,8 +376,7 @@
    * (identifier) attribute of a Compartment is required to have a value.
    * Thus, callers are cautioned to assign a value after calling this
    * constructor.  Setting the identifier can be accomplished using the
-   * method
-   * @if clike setId()@endif@... python setId()@endif@... java Compartment::setId(String id)@endif.
+   * method @if java Compartment::setId(String id)@else setId()@endif.
    *
    * @param sbmlns an SBMLNamespaces object.
    *
@@ -522,14 +521,14 @@
    * Get the size of this Compartment.
    *
    * This method is identical to
-   * @if clike getVolume()@endif@... python getVolume()@endif@... java Compartment::getVolume()@endif.
+   * @if java Compartment::getVolume()@else getVolume()@endif.
    * In SBML Level&nbsp;1, compartments are always three-dimensional
    * constructs and only have volumes, whereas in SBML Level&nbsp;2,
    * compartments may be other than three-dimensional and therefore the
    * "volume" attribute is named "size" in Level&nbsp;2.  LibSBML provides
    * both
-   * @if clike getSize()@endif@... python getSize()@endif@... java Compartment::getSize()@endif and
-   * @if clike getVolume()@endif@... python getVolume()@endif@... java Compartment::getVolume()@endif for
+   * @if java Compartment::getSize()@else getSize()@endif and
+   * @if java Compartment::getVolume()@else getVolume()@endif for
    * easier compatibility between SBML Levels.
    *
    * @return the value of the "size" attribute ("volume" in Level&nbsp;1) of
@@ -545,14 +544,14 @@
    * Get the volume of this Compartment.
    * 
    * This method is identical to
-   * @if clike getSize()@endif@... python getSize()@endif@... java Compartment::getSize()@endif.  In
+   * @if java Compartment::getSize()@else getSize()@endif.  In
    * SBML Level&nbsp;1, compartments are always three-dimensional
    * constructs and only have volumes, whereas in SBML Level&nbsp;2,
    * compartments may be other than three-dimensional and therefore the
    * "volume" attribute is named "size" in Level&nbsp;2.  LibSBML provides
    * both
-   * @if clike getSize()@endif@... python getSize()@endif@... java Compartment::getSize()@endif and
-   * @if clike getVolume()@endif@... python getVolume()@endif@... java Compartment::getVolume()@endif
+   * @if java Compartment::getSize()@else getSize()@endif and
+   * @if java Compartment::getVolume()@else getVolume()@endif
    * for easier compatibility between SBML Levels.
    *
    * @return the value of the "volume" attribute ("size" in Level&nbsp;2) of
@@ -581,7 +580,7 @@
    * @note @htmlinclude unassigned-units-are-not-a-default.html
    *
    * @see isSetUnits()
-   * @see @if clike setUnits()@endif@... python setUnits()@endif@... java Compartment::setUnits(String sid)@endif
+   * @see @if java Compartment::setUnits(String sid)@else setUnits()@endif
    * @see getSize()
    */
   const std::string& getUnits () const;
@@ -647,14 +646,12 @@
    * Compartment's "size" attribute is set.
    *
    * This method is similar but not identical to
-   * @if clike isSetVolume()@endif@... python isSetVolume()@endif@... java Compartment::isSetVolume()@endif.  The latter
+   * @if java Compartment::isSetVolume()@else isSetVolume()@endif.  The latter
    * should be used in the context of SBML Level&nbsp;1 models instead of
-   * @if clike isSetSize()@endif@... python isSetSize()@endif@... java Compartment::isSetSize()@endif
-   * because
-   * @if clike isSetVolume()@endif@... python isSetVolume()@endif@... java Compartment::isSetVolume()@endif
-   * performs extra processing to take
-   * into account the difference in default values between SBML Levels 1
-   * and 2.
+   * @if java Compartment::isSetSize()@else isSetSize()@endif
+   * because @if java Compartment::isSetVolume()@else isSetVolume()@endif
+   * performs extra processing to take into account the difference in
+   * default values between SBML Levels 1 and 2.
    * 
    * @return @c true if the "size" attribute ("volume" in Level&nbsp;2) of
    * this Compartment is set, @c false otherwise.
@@ -670,7 +667,7 @@
    * "volume" attribute is set.
    * 
    * This method is similar but not identical to
-   * @if clike isSetSize()@endif@... python isSetSize()@endif@... java Compartment::isSetSize()@endif.  The latter
+   * @if java Compartment::isSetSize()@else isSetSize()@endif.  The latter
    * should not be used in the context of SBML Level&nbsp;1 models because this
    * method performs extra processing to take into account
    * the difference in default values between SBML Levels 1 and 2.
@@ -687,7 +684,7 @@
    * therefore may or may not be set.
    *
    * @see isSetSize()
-   * @see @if clike setVolume()@endif@... python setVolume()@endif@... java Compartment::setVolume(double value)@endif
+   * @see @if java Compartment::setVolume(double value)@else setVolume()@endif
    */
   bool isSetVolume () const;
 
@@ -831,7 +828,7 @@
    * Compartment.
    *
    * This method is identical to
-   * @if clike setVolume()@endif@... python setVolume()@endif@... java Compartment::setVolume(double value)@endif
+   * @if java Compartment::setVolume(double value)@else setVolume()@endif
    * and is provided for compatibility between
    * SBML Level&nbsp;1 and Level&nbsp;2.
    *
@@ -855,7 +852,7 @@
    * Compartment.
    *
    * This method is identical to
-   * @if clike setVolume()@endif@... python setVolume()@endif@... java Compartment::setVolume(double value)@endif
+   * @if java Compartment::setVolume(double value)@else setVolume()@endif
    * and is provided for compatibility between SBML Level&nbsp;1 and
    * Level&nbsp;2.
    * 
@@ -1050,7 +1047,7 @@
    *
    * Note that unit declarations for Compartment objects are specified in
    * terms of the @em identifier of a unit (e.g., using
-   * @if clike setUnits()@endif@... python setUnits()@endif@... java Compartment::setUnits(String sid)@endif), but
+   * @if java Compartment::setUnits(String sid)@else setUnits()@endif), but
    * @em this method returns a UnitDefinition object, not a unit
    * identifier.  It does this by constructing an appropriate
    * UnitDefinition.  For SBML Level&nbsp;2 models, it will do this even

Modified: trunk/libsbml/src/sbml/CompartmentType.h
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/CompartmentType.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -172,7 +172,7 @@
    * (identifier) attribute of a CompartmentType is required to have a value.
    * Thus, callers are cautioned to assign a value after calling this
    * constructor.  Setting the identifier can be accomplished using the
-   * method @if clike setId() @endif@... python setId() @endif@... java setId(String id) @endif.
+   * method setId(@if java String id@...).
    *
    * @param sbmlns an SBMLNamespaces object.
    *

Modified: trunk/libsbml/src/sbml/InitialAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/InitialAssignment.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -400,7 +400,7 @@
    * The units are calculated based on the mathematical expression in the
    * InitialAssignment and the model quantities referenced by
    * <code>&lt;ci&gt;</code> elements used within that expression.  The
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java InitialAssignment::getDerivedUnitDefinition()@endif
+   * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * method returns the calculated units.
    *
    * Note that the functionality that facilitates unit analysis depends 
@@ -413,13 +413,13 @@
    * units.  In those cases, it is not possible to calculate the units of
    * the overall expression without making assumptions.  LibSBML does not
    * make assumptions about the units, and
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java InitialAssignment::getDerivedUnitDefinition()@endif
+   * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * only returns the units as far as it is able to determine them.  For
    * example, in an expression <em>X + Y</em>, if <em>X</em> has
    * unambiguously-defined units and <em>Y</em> does not, it will return
    * the units of <em>X</em>.  <strong>It is important that callers also
    * invoke the method</strong>
-   * @if clike containsUndeclaredUnits()@endif@... python containsUndeclaredUnits()@endif@... java InitialAssignment::containsUndeclaredUnits()@endif
+   * @if java InitialAssignment::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
    * <strong>to determine whether this situation holds</strong>.  Callers
    * may wish to take suitable actions in those scenarios.
    * 
@@ -439,7 +439,7 @@
    * The units are calculated based on the mathematical expression in the
    * InitialAssignment and the model quantities referenced by
    * <code>&lt;ci&gt;</code> elements used within that expression.  The
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java InitialAssignment::getDerivedUnitDefinition()@endif
+   * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * method returns the calculated units.
    *
    * Note that the functionality that facilitates unit analysis depends 
@@ -452,13 +452,13 @@
    * units.  In those cases, it is not possible to calculate the units of
    * the overall expression without making assumptions.  LibSBML does not
    * make assumptions about the units, and
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java InitialAssignment::getDerivedUnitDefinition()@endif
+   * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * only returns the units as far as it is able to determine them.  For
    * example, in an expression <em>X + Y</em>, if <em>X</em> has
    * unambiguously-defined units and <em>Y</em> does not, it will return
    * the units of <em>X</em>.  <strong>It is important that callers also
    * invoke the method</strong>
-   * @if clike containsUndeclaredUnits()@endif@... python containsUndeclaredUnits()@endif@... java InitialAssignment::containsUndeclaredUnits()@endif
+   * @if java InitialAssignment::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
    * <strong>to determine whether this situation holds</strong>.  Callers
    * may wish to take suitable actions in those scenarios.
    * 
@@ -481,7 +481,7 @@
    *
    * @note A return value of @c true indicates that the UnitDefinition
    * returned by
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java InitialAssignment::getDerivedUnitDefinition()@endif
+   * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * may not accurately represent the units of the expression.
    *
    * @see getDerivedUnitDefinition()
@@ -500,7 +500,7 @@
    *
    * @note A return value of @c true indicates that the UnitDefinition
    * returned by
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java InitialAssignment::getDerivedUnitDefinition()@endif
+   * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * may not accurately represent the units of the expression.
    *
    * @see getDerivedUnitDefinition()

Modified: trunk/libsbml/src/sbml/KineticLaw.h
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/KineticLaw.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -226,7 +226,7 @@
    * it as as a text string.
    *
    * This is fundamentally equivalent to
-   * @if clike getMath()@endif@... python getMath()@endif@... java KineticLaw::getMath()@endif.
+   * @if java KineticLaw::getMath()@else getMath()@endif.
    * This variant is provided principally for compatibility compatibility
    * with SBML Level&nbsp;1.
    * 
@@ -244,7 +244,7 @@
    * it as as an AST.
    *
    * This is fundamentally equivalent to
-   * @if clike getFormula()@endif@... python getFormula()@endif@... java KineticLaw::getFormula()@endif.
+   * @if java KineticLaw::getFormula()@else getFormula()@endif.
    * The latter is provided principally for compatibility compatibility
    * with SBML Level&nbsp;1, which represented mathematical formulas in
    * text-string form.
@@ -291,10 +291,10 @@
    * KineticLaw's "formula" attribute is set.
    *
    * This is functionally identical to the method
-   * @if clike isSetMath()@endif@... python isSetMath()@endif@... java KineticLaw::isSetMath()@endif.  It is
+   * @if java KineticLaw::isSetMath()@else isSetMath()@endif.  It is
    * provided in order to mirror the parallel between
-   * @if clike getFormula()@endif@... python getFormula()@endif@... java KineticLaw::getFormula()@endif and
-   * @if clike getMath()@endif@... python getMath()@endif@... java KineticLaw::getMath()@endif.
+   * @if java KineticLaw::getFormula()@else getFormula()@endif and
+   * @if java KineticLaw::getMath()@else getMath()@endif.
    *
    * @return @c true if the formula (meaning the @c math subelement) of
    * this KineticLaw is set, @c false otherwise.
@@ -311,10 +311,10 @@
    * Kinetic's "math" subelement is set.
    *
    * This is identical to the method
-   * @if clike isSetFormula()@endif@... python isSetFormula()@endif@... java KineticLaw::isSetFormula()@endif.
+   * @if java KineticLaw::isSetFormula()@else isSetFormula()@endif.
    * It is provided in order to mirror the parallel between
-   * @if clike getFormula()@endif@... python getFormula()@endif@... java KineticLaw::getFormula()@endif and
-   * @if clike getMath()@endif@... python getMath()@endif@... java KineticLaw::getMath()@endif.
+   * @if java KineticLaw::getFormula()@else getFormula()@endif and
+   * @if java KineticLaw::getMath()@else getMath()@endif.
    * 
    * @return @c true if the formula (meaning the @c math subelement) of
    * this KineticLaw is set, @c false otherwise.
@@ -384,7 +384,7 @@
    * of the given ASTNode.
    *
    * This is fundamentally identical to
-   * @if clike getFormula()@endif@... python getFormula()@endif@... java KineticLaw::setFormula(String formula)@endif.
+   * @if java KineticLaw::setFormula(String formula)@else getFormula()@endif.
    * The latter is provided principally for compatibility compatibility with
    * SBML Level&nbsp;1, which represented mathematical formulas in text-string
    * form.
@@ -511,7 +511,7 @@
    * instance in the KineticLaw</em>.  In addition, the caller should make
    * sure to free the original object if it is no longer being used, or
    * else a memory leak will result.  Please see
-   * @if clike createParameter()@endif@... python createParameter()@endif@... java KineticLaw::createParameter()@endif
+   * @if java KineticLaw::createParameter()@else createParameter()@endif
    * for a method that does not lead to these issues.
    *
    * @see createParameter()
@@ -543,7 +543,7 @@
    * instance in the KineticLaw</em>.  In addition, the caller should make
    * sure to free the original object if it is no longer being used, or
    * else a memory leak will result.  Please see
-   * @if clike createParameter()@endif@... python createParameter()@endif@... java KineticLaw::createParameter()@endif
+   * @if java KineticLaw::createParameter()@else createParameter()@endif
    * for a method that does not lead to these issues.
    *
    * @see createLocalParameter()
@@ -717,7 +717,7 @@
    * The units are calculated based on the mathematical expression in the
    * KineticLaw and the model quantities referenced by
    * <code>&lt;ci&gt;</code> elements used within that expression.  The
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java KineticLaw::getDerivedUnitDefinition()@endif
+   * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * method returns the calculated units.
    *
    * Note that the functionality that facilitates unit analysis depends 
@@ -730,13 +730,13 @@
    * units.  In those cases, it is not possible to calculate the units of
    * the overall expression without making assumptions.  LibSBML does not
    * make assumptions about the units, and
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java KineticLaw::getDerivedUnitDefinition()@endif
+   * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * only returns the units as far as it is able to determine them.  For
    * example, in an expression <em>X + Y</em>, if <em>X</em> has
    * unambiguously-defined units and <em>Y</em> does not, it will return
    * the units of <em>X</em>.  <strong>It is important that callers also
    * invoke the method</strong>
-   * @if clike containsUndeclaredUnits()@endif@... java KineticLaw::containsUndeclaredUnits()@endif
+   * @if java KineticLaw::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
    * <strong>to determine whether this situation holds</strong>.  Callers may
    * wish to take suitable actions in those scenarios.
    *
@@ -756,7 +756,7 @@
    * The units are calculated based on the mathematical expression in the
    * KineticLaw and the model quantities referenced by
    * <code>&lt;ci&gt;</code> elements used within that expression.  The
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java KineticLaw::getDerivedUnitDefinition()@endif
+   * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * method returns the calculated units.
    *
    * Note that the functionality that facilitates unit analysis depends 
@@ -769,13 +769,13 @@
    * units.  In those cases, it is not possible to calculate the units of
    * the overall expression without making assumptions.  LibSBML does not
    * make assumptions about the units, and
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java KineticLaw::getDerivedUnitDefinition()@endif
+   * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * only returns the units as far as it is able to determine them.  For
    * example, in an expression <em>X + Y</em>, if <em>X</em> has
    * unambiguously-defined units and <em>Y</em> does not, it will return
    * the units of <em>X</em>.  <strong>It is important that callers also
    * invoke the method</strong>
-   * @if clike containsUndeclaredUnits()@endif@... java KineticLaw::containsUndeclaredUnits()@endif
+   * @if java KineticLaw::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
    * <strong>to determine whether this situation holds</strong>.  Callers
    * may wish to take suitable actions in those scenarios.
    *
@@ -798,7 +798,7 @@
    *
    * @note A return value of @c true indicates that the UnitDefinition
    * returned by
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java KineticLaw::getDerivedUnitDefinition()@endif
+   * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * may not accurately represent the units of the expression.
    *
    * @see getDerivedUnitDefinition()
@@ -817,7 +817,7 @@
    *
    * @note A return value of @c true indicates that the UnitDefinition
    * returned by
-   * @if clike getDerivedUnitDefinition()@endif@... python getDerivedUnitDefinition()@endif@... java KineticLaw::getDerivedUnitDefinition()@endif
+   * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
    * may not accurately represent the units of the expression.
    *
    * @see getDerivedUnitDefinition()

Modified: trunk/libsbml/src/sbml/LocalParameter.h
===================================================================
--- trunk/libsbml/src/sbml/LocalParameter.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/LocalParameter.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -201,7 +201,7 @@
    * Thus, callers are cautioned to assign a value after calling this
    * constructor if no identifier is provided as an argument.  Setting the
    * identifier can be accomplished using the method
-   * @if clike setId()@endif@... python setId()@endif@... java setId(String id)@endif.
+   * @if java setId(String id)@else setId()@endif.
    *
    * @param sbmlns an SBMLNamespaces object.
    *

Modified: trunk/libsbml/src/sbml/Model.h
===================================================================
--- trunk/libsbml/src/sbml/Model.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Model.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -94,7 +94,8 @@
  * @section approaches Approaches to creating objects using the libSBML API
  *
  * LibSBML provides two main mechanisms for creating objects: class
- * constructors (e.g., @if clike @link Species::Species() Species() @endlink @endif@... python @link Species::Species() Species() @endlink @endif@... java <a href="org/sbml/libsbml/Species.html">Species()</a> @endif), 
+ * constructors
+ * (e.g., @if java <a href="org/sbml/libsbml/Species.html">Species()</a> @else Species::Species() @endif), 
  * and <code>create<span class="placeholder"><em>Object</em></span>()</code>
  * methods (such as Model::createSpecies()) provided by certain <span
  * class="placeholder"><em>Object</em></span> classes such as Model.  These
@@ -127,7 +128,7 @@
 Species *sp = model->createSpecies();
 sp->setId(&#34;MySpecies&#34;);
 @endverbatim
-@... java
+ * @endif@... java
 @verbatim
 // Create an SBMLDocument object in Level 3 Version 1 format:
 
@@ -149,7 +150,7 @@
 Species sp = model.createSpecies();
 sp.setId(&#34;BestSpeciesEver&#34;);
 @endverbatim
-@...
+ * @endif
  * 
  * The <code>create<span
  * class="placeholder"><em>Object</em></span>()</code> methods return a
@@ -183,7 +184,7 @@
 
 delete newsp;
 @endverbatim
-@... java
+ * @endif@... java
 @verbatim
 // Create a Species object and add it to the model.
 // This uses the Species class constructor:
@@ -197,14 +198,14 @@
 
 newsp.setId(&#34;NewId&#34;);    // Warning -- doesn't change the species in 'model'!
 @endverbatim
-@...
+ * @endif
  * 
- * The key point of the example above is that, because the @if clike Model::addSpecies() @endif@... python Model::addSpecies() @endif@... java Model::addSpecies(Species s) @endif
+ * The key point of the example above is that, because the
+ * @if java Model::addSpecies(Species s)@else Model::addSpecies()@endif
  * call makes a copy of the object handed to it, care is needed
- * @if clike both when
- * attempting to make changes to the object, and when the original object
- * is no longer needed.@... java when
- * attempting to make changes to the object.@...
+ * @if clike both when attempting to make changes to the object, and when
+ * the original object is no longer needed.@... when attempting to make
+ * changes to the object.@...
  *
  * @section checking Consistency and adherence to SBML specifications
  *

Modified: trunk/libsbml/src/sbml/Parameter.h
===================================================================
--- trunk/libsbml/src/sbml/Parameter.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Parameter.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -229,7 +229,7 @@
    * Thus, callers are cautioned to assign a value after calling this
    * constructor if no identifier is provided as an argument.  Setting the
    * identifier can be accomplished using the method
-   * @if clike setId()@endif@... python setId()@endif@... java setId(String id)@endif.
+   * @if java setId(String id)@else setId()@endif.
    *
    * @param sbmlns an SBMLNamespaces object.
    *

Modified: trunk/libsbml/src/sbml/Rule.h
===================================================================
--- trunk/libsbml/src/sbml/Rule.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Rule.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -174,7 +174,7 @@
  * Level&nbsp;3 for distinguishing rules; specifically, it uses an
  * attribute whose value is drawn from an enumeration of 3 values.  LibSBML
  * supports this using methods that work @if clike a libSBML enumeration
- * type, #RuleType_t, whose values are @endif@... notcpp  with the enumeration
+ * type, #RuleType_t, whose values are @else with the enumeration
  * values @endif listed in the following table.  
  * 
  * <p>
@@ -367,7 +367,7 @@
  * Level&nbsp;3 for distinguishing rules; specifically, it uses an
  * attribute whose value is drawn from an enumeration of 3 values.  LibSBML
  * supports this using methods that work @if clike a libSBML enumeration
- * type, #RuleType_t, whose values are @endif@... notcpp  with the enumeration
+ * type, #RuleType_t, whose values are @else with the enumeration
  * values @endif listed in the following table.  
  * 
  * <p>
@@ -604,7 +604,7 @@
  * Level&nbsp;3 for distinguishing rules; specifically, it uses an
  * attribute whose value is drawn from an enumeration of 3 values.  LibSBML
  * supports this using methods that work @if clike a libSBML enumeration
- * type, #RuleType_t, whose values are @endif@... notcpp  with the enumeration
+ * type, #RuleType_t, whose values are @else with the enumeration
  * values @endif listed in the following table.  
  * 
  * <p>
@@ -818,7 +818,7 @@
  * Level&nbsp;3 for distinguishing rules; specifically, it uses an
  * attribute whose value is drawn from an enumeration of 3 values.  LibSBML
  * supports this using methods that work @if clike a libSBML enumeration
- * type, #RuleType_t, whose values are @endif@... notcpp  with the enumeration
+ * type, #RuleType_t, whose values are @else with the enumeration
  * values @endif listed in the following table.  
  * 
  * <p>
@@ -962,7 +962,7 @@
    * Returns the mathematical expression of this Rule in text-string form.
    *
    * The text string is produced by
-   * @if clike SBML_formulaToString()@endif@... python SBML_formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif; please consult
+   * @if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@else SBML_formulaToString()@endif; please consult
    * the documentation for that function to find out more about the format
    * of the text-string formula.
    * 
@@ -1244,7 +1244,7 @@
    * unambiguously-defined units and <em>Y</em> does not, it will return
    * the units of <em>X</em>.  <strong>It is important that callers also
    * invoke the method</strong>
-   * @if clike containsUndeclaredUnits()@endif@... python containsUndeclaredUnits()@endif@... java Rule::containsUndeclaredUnits()@endif
+   * @if java Rule::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
    * <strong>to determine whether this situation holds</strong>.  Callers may
    * wish to take suitable actions in those scenarios.
    * 
@@ -1280,7 +1280,7 @@
    * unambiguously-defined units and <em>Y</em> does not, it will return
    * the units of <em>X</em>.  <strong>It is important that callers also
    * invoke the method</strong>
-   * @if clike containsUndeclaredUnits()@endif@... python containsUndeclaredUnits()@endif@... java Rule::containsUndeclaredUnits()@endif
+   * @if java Rule::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
    * <strong>to determine whether this situation holds</strong>.  Callers
    * may wish to take suitable actions in those scenarios.
    * 
@@ -1644,7 +1644,7 @@
    * AlgebraicRule
    * 
    * @note Upon the addition of an AlgebraicRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if clike Model::addRule()@endif@... python Model::addRule()@endif@... java Model::addRule(Rule r)@endif), the SBML Level, SBML Version
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif), the SBML Level, SBML Version
    * and XML namespace of the document @em override the values used
    * when creating the AlgebraicRule object via this constructor.  This is
    * necessary to ensure that an SBML document is a consistent structure.
@@ -1671,7 +1671,7 @@
    * @param sbmlns an SBMLNamespaces object.
    *
    * @note Upon the addition of a AlgebraicRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if clike Model::addRule()@endif@... python Model::addRule()@endif@... java Model::addRule(Rule r)@endif, the SBML XML namespace of the
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML XML namespace of the
    * document @em overrides the value used when creating the AlgebraicRule
    * object via this constructor.  This is necessary to ensure that an SBML
    * document is a consistent structure.  Nevertheless, the ability to
@@ -1786,7 +1786,7 @@
    * AssignmentRule
    * 
    * @note Upon the addition of an AssignmentRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if clike Model::addRule()@endif@... python Model::addRule()@endif@... java Model::addRule(Rule r)@endif, the SBML Level, SBML Version
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML Level, SBML Version
    * and XML namespace of the document @em override the values used
    * when creating the AssignmentRule object via this constructor.  This is
    * necessary to ensure that an SBML document is a consistent structure.
@@ -1813,7 +1813,7 @@
    * @param sbmlns an SBMLNamespaces object.
    *
    * @note Upon the addition of a AssignmentRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if clike Model::addRule()@endif@... python Model::addRule()@endif@... java Model::addRule(Rule r)@endif, the SBML XML namespace of
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML XML namespace of
    * the document @em overrides the value used when creating the
    * AssignmentRule object via this constructor.  This is necessary to
    * ensure that an SBML document is a consistent structure.  Nevertheless,
@@ -1918,7 +1918,7 @@
    * RateRule
    * 
    * @note Upon the addition of a RateRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if clike Model::addRule()@endif@... python Model::addRule()@endif@... java Model::addRule(Rule r)@endif, the SBML Level, SBML Version
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML Level, SBML Version
    * and XML namespace of the document @em override the values used
    * when creating the RateRule object via this constructor.  This is
    * necessary to ensure that an SBML document is a consistent structure.
@@ -1945,7 +1945,7 @@
    * @param sbmlns an SBMLNamespaces object.
    *
    * @note Upon the addition of a RateRule object to an SBMLDocument (e.g.,
-   * using @if clike Model::addRule()@endif@... python Model::addRule()@endif@... java Model::addRule(Rule r)@endif, the SBML XML namespace of the document
+   * using @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML XML namespace of the document
    * @em overrides the value used when creating the RateRule object via
    * this constructor.  This is necessary to ensure that an SBML document
    * is a consistent structure.  Nevertheless, the ability to supply the

Modified: trunk/libsbml/src/sbml/SBMLDocument.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/SBMLDocument.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -80,8 +80,7 @@
  * @verbatim
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
   ...
-</sbml>
-@...
+</sbml>@endverbatim
  * 
  * SBMLDocument is derived from SBase, and therefore contains the usual SBase
  * attributes (in SBML Level&nbsp;2 and Level&nbsp;3) of "metaid" and "sboTerm", as
@@ -161,7 +160,7 @@
  * calling SBMLDocument::getNumErrors()</li>
  * 
  * <li style="margin-bottom: 0.5em">
- * Call @if clike SBMLDocument::setConsistencyChecks() @endif@... python SBMLDocument::setConsistencyChecks() @endif@... java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @endif to configure which checks
+ * Call @if java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @else SBMLDocument::setConsistencyChecks() @endif to configure which checks
  * will be performed by SBMLDocument::checkConsistency()</li>
  * 
  * <li>Call SBMLDocument::checkConsistency(), then inquire about the results by
@@ -176,7 +175,7 @@
  * to inquire about the results by using SBMLDocument::getNumErrors()</li>
  * 
  * <li style="margin-bottom: 0.5em">
- * Call @if clike SBMLDocument::setConsistencyChecks() @endif@... python SBMLDocument::setConsistencyChecks() @endif@... java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @endif to configure which
+ * Call @if java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @else SBMLDocument::setConsistencyChecks() @endif to configure which
  * checks are performed by SBMLDocument::checkConsistency()</li>
  * 
  * <li>Call SBMLDocument::checkConsistency(), then inquire about the results
@@ -194,18 +193,18 @@
  *
  * LibSBML provides facilities for limited translation of SBML between
  * Levels and Versions of the SBML specifications.  The method for doing is
- * is @if clike setLevelAndVersion() @endif@... python setLevelAndVersion() @endif@... java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @endif.  In 
+ * is @if java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @else setLevelAndVersion() @endif.  In 
  * general, models can be converted upward without difficulty (e.g., from
  * SBML Level&nbsp;1 to Level&nbsp;2, or from an earlier Version of
  * Level&nbsp;2 to the latest Version of Level&nbsp;2).  Sometimes models
  * can be translated downward as well, if they do not use constructs
  * specific to more advanced Levels of SBML.
  *
- * Calling @if clike SBMLDocument::setLevelAndVersion() @endif@... python SBMLDocument::setLevelAndVersion() @endif@... java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @endif will not @em necessarily lead
+ * Calling @if java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @else SBMLDocument::setLevelAndVersion() @endif will not @em necessarily lead
  * to a successful conversion.  The method will return a boolean value
  * to indicate success or failure.  Callers must check the error log (see 
  * next section) attached to the SBMLDocument object after calling
- * @if clike SBMLDocument::setLevelAndVersion() @endif@... python SBMLDocument::setLevelAndVersion() @endif@... java SBMLDocument::setLevelAndVersion(long lev, long ver) @endif in order to assess whether any
+ * @if java SBMLDocument::setLevelAndVersion(long lev, long ver) @else SBMLDocument::setLevelAndVersion() @endif in order to assess whether any
  * problems arose.
  *
  * If an application is interested in translating to a lower Level and/or
@@ -239,7 +238,7 @@
  * reported through a single common interface involving the object class
  * SBMLError.
  *
- * The methods SBMLDocument::getNumErrors(), @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif and
+ * The methods SBMLDocument::getNumErrors(), @if java SBMLDocument::getError(long n) @else SBMLDocument::getError() @endif and
  * SBMLDocument::printErrors() allow callers to interact with the warnings
  * or errors logged.  Alternatively, callers may retrieve the entire log as
  * an SBMLErrorLog object using the method SBMLDocument::getErrorLog().
@@ -357,11 +356,13 @@
    * object has no associated XML attributes, including (but not limited
    * to) an XML namespace declaration.  The XML namespace declaration is
    * not added until the model is written out, <em>or</em> the method
-   * @if clike SBMLDocument::setLevelAndVersion() @endif@... python SBMLDocument::setLevelAndVersion() @endif@... java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @endif is called.  This may be important to keep in mind
+   * SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@...)
+   * is called.  This may be important to keep in mind
    * if an application needs to add additional XML namespace declarations
    * on the <code>&lt;sbml&gt;</code> element.  Application writers should
    * either provide values for @p level and @p version on the call to this
-   * constructor, or else call @if clike SBMLDocument::setLevelAndVersion() @endif@... python SBMLDocument::setLevelAndVersion() @endif@... java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @endif shortly after creating
+   * constructor, or else call
+   * SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@...) shortly after creating
    * the SBMLDocument object.
    *
    * @param level an integer for the SBML Level
@@ -370,7 +371,7 @@
    *
    * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
    *
-   * @if clike @see SBMLDocument::setLevelAndVersion() @endif@... python @see SBMLDocument::setLevelAndVersion() @endif@... java @see SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @endif
+   * @see SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@...)
    * @see getDefaultLevel()
    * @see getDefaultVersion()
    */
@@ -393,8 +394,7 @@
    * (identifier) attribute of a Compartment is required to have a value.
    * Thus, callers are cautioned to assign a value after calling this
    * constructor.  Setting the identifier can be accomplished using the
-   * method
-   * @if clike setId()@endif@... python setId()@endif@... java Compartment::setId(String id)@endif.
+   * method Compartment::setId(@if java String id@...).
    *
    * @param sbmlns an SBMLNamespaces object.
    *
@@ -454,7 +454,7 @@
    * It is important to note that this method <em>does not create</em> a
    * Model instance.  The model in the SBMLDocument must have been created
    * at some prior time, for example using SBMLDocument::createModel() 
-   * or @if clike SBMLDocument::setModel() @endif@... python SBMLDocument::setModel() @endif@... java SBMLDocument::setModel(Model m) @endif.
+   * or SBMLDocument::setModel(@if java Model m@...).
    * This method returns @c NULL if a model does not yet exist.
    * 
    * @return the Model contained in this SBMLDocument.
@@ -470,7 +470,7 @@
    * It is important to note that this method <em>does not create</em> a
    * Model instance.  The model in the SBMLDocument must have been created
    * at some prior time, for example using SBMLDocument::createModel() 
-   * or @if clike SBMLDocument::setModel() @endif@... python SBMLDocument::setModel() @endif@... java SBMLDocument::setModel(Model m) @endif.
+   * or SBMLDocument::setModel(@if java Model m@...).
    * This method returns @c NULL if a model does not yet exist.
    * 
    * @return the Model contained in this SBMLDocument.
@@ -635,7 +635,7 @@
    * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
    *
    * @see getModel()
-   * @see @if clike SBMLDocument::setModel() @endif@... python SBMLDocument::setModel() @endif@... java SBMLDocument::setModel(Model m) @endif
+   * @see SBMLDocument::setModel(@if java Model m@...)
    */
   Model* createModel (const std::string& sid = "");
 
@@ -714,16 +714,20 @@
    * </ul>
    * 
    * <em>By default, all validation checks are applied</em> to the model in
-   * an SBMLDocument object @em unless @if clike SBMLDocument::setConsistencyChecks() @endif@... python SBMLDocument::setConsistencyChecks() @endif@... java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @endif is called to
-   * indicate that only a subset should be applied.  Further, this default
-   * (i.e., performing all checks) applies separately to <em>each new
-   * SBMLDocument object</em> created.  In other words, each time a model
-   * is read using @if clike SBMLReader::readSBML() @endif@... python SBMLReader::readSBML() @endif@... java SBMLReader::readSBML(String filename) @endif, @if clike SBMLReader::readSBMLFromString() @endif@... python SBMLReader::readSBMLFromString() @endif@... java SBMLReader::readSBMLFromString(String xml) @endif,
+   * an SBMLDocument object @em unless
+   * SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@...)
+   * is called to indicate that only a subset should be applied.  Further,
+   * this default (i.e., performing all checks) applies separately to
+   * <em>each new SBMLDocument object</em> created.  In other words, each
+   * time a model is read using SBMLReader::readSBML(@if java String filename@...),
+   * SBMLReader::readSBMLFromString(@if java String xml@...),
    * or the global functions readSBML() and readSBMLFromString(), a new
    * SBMLDocument is created and for that document, a call to
    * SBMLDocument::checkConsistency() will default to applying all possible checks.
-   * Calling programs must invoke @if clike SBMLDocument::setConsistencyChecks() @endif@... python SBMLDocument::setConsistencyChecks() @endif@... java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @endif for each such new
-   * model if they wish to change the consistency checks applied.
+   * Calling programs must invoke
+   * SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@...)
+   * for each such new model if they wish to change the consistency checks
+   * applied.
    * 
    * @param category a value drawn from #SBMLErrorCategory_t indicating the
    * consistency checking/validation to be turned on or off
@@ -810,16 +814,20 @@
    * </ul>
    * 
    * <em>By default, all validation checks are applied</em> to the model in
-   * an SBMLDocument object @em unless @if clike SBMLDocument::setConsistencyChecks() @endif@... python SBMLDocument::setConsistencyChecks() @endif@... java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @endif is called to
-   * indicate that only a subset should be applied.  Further, this default
-   * (i.e., performing all checks) applies separately to <em>each new
-   * SBMLDocument object</em> created.  In other words, each time a model
-   * is read using @if clike SBMLReader::readSBML() @endif@... python SBMLReader::readSBML() @endif@... java SBMLReader::readSBML(String filename) @endif, @if clike SBMLReader::readSBMLFromString() @endif@... python SBMLReader::readSBMLFromString() @endif@... java SBMLReader::readSBMLFromString(String xml) @endif,
+   * an SBMLDocument object @em unless
+   * SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@...)
+   * is called to indicate that only a subset should be applied.  Further,
+   * this default (i.e., performing all checks) applies separately to
+   * <em>each new SBMLDocument object</em> created.  In other words, each
+   * time a model is read using SBMLReader::readSBML(@if java String filename@...),
+   * SBMLReader::readSBMLFromString(@if java String xml@...),
    * or the global functions readSBML() and readSBMLFromString(), a new
    * SBMLDocument is created and for that document, a call to
    * SBMLDocument::checkConsistency() will default to applying all possible checks.
-   * Calling programs must invoke @if clike SBMLDocument::setConsistencyChecks() @endif@... python SBMLDocument::setConsistencyChecks() @endif@... java SBMLDocument::setConsistencyChecks(int categ, boolean onoff) @endif for each such new
-   * model if they wish to change the consistency checks applied.
+   * Calling programs must invoke
+   * SBMLDocument::setConsistencyChecks(@if java int categ, boolean onoff@...)
+   * for each such new model if they wish to change the consistency checks
+   * applied.
    * 
    * @param category a value drawn from #SBMLErrorCategory_t indicating the
    * consistency checking/validation to be turned on or off
@@ -827,7 +835,7 @@
    * @param apply a boolean indicating whether the checks indicated by
    * @p category should be applied or not.
    *
-   * @see @if clike SBMLDocument::setLevelAndVersion() @endif@... python SBMLDocument::setLevelAndVersion() @endif@... java SBMLDocument::setLevelAndVersion(long lev, long ver, boolean strict) @endif
+   * @see SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@...)
    */
   void setConsistencyChecksForConversion(SBMLErrorCategory_t category, 
                                          bool apply);
@@ -840,7 +848,7 @@
    * consistency checks have failed for SBML document), the failures may be
    * due to warnings @em or errors.  Callers should inspect the severity
    * flag in the individual SBMLError objects returned by
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif to determine the nature of the failures.
+   * SBMLDocument::getError(@if java long n@...) to determine the nature of the failures.
    *
    * @return the number of failed checks (errors) encountered.
    *
@@ -854,7 +862,7 @@
    * an SBML Model.
    *
    * Callers should query the results of the consistency check by calling
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif.
+   * SBMLDocument::getError(@if java long n@...).
    *
    * @return the number of failed checks (errors) encountered.
    *
@@ -877,7 +885,7 @@
    * to Level&nbsp;1.
    *
    * Callers should query the results of the consistency check by calling
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif.
+   * SBMLDocument::getError(@if java long n@...).
    *
    * @return the number of failed checks (errors) encountered.
    */
@@ -890,7 +898,7 @@
    * be converted to Level&nbsp;2 Version&nbsp;1.
    *
    * Callers should query the results of the consistency check by calling
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif.
+   * SBMLDocument::getError(@if java long n@...).
    *
    * @return the number of failed checks (errors) encountered.
    */
@@ -903,7 +911,7 @@
    * be converted to Level&nbsp;2 Version&nbsp;2.
    *
    * Callers should query the results of the consistency check by calling
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif.
+   * SBMLDocument::getError(@if java long n@...).
    *
    * @return the number of failed checks (errors) encountered.
    */
@@ -916,7 +924,7 @@
    * be converted to Level&nbsp;2 Version&nbsp;3.
    *
    * Callers should query the results of the consistency check by calling
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif.
+   * SBMLDocument::getError(@if java long n@...).
    *
    * @return the number of failed checks (errors) encountered.
    */
@@ -929,7 +937,7 @@
    * be converted to Level&nbsp;2 Version&nbsp;4.
    *
    * Callers should query the results of the consistency check by calling
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif.
+   * SBMLDocument::getError(@if java long n@...).
    *
    * @return the number of failed checks (errors) encountered.
    */
@@ -942,7 +950,7 @@
    * be converted to Level&nbsp;3 Version&nbsp;1.
    *
    * Callers should query the results of the consistency check by calling
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif.
+   * SBMLDocument::getError(@if java long n@...).
    *
    * @return the number of failed checks (errors) encountered.
    */

Modified: trunk/libsbml/src/sbml/SBMLError.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLError.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/SBMLError.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -1054,7 +1054,7 @@
    * filled-in as well from the enumerations <a class="el"
    * href="#SBMLErrorSeverity_t">SBMLErrorSeverity_t</a> and <a class="el"
    * href="#SBMLErrorCategory_t">SBMLErrorCategory_t</a>,
-   * respectively. @endif@... notcpp set of constants.  If it @em
+   * respectively. @else set of constants.  If it @em
    * is one of the predefined error identifiers, the SBMLError class
    * assumes the error is a low-level system or SBML layer error and
    * <em>prepends</em> a built-in, predefined error message to any string
@@ -1087,7 +1087,7 @@
    * href="#SBMLErrorSeverity_t">SBMLErrorSeverity_t</a> and <a class="el"
    * href="#SBMLErrorCategory_t">SBMLErrorCategory_t</a>, but their own
    * special values) for @p severity and 
-   * @p category. @endif@... notcpp As mentioned above, 
+   * @p category. @else As mentioned above, 
    * there are additional constants defined for <a class="el"
    * href="#SBMLErrorSeverity_t">standard severity</a> and <a class="el"
    * href="#SBMLErrorCategory_t">standard category</a> codes, and every predefined 

Modified: trunk/libsbml/src/sbml/SBMLErrorLog.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorLog.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/SBMLErrorLog.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -43,18 +43,18 @@
  * SBMLErrorLog is derived from XMLErrorLog, an object class that serves
  * exactly the same purpose but for the XML parsing layer.  XMLErrorLog
  * provides crucial methods such as
- * @if clike getNumErrors()@endif@... python getNumErrors()@endif@... java XMLErrorLog::getNumErrors()@endif
+ * @if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif
  * for determining how many SBMLError or XMLError objects are in the log.
  * SBMLErrorLog inherits these methods.
  *
  * The general approach to working with SBMLErrorLog in user programs
  * involves first obtaining a pointer to a log from a libSBML object such
  * as SBMLDocument.  Callers should then use
- * @if clike getNumErrors()@endif@... python getNumErrors()@endif@... java XMLErrorLog::getNumErrors()@endif to inquire how
+ * @if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif to inquire how
  * many objects there are in the list.  (The answer may be 0.)  If there is
  * at least one SBMLError object in the SBMLErrorLog instance, callers can
  * then iterate over the list using
- * @if clike getError(unsigned int)@endif@... python getError(unsigned int)@endif@... java SBMLErrorLog::getError(long n)@endif@... clike const@...,
+ * SBMLErrorLog::getError(@if java long n@... clike const@...,
  * using methods provided by the SBMLError class to find out the error code
  * and associated information such as the error severity, the message, and
  * the line number in the input.
@@ -90,7 +90,7 @@
    *
    * Index @p n is counted from 0.  Callers should first inquire about the
    * number of items in the log by using the
-   * @if clike getNumErrors()@endif@... python getNumErrors()@endif@... java XMLErrorLog::getNumErrors()@endif method.
+   * @if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif method.
    * Attempts to use an error index number that exceeds the actual number
    * of errors in the log will result in a @c NULL being returned.
    *
@@ -99,7 +99,7 @@
    *
    * @return the <i>n</i>th SBMLError in this log, or @c NULL if @p n is
    * greater than or equal to
-   * @if clike getNumErrors()@endif@... python getNumErrors()@endif@... java XMLErrorLog::getNumErrors()@endif.
+   * @if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif.
    *
    * @see getNumErrors()
    */

Modified: trunk/libsbml/src/sbml/SBMLNamespaces.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLNamespaces.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/SBMLNamespaces.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -253,7 +253,7 @@
     // Handle another truly exceptional situation.
 }
 @endverbatim
-@... java
+   * @endif@... java
 @verbatim
 SBMLDocument sd;
 try 
@@ -276,9 +276,9 @@
 else
 {
     // Handle another truly exceptional situation.
-}
+ }
 @endverbatim
-@...
+   * @endif
    * 
    * @param xmlns the XML namespaces to be added.
    */

Modified: trunk/libsbml/src/sbml/SBMLReader.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLReader.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/SBMLReader.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -46,12 +46,12 @@
  *
  * For convenience as well as easy access from other languages besides C++,
  * this file also defines two global functions,
- * @if clike readSBMLFromFile()@endif@... python readSBMLFromFile()@endif@... java libsbml::readSBML(String filename)@endif
- * and @if clike readSBMLFromString()@endif@... python readSBMLFromString()@endif@... java libsbml::readSBMLFromString(String xml)@endif.
+ * libsbml::readSBML(@if java String filename@...)
+ * and libsbml::readSBMLFromString(@if java String xml@...).
  * They are equivalent to creating an SBMLReader
  * object and then calling the
- * @if clike SBMLReader::readSBML()@endif@... python SBMLReader::readSBML()@endif@... java SBMLReader::readSBML(String filename)@endif or
- * @if clike SBMLReader::readSBMLFromString()@endif@... python SBMLReader::readSBMLFromString()@endif@... java SBMLReader::readSBMLFromString(String xml)@endif
+ * SBMLReader::readSBML(@if java String filename@...) or
+ * SBMLReader::readSBMLFromString(@if java String xml@...)
  * methods, respectively.
  *
  * @section compression Support for reading compressed files
@@ -72,8 +72,8 @@
  * zip formats) and/or @em bzip2 (for @em bzip2 format) be available on the
  * system running libSBML, and that libSBML was configured with their
  * support compiled-in.  Please see the libSBML @if clike <a href="libsbml-installation.html">installation instructions</a> @endif@... python <a href="libsbml-installation.html">installation instructions</a> @endif@... java  <a href="../../../libsbml-installation.html">installation instructions</a> @endif for more information about this.  The methods
- * @if clike hasZlib()@endif@... python hasZlib()@endif@... java SBMLReader::hasZlib()@endif and
- * @if clike hasBzip2()@endif@... python hasBzip2()@endif@... java SBMLReader::hasBzip2()@endif
+ * @if java SBMLReader::hasZlib()@else hasZlib()@endif and
+ * @if java SBMLReader::hasBzip2()@else hasBzip2()@endif
  * can be used by an application to query at run-time whether support
  * for the compression libraries is available in the present copy of
  * libSBML.
@@ -130,8 +130,8 @@
    * valid SBML, one or more errors will be logged with the SBMLDocument
    * object returned by this method.  Callers can use the methods on
    * SBMLDocument such as SBMLDocument::getNumErrors() and
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif to get the errors.  The object returned by
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif is an SBMLError object, and it has methods to
+   * SBMLDocument::getError(@if java long n@...) to get the errors.  The object returned by
+   * SBMLDocument::getError(@if java long n@...) is an SBMLError object, and it has methods to
    * get the error code, category, and severity level of the problem, as
    * well as a textual description of the problem.  The possible severity
    * levels range from informational messages to fatal errors; see the
@@ -146,63 +146,63 @@
    * by the underlying operating system.  Callers can check for these
    * situations using a program fragment such as the following:
    * @if clike
-@...
-SBMLReader* reader = new SBMLReader();
-SBMLDocument* doc  = reader.readSBMLFromFile(filename);
-
-if (doc->getNumErrors() > 0)
-{
-  if (doc->getError(0)->getErrorId() == XMLError::FileUnreadable)
-  {
-    // Handle case of unreadable file here.
-  } 
-  else if (doc->getError(0)->getErrorId() == XMLError::FileOperationError)
-  {
-    // Handle case of other file operation error here.
-  }
-  else
-  {
-    // Handle other cases -- see error codes defined in XMLErrorCode_t
-    // for other possible cases to check.
-  }
-}
-@...
-@... java
-@...
-SBMLReader reader = new SBMLReader();
-SBMLDocument doc  = reader.readSBMLFromFile(filename);
-
-if (doc.getNumErrors() > 0)
-{
-    if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileUnreadable)
-    {
-        // Handle case of unreadable file here.
-    } 
-    else if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileOperationError)
-    {
-        // Handle case of other file operation error here.
-    }
-    else
-    {
-        // Handle other error cases.
-    }
-}
-@...
-@... python
-@...
-reader = SBMLReader()
-doc    = reader.readSBMLFromFile(filename)
-
-if doc.getNumErrors() > 0:
-  if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
-    # Handle case of unreadable file here.
-  elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
-    # Handle case of other file error here.
-  else:
-    # Handle other error cases here.
-  
-@...
-@...
+ @verbatim
+ SBMLReader* reader = new SBMLReader();
+ SBMLDocument* doc  = reader.readSBMLFromFile(filename);
+ 
+ if (doc->getNumErrors() > 0)
+ {
+   if (doc->getError(0)->getErrorId() == XMLError::FileUnreadable)
+   {
+     // Handle case of unreadable file here.
+   } 
+   else if (doc->getError(0)->getErrorId() == XMLError::FileOperationError)
+   {
+     // Handle case of other file operation error here.
+   }
+   else
+   {
+     // Handle other cases -- see error codes defined in XMLErrorCode_t
+     // for other possible cases to check.
+   }
+ }
+ @endverbatim
+ @endif@... java
+ @verbatim
+ SBMLReader reader = new SBMLReader();
+ SBMLDocument doc  = reader.readSBMLFromFile(filename);
+ 
+ if (doc.getNumErrors() > 0)
+ {
+     if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileUnreadable)
+     {
+         // Handle case of unreadable file here.
+     } 
+     else if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileOperationError)
+     {
+         // Handle case of other file operation error here.
+     }
+     else
+     {
+         // Handle other error cases.
+     }
+ }
+ @endverbatim
+ @endif@... python
+ @verbatim
+ reader = SBMLReader()
+ doc    = reader.readSBMLFromFile(filename)
+ 
+ if doc.getNumErrors() > 0:
+   if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
+     # Handle case of unreadable file here.
+   elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
+     # Handle case of other file error here.
+   else:
+     # Handle other error cases here.
+   
+ @endverbatim
+ @endif
    *
    * If the given filename ends with the suffix @c ".gz" (for example, @c
    * "myfile.xml.gz"), the file is assumed to be compressed in @em gzip
@@ -250,8 +250,8 @@
    * valid SBML, one or more errors will be logged with the SBMLDocument
    * object returned by this method.  Callers can use the methods on
    * SBMLDocument such as SBMLDocument::getNumErrors() and
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif to get the errors.  The object returned by
-   * @if clike SBMLDocument::getError() @endif@... python SBMLDocument::getError() @endif@... java SBMLDocument::getError(long n) @endif is an SBMLError object, and it has methods to
+   * SBMLDocument::getError(@if java long n@...) to get the errors.  The object returned by
+   * SBMLDocument::getError(@if java long n@...) is an SBMLError object, and it has methods to
    * get the error code, category, and severity level of the problem, as
    * well as a textual description of the problem.  The possible severity
    * levels range from informational messages to fatal errors; see the
@@ -266,63 +266,63 @@
    * by the underlying operating system.  Callers can check for these
    * situations using a program fragment such as the following:
    * @if clike
-@...
-SBMLReader* reader = new SBMLReader();
-SBMLDocument* doc  = reader.readSBML(filename);
-
-if (doc->getNumErrors() > 0)
-{
-  if (doc->getError(0)->getErrorId() == XMLError::FileUnreadable)
-  {
-    // Handle case of unreadable file here.
-  } 
-  else if (doc->getError(0)->getErrorId() == XMLError::FileOperationError)
-  {
-    // Handle case of other file operation error here.
-  }
-  else
-  {
-    // Handle other cases -- see error codes defined in XMLErrorCode_t
-    // for other possible cases to check.
-  }
-}
-@...
-@... java
-@...
-SBMLReader reader = new SBMLReader();
-SBMLDocument doc  = reader.readSBMLFromFile(filename);
-
-if (doc.getNumErrors() > 0)
-{
-    if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileUnreadable)
-    {
-        // Handle case of unreadable file here.
-    } 
-    else if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileOperationError)
-    {
-        // Handle case of other file operation error here.
-    }
-    else
-    {
-        // Handle other error cases.
-    }
-}
-@...
-@... python
-@...
-reader = SBMLReader()
-doc    = reader.readSBMLFromFile(filename)
-
-if doc.getNumErrors() > 0:
-  if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
-    # Handle case of unreadable file here.
-  elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
-    # Handle case of other file error here.
-  else:
-    # Handle other error cases here.
-  
-@...
-@...
+ @verbatim
+ SBMLReader* reader = new SBMLReader();
+ SBMLDocument* doc  = reader.readSBML(filename);
+ 
+ if (doc->getNumErrors() > 0)
+ {
+   if (doc->getError(0)->getErrorId() == XMLError::FileUnreadable)
+   {
+     // Handle case of unreadable file here.
+   } 
+   else if (doc->getError(0)->getErrorId() == XMLError::FileOperationError)
+   {
+     // Handle case of other file operation error here.
+   }
+   else
+   {
+     // Handle other cases -- see error codes defined in XMLErrorCode_t
+     // for other possible cases to check.
+   }
+ }
+ @endverbatim
+ @endif@... java
+ @verbatim
+ SBMLReader reader = new SBMLReader();
+ SBMLDocument doc  = reader.readSBMLFromFile(filename);
+ 
+ if (doc.getNumErrors() > 0)
+ {
+     if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileUnreadable)
+     {
+         // Handle case of unreadable file here.
+     } 
+     else if (doc.getError(0).getErrorId() == libsbmlConstants.XMLFileOperationError)
+     {
+         // Handle case of other file operation error here.
+     }
+     else
+     {
+         // Handle other error cases.
+     }
+ }
+ @endverbatim
+ @endif@... python
+ @verbatim
+ reader = SBMLReader()
+ doc    = reader.readSBMLFromFile(filename)
+ 
+ if doc.getNumErrors() > 0:
+   if doc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
+     # Handle case of unreadable file here.
+   elif doc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
+     # Handle case of other file error here.
+   else:
+     # Handle other error cases here.
+   
+ @endverbatim
+ @endif
    *
    * If the given filename ends with the suffix @c ".gz" (for example, @c
    * "myfile.xml.gz"), the file is assumed to be compressed in @em gzip
@@ -373,14 +373,14 @@
    *
    * This method will log a fatal error if the content given in the
    * parameter @p xml is not SBML.  See the method documentation for
-   * @if clike SBMLReader::readSBML()@endif@... python SBMLReader::readSBML()@endif@... java SBMLReader::readSBML(String filename)@endif
+   * SBMLReader::readSBML(@if java String filename@...)
    * for an example of code for testing the returned error code.
    *
    * @param xml a string containing a full SBML model
    *
    * @return a pointer to the SBMLDocument created from the SBML content.
    *
-   * @if clike @see SBMLReader::readSBML()@endif@... python @see SBMLReader::readSBML()@endif@... java @see SBMLReader::readSBML(String filename)@endif
+   * @see SBMLReader:@if java :readSBML(String filename@...)
    */
   SBMLDocument* readSBMLFromString (const std::string& xml);
 

Modified: trunk/libsbml/src/sbml/SBMLWriter.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLWriter.h	2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/SBMLWriter.h	2011-02-27 05:16:27 UTC (rev 13063)
@@ -60,8 +60,8 @@
  * system running libSBML, and that libSBML was configured with their
  * support compiled-in.  Please see the libSBML @if clike <a href="libsbml-installation.html">installation instructions</a>@endif@... python <a href="libsbml-installation.html">installation instructions</a>@endif@... java  <a href="../../../libsbml-installation.html">installation instructions</a>@endif for 
  * more information about this.  The methods
- * @if clike hasZlib()@endif@... python hasZlib()@endif@... java SBMLWriter::hasZlib()@endif and
- * @if clike hasBzip2()@endif@... python hasBzip2()@endif@... java SBMLWriter::hasBzip2()@endif
+ * SBMLWriter::hasZlib() and
+ * SBMLWriter::hasBzip2()
  * can be used by an application to query at run-time whether support
  * for the compression libraries is available in the present copy of
  * libSBML.
@@ -114,7 +114,7 @@
    * write out the SBMLDocument.
    *
    * If the program name and version are set (see
-   * @if clike setProgramVersion()@endif@... python setProgramVersion()@endif@... java SBMLWriter::setProgramVersion(String version)@endif), the
+   * SBMLWriter::setProgramVersion(@if java String version@...)), the
    * following XML comment, intended for human consumption, will be written
    * at the beginning of the XML document:
    * @verbatim
@@ -143,7 +143,7 @@
    * write out the SBMLDocument.
    *
    * If the program version and name are set (see
-   * @if clike setProgramName()@endif@... python setProgramName()@endif@... java SBMLWriter::setProgramName(String name)@endif), the
+   * SBMLWriter::setProgramName(@if java String name@...)), the
    * following XML comment, intended for human consumption, will be written
    * at the beginning of the document:
    * @verbatim
@@ -449,8 +449,8 @@
  * should be freed (with the normal string <code>free()</code> C++
  * function) after it is no longer needed.@...
  *
- * @if clike @see hasZlib()@endif@... python @see hasZlib()@endif@... java @see SBMLWriter::hasZlib()@endif
- * @if clike @see hasBzip2()@endif@... python @see hasBzip2()@endif@... java @see SBMLWriter::hasBzip2()@endif
+ * @see SBMLWriter::hasZlib()
+ * @see SBMLWriter::hasBzip2()
  */
 LIBSBML_EXTERN
 int
@@ -505,8 +505,8 @@
  * should be freed (with the normal string <code>free()</code> C++
  * function) after it is no longer needed.@...
  *
- * @if clike @see hasZlib()@endif@... python @see hasZlib()@endif@... java @see SBMLWriter::hasZlib()@endif
- * @if clike @see hasBzip2()@endif@... python @see hasBzip2()@endif@... java @see SBMLWriter::hasBzip2()@endif
+ * @see SBMLWriter::hasZlib()
+ * @see SBMLWriter::hasBzip2()
  */
 LIBSBML_EXTERN
 int

Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h	2011-02-27 05:14:17 UTC (rev 13062)

@@ Diff output truncated at 100000 characters. @@

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 13064
          http://sbml.svn.sourceforge.net/sbml/?rev=13064&view=rev
Author:   mhucka
Date:     2011-02-27 05:53:08 +0000 (Sun, 27 Feb 2011)

Log Message:
-----------
Added code examples for python.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/Model.h
    trunk/libsbml/src/sbml/SBMLNamespaces.h
    trunk/libsbml/src/xml/XMLNode.h

Modified: trunk/libsbml/src/sbml/Model.h
===================================================================
--- trunk/libsbml/src/sbml/Model.h	2011-02-27 05:16:27 UTC (rev 13063)
+++ trunk/libsbml/src/sbml/Model.h	2011-02-27 05:53:08 UTC (rev 13064)
@@ -118,7 +118,7 @@
 // of the object attached to the model (as expected).
 
 Model* model = sbmlDoc->createModel();
-model->setId("BestModelEver");
+model->setId("BestModelEver");
 
 // Create a Species object inside the Model and set its identifier.
 // Similar to the lines above, this call returns a pointer to the Species
@@ -126,7 +126,7 @@
 // of the object attached to the model (as expected).
 
 Species *sp = model->createSpecies();
-sp->setId("MySpecies");
+sp->setId("MySpecies");
 @endverbatim
  * @endif@... java
 @verbatim
@@ -137,7 +137,9 @@
 // Create a Model object inside the SBMLDocument object and set
 // its identifier.  The call returns a pointer to the Model object
 // created, and methods called on that object affect the attributes
-// of the object attached to the model (as expected).
+// of the object attached to the model (as expected).  Note that
+// the call to setId() returns a status code, and a real program
+// should check this status code to make sure everything went okay.
 
 Model model = sbmlDoc.createModel();
 model.setId("BestModelEver");
@@ -145,67 +147,49 @@
 // Create a Species object inside the Model and set its identifier.
 // Similar to the lines above, this call returns a pointer to the Species
 // object created, and methods called on that object affect the attributes
-// of the object attached to the model (as expected).
+// of the object attached to the model (as expected).  Note that, like
+// with Model, the call to setId() returns a status code, and a real program
+// should check this status code to make sure everything went okay.
 
 Species sp = model.createSpecies();
 sp.setId("BestSpeciesEver");
 @endverbatim
+ * @endif@... python
+@verbatim
+# Create an SBMLDocument object in Level 3 Version 1 format:
+
+sbmlDoc = SBMLDocument(3, 1)
+
+# Create a Model object inside the SBMLDocument object and set
+# its identifier.  The call to setId() returns a status code
+# to indicate whether the assignment was successful.  Code 0
+# means success; see the documentation for Model's setId() for 
+# more information.
+
+model = sbmlDoc.createModel()
+model.setId("BestModelEver")
+
+# Create a Species object inside the Model and set its identifier.
+# Again, the setId() returns a status code to indicate whether the
+# assignment was successful.  Code 0 means success; see the
+# documentation for Specie's setId() for more information.
+
+sp = model.createSpecies()
+sp.setId("BestSpeciesEver")
+@endverbatim
  * @endif
  * 
  * The <code>create<span
  * class="placeholder"><em>Object</em></span>()</code> methods return a
  * pointer to the object created, but they also add the object to the
  * relevant list of object instances contained in the parent.  (These lists
- * become the <code>&lt;listOf<i>Object</i>s&gt;</code> elements in the
+ * become the <code>&lt;listOf<span
+ * class="placeholder"><em>Object</em></span>s&gt;</code> elements in the
  * finished XML rendition of SBML.)  In the example above,
  * Model::createSpecies() adds the created species directly to the
  * <code>&lt;listOfSpecies<i></i>&gt;</code> list in the model.  Subsequently,
  * methods called on the species change the species in the model (which is
  * what is expected in most situations).
- * 
- * By contrast, the other main way of creating an object and adding it to a
- * parent makes a @em copy of the object, and requires more care on the
- * part of the caller.  Here is an example of this alternative approach: @if clike
- * @verbatim
-// Create a Species object and add it to the model.
-// This uses the Species class constructor:
-
-Species *newsp = Species(&#34;BestSpeciesEver&#34;);
-model->addSpecies(newsp); // Warning! This makes a COPY inside 'model'.
-
-// addSpecies(...) copies the object, with the result that
-// 'newsp' still refers to the original.  The following may not
-// do what is expected:
-
-newsp->setId(&#34;NewId&#34;);    // Warning -- doesn't change the species in 'model'!
-
-// If 'newsp' object is not going to be used further, it needs
-// to be deleted to avoid a memory leak.
-
-delete newsp;
-@...
- * @endif@... java
-@...
-// Create a Species object and add it to the model.
-// This uses the Species class constructor:
-
-Species newsp = Species(&#34;BestSpeciesEver&#34;);
-model.addSpecies(newsp); // Warning! This makes a COPY inside 'model'.
-
-// addSpecies(...) copies the object, with the result that
-// 'newsp' still refers to the original.  The following may not
-// do what is expected:
-
-newsp.setId(&#34;NewId&#34;);    // Warning -- doesn't change the species in 'model'!
-@...
- * @endif
- * 
- * The key point of the example above is that, because the
- * @if java Model::addSpecies(Species s)@else Model::addSpecies()@endif
- * call makes a copy of the object handed to it, care is needed
- * @if clike both when attempting to make changes to the object, and when
- * the original object is no longer needed.@... when attempting to make
- * changes to the object.@...
  *
  * @section checking Consistency and adherence to SBML specifications
  *

Modified: trunk/libsbml/src/sbml/SBMLNamespaces.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLNamespaces.h	2011-02-27 05:16:27 UTC (rev 13063)
+++ trunk/libsbml/src/sbml/SBMLNamespaces.h	2011-02-27 05:53:08 UTC (rev 13064)
@@ -278,6 +278,23 @@
     // Handle another truly exceptional situation.
  }
 @endverbatim
+   * @endif@... python
+@verbatim
+sbmlDoc = SBMLDocument(3, 1)
+if sbmlDoc == None:
+  # Do something to handle exceptional situation.  Candidate
+  # causes include invalid combinations of SBML Level and Version
+  # (impossible if hardwired as given here), running out of memory, and
+  # unknown system exceptions.
+
+namespaces = sbmlDoc.getNamespaces()
+if namespaces == None:
+  # Do something to handle exceptional situation.
+
+status = namespaces.add("http://www.w3.org/1999/xhtml", "html")
+if status != LIBSBML_OPERATION_SUCCESS:
+  # Do something to handle exceptional situation.
+@endverbatim
    * @endif
    * 
    * @param xmlns the XML namespaces to be added.

Modified: trunk/libsbml/src/xml/XMLNode.h
===================================================================
--- trunk/libsbml/src/xml/XMLNode.h	2011-02-27 05:16:27 UTC (rev 13063)
+++ trunk/libsbml/src/xml/XMLNode.h	2011-02-27 05:53:08 UTC (rev 13064)
@@ -125,8 +125,19 @@
   ...
 }
 @endverbatim
+ * @endif@... python
+@verbatim
+xn = XMLNode.convertStringToXMLNode("<p></p>")
+if xn == None:
+  # Do something to handle exceptional situation.
+
+elif xn.isEOF():
+  # Node is a dummy node.
+
+else:
+  # None is not a dummy node.
+@endverbatim
  * @endif
- *
  */
 
 #ifndef XMLNode_h


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 13252
          http://sbml.svn.sourceforge.net/sbml/?rev=13252&view=rev
Author:   sarahkeating
Date:     2011-03-19 15:02:07 +0000 (Sat, 19 Mar 2011)

Log Message:
-----------
beginnings of logging an error for a required package and a warning for a non required package but not all the unknown element errors

NOTE: not working for layout yet as layout is special because libsbml-4 does already recognise the elements

Modified Paths:
--------------
    trunk/libsbml/src/sbml/SBMLDocument.cpp
    trunk/libsbml/src/sbml/SBMLError.h
    trunk/libsbml/src/sbml/SBMLErrorTable.h
    trunk/libsbml/src/sbml/SBMLNamespaces.cpp
    trunk/libsbml/src/sbml/SBMLNamespaces.h
    trunk/libsbml/src/sbml/SBase.cpp

Added Paths:
-----------
    trunk/libsbml/src/validator/test/test-data/10102-fail-01-27.xml
    trunk/libsbml/src/validator/test/test-data/10102-fail-01-28.xml
    trunk/libsbml/src/validator/test/test-data/10102-fail-01-29.xml
    trunk/libsbml/src/validator/test/test-data/99107-fail-01-02.xml
    trunk/libsbml/src/validator/test/test-data/99107-fail-01-03.xml
    trunk/libsbml/src/validator/test/test-data/99107-fail-01-04-10102.xml
    trunk/libsbml/src/validator/test/test-data/99108-fail-01-01.xml
    trunk/libsbml/src/validator/test/test-data/99108-fail-01-02.xml
    trunk/libsbml/src/validator/test/test-data/99108-fail-02-03-99107.xml

Removed Paths:
-------------
    trunk/libsbml/src/validator/test/test-data/10102-fail-01-26.xml
    trunk/libsbml/src/validator/test/test-data/99107-fail-01-01-10102.xml
    trunk/libsbml/src/validator/test/test-data/99107-fail-01-02-10102.xml

Modified: trunk/libsbml/src/sbml/SBMLDocument.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.cpp	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/sbml/SBMLDocument.cpp	2011-03-19 15:02:07 UTC (rev 13252)
@@ -2593,26 +2593,40 @@
     {
       // look for a required package and report that one exists
       bool required = false;
-      int ns = 0;
+      int j = 0;
       do
       {
-        if (attributes.getName(ns) == "required")
+        if (attributes.getName(j) == "required")
         {
-          const XMLTriple *triple = new XMLTriple(attributes.getName(ns), 
-            attributes.getURI(ns), attributes.getPrefix(ns));
+          const XMLTriple *triple = new XMLTriple(attributes.getName(j), 
+            attributes.getURI(j), attributes.getPrefix(j));
           attributes.readInto(*triple, required);
+          // look to see if the namespace might be a valid L3 package
+          size_t pos = attributes.getURI(j).find(
+                                    "http://www.sbml.org/sbml/level3/version");
+          if (pos == 0)
+          { // we have found a URI that could be L3 package
+            mSBMLNamespaces->addPackagePrefix(attributes.getPrefix(j));
+       
+            ostringstream msg;
+          
+            if (required)
+            {
+              msg << "Package '" << attributes.getPrefix(j) << 
+                "' is a required package.";
+              logError(RequiredPackagePresent, mLevel, mVersion, msg.str());
+            }
+            else
+            {
+              msg << "Package '" << attributes.getPrefix(j) << 
+                "' is not a required package.";
+              logError(UnrequiredPackagePresent, mLevel, mVersion, msg.str());
+            }
+          }
         }
-        ns++;
-      } while (!required && ns < attributes.getLength());
+        j++;
+      } while (j < attributes.getLength());
 
-      if (required)
-      {
-        ostringstream msg;
-
-        msg << "Package '" << attributes.getPrefix(ns-1) << "' is a required package.";
-            
-        logError(RequiredPackagePresent, mLevel, mVersion, msg.str());
-      }
     }
 
   }

Modified: trunk/libsbml/src/sbml/SBMLError.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLError.h	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/sbml/SBMLError.h	2011-03-19 15:02:07 UTC (rev 13252)
@@ -821,6 +821,7 @@
  , AnnotationNotesNotAllowedLevel1       = 99104 /*!< Annotation on <code>&lt;sbml&gt;</code> not permitted in SBML Level&nbsp;1 */
  , InvalidRuleOrdering                   = 99106 /*!< Invalid ordering of rules */
  , RequiredPackagePresent                = 99107 /*!< Model requires an L3 package */
+ , UnrequiredPackagePresent              = 99108 /*!< Possible L3 package detected */
 
  , SubsUnitsAllowedInKL                  = 99127 /*!< Disallowed value for attribute <code>substanceUnits</code> */
  , TimeUnitsAllowedInKL                  = 99128 /*!< Disallowed value for attribute <code>timeUnits</code> */

Modified: trunk/libsbml/src/sbml/SBMLErrorTable.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorTable.h	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/sbml/SBMLErrorTable.h	2011-03-19 15:02:07 UTC (rev 13252)
@@ -7829,6 +7829,25 @@
     "mathematical interpretation of the model. (L3V1 Section 4.1.2)."
   },
 
+  //99108
+  {
+    UnrequiredPackagePresent,
+    "Possible L3 package detected",
+    LIBSBML_CAT_GENERAL_CONSISTENCY,
+    LIBSBML_SEV_NOT_APPLICABLE,
+    LIBSBML_SEV_NOT_APPLICABLE,
+    LIBSBML_SEV_NOT_APPLICABLE,
+    LIBSBML_SEV_NOT_APPLICABLE,
+    LIBSBML_SEV_NOT_APPLICABLE,
+    LIBSBML_SEV_NOT_APPLICABLE,
+    LIBSBML_SEV_WARNING,
+    "Every SBML Level 3 package is identified uniquely by an XML namespace "
+    "URI and defines the attribute named 'required'. LibSBML has detected "
+    "what appears to be an L3 unrequired package. The model will be correct "
+    "but the user should be aware that libSBML-4 does not attempt to read "
+    "or even store information from L3 packages(L3V1 Section 4.1.2)."
+  },
+
   //99127
   {
     SubsUnitsAllowedInKL,

Modified: trunk/libsbml/src/sbml/SBMLNamespaces.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLNamespaces.cpp	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/sbml/SBMLNamespaces.cpp	2011-03-19 15:02:07 UTC (rev 13252)
@@ -46,7 +46,9 @@
   mLevel = level;
   mVersion = version;
   mNamespaces = new XMLNamespaces();
+  mPackagePrefixes.clear();
 
+
   switch (level)
   {
   case 1:
@@ -123,6 +125,8 @@
             new XMLNamespaces(*const_cast<SBMLNamespaces&>(orig).mNamespaces);
     else
       this->mNamespaces = NULL;
+
+    mPackagePrefixes = orig.mPackagePrefixes;
   }
 }
 
@@ -161,6 +165,7 @@
             new XMLNamespaces(*const_cast<SBMLNamespaces&>(rhs).mNamespaces);
     else
       this->mNamespaces = NULL;
+    mPackagePrefixes = rhs.mPackagePrefixes;
   }
 
   return *this;
@@ -306,6 +311,35 @@
   else
     mNamespaces = NULL;
 }
+
+void 
+SBMLNamespaces::addPackagePrefix(std::string package_prefix)
+{
+  mPackagePrefixes.push_back(package_prefix);
+}
+
+std::string 
+SBMLNamespaces::getPackagePrefix(unsigned int index)
+{
+  return mPackagePrefixes.at(index);
+}
+
+bool 
+SBMLNamespaces::containsPackagePrefix(std::string package_prefix)
+{
+  bool found = false;
+  unsigned int i = 0;
+  while (!found && i < mPackagePrefixes.size())
+  {
+    if (mPackagePrefixes.at(i) == package_prefix)
+    {
+      found = true;
+    }
+    i++;
+  }
+  return found;
+}
+
 /** @endcond */
 /** @cond doxygen-c-only */
 

Modified: trunk/libsbml/src/sbml/SBMLNamespaces.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLNamespaces.h	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/sbml/SBMLNamespaces.h	2011-03-19 15:02:07 UTC (rev 13252)
@@ -335,6 +335,13 @@
 
 
   void setNamespaces(XMLNamespaces * xmlns);
+
+  void addPackagePrefix(std::string package_prefix);
+
+  std::string getPackagePrefix(unsigned int index);
+  
+  bool containsPackagePrefix(std::string package_prefix);
+
   /** @endcond */
 
 protected:  
@@ -343,6 +350,7 @@
   unsigned int    mLevel;
   unsigned int    mVersion;
   XMLNamespaces * mNamespaces;
+  std::vector<std::string> mPackagePrefixes;
 
   /** @endcond */
 };

Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/sbml/SBase.cpp	2011-03-19 15:02:07 UTC (rev 13252)
@@ -2944,7 +2944,12 @@
                    || readAnnotation(stream)
                    || readNotes(stream) ))
       {
-        logUnknownElement(next.getName(), getLevel(), getVersion());
+        // if this is an unknown element from possibly a L3 package we want 
+        // a different warning/error
+        if (!(mSBMLNamespaces->containsPackagePrefix(next.getPrefix())))
+        {
+          logUnknownElement(next.getName(), getLevel(), getVersion());
+        }
         stream.skipPastEnd( stream.next() );
       }
     }

Deleted: trunk/libsbml/src/validator/test/test-data/10102-fail-01-26.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10102-fail-01-26.xml	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/validator/test/test-data/10102-fail-01-26.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
-xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
-      appear:required="false">
-  <model>
-    <listOfCompartments>
-      <compartment id="c" constant="true" appear:shape="circle"/>
-    </listOfCompartments>
-    <appear:listOfShapes>
-      <appear:shape appear:id="circle"/>
-    </appear:listOfShapes>
-  </model>
-</sbml>

Added: trunk/libsbml/src/validator/test/test-data/10102-fail-01-27.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10102-fail-01-27.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10102-fail-01-27.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/version1">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Added: trunk/libsbml/src/validator/test/test-data/10102-fail-01-28.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10102-fail-01-28.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10102-fail-01-28.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/version1"
+      appear:required="false">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Added: trunk/libsbml/src/validator/test/test-data/10102-fail-01-29.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10102-fail-01-29.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10102-fail-01-29.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/version1"
+      appear:required="true">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Deleted: trunk/libsbml/src/validator/test/test-data/99107-fail-01-01-10102.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99107-fail-01-01-10102.xml	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/validator/test/test-data/99107-fail-01-01-10102.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
-xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
-      appear:required="false"
-xmlns:appear1="http://www.sbml.org/sbml/level3/version1/appear1/version1"
-      appear1:required="false"
-xmlns:appear2="http://www.sbml.org/sbml/level3/version1/appear2/version1"
-      appear2:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="c" constant="true" appear:shape="circle"/>
-    </listOfCompartments>
-    <appear:listOfShapes>
-      <appear:shape appear:id="circle"/>
-    </appear:listOfShapes>
-  </model>
-</sbml>

Deleted: trunk/libsbml/src/validator/test/test-data/99107-fail-01-02-10102.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99107-fail-01-02-10102.xml	2011-03-18 23:32:25 UTC (rev 13251)
+++ trunk/libsbml/src/validator/test/test-data/99107-fail-01-02-10102.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
-xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
-      appear:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="c" constant="true" appear:shape="circle"/>
-    </listOfCompartments>
-    <appear:listOfShapes>
-      <appear:shape appear:id="circle"/>
-    </appear:listOfShapes>
-  </model>
-</sbml>

Added: trunk/libsbml/src/validator/test/test-data/99107-fail-01-02.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99107-fail-01-02.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99107-fail-01-02.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
+      appear:required="true">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Added: trunk/libsbml/src/validator/test/test-data/99107-fail-01-03.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99107-fail-01-03.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99107-fail-01-03.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
+      appear:required="true">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Added: trunk/libsbml/src/validator/test/test-data/99107-fail-01-04-10102.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99107-fail-01-04-10102.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99107-fail-01-04-10102.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear1="http://www.sbml.org/sbml/level3/version1/appear/version1"
+      appear1:required="true" xmlns:appear="http://anything">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle" units="litre"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Added: trunk/libsbml/src/validator/test/test-data/99108-fail-01-01.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99108-fail-01-01.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99108-fail-01-01.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
+      appear:required="false">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle" size="1" units="litre"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Added: trunk/libsbml/src/validator/test/test-data/99108-fail-01-02.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99108-fail-01-02.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99108-fail-01-02.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
+      appear:required="false">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>

Added: trunk/libsbml/src/validator/test/test-data/99108-fail-02-03-99107.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99108-fail-02-03-99107.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99108-fail-02-03-99107.xml	2011-03-19 15:02:07 UTC (rev 13252)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"  level="3" version="1" 
+xmlns:appear="http://www.sbml.org/sbml/level3/version1/appear/version1"
+      appear:required="false"
+xmlns:appear1="http://www.sbml.org/sbml/level3/version1/appear1/version1"
+      appear1:required="false"
+xmlns:appear2="http://www.sbml.org/sbml/level3/version1/appear2/version1"
+      appear2:required="true">
+  <model>
+    <listOfCompartments>
+      <compartment id="c" constant="true" appear:shape="circle"/>
+    </listOfCompartments>
+    <appear:listOfShapes>
+      <appear:shape appear:id="circle"/>
+    </appear:listOfShapes>
+  </model>
+</sbml>


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Revision: 13253
          http://sbml.svn.sourceforge.net/sbml/?rev=13253&view=rev
Author:   sarahkeating
Date:     2011-03-20 10:30:47 +0000 (Sun, 20 Mar 2011)

Log Message:
-----------
finished the logging an error for a required package and a warning for a non required package but not all the unknown element errors

Modified Paths:
--------------
    trunk/libsbml/src/sbml/Model.cpp
    trunk/libsbml/src/sbml/SBMLDocument.cpp
    trunk/libsbml/src/sbml/SBMLErrorTable.h

Added Paths:
-----------
    trunk/libsbml/src/validator/test/test-data/99107-fail-01-05.xml
    trunk/libsbml/src/validator/test/test-data/99108-fail-01-04.xml

Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp	2011-03-19 15:02:07 UTC (rev 13252)
+++ trunk/libsbml/src/sbml/Model.cpp	2011-03-20 10:30:47 UTC (rev 13253)
@@ -4116,7 +4116,12 @@
     }
   }
 #ifdef USE_LAYOUT
-  else if ( name == "listOfLayouts"             ) object = &mLayouts;
+  else if ( name == "listOfLayouts"             ) 
+    // do not create an object in L3
+    if (level < 3)
+    {
+      object = &mLayouts;
+    }
 #endif /* USE_LAYOUT */  
 
   return object;

Modified: trunk/libsbml/src/sbml/SBMLDocument.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.cpp	2011-03-19 15:02:07 UTC (rev 13252)
+++ trunk/libsbml/src/sbml/SBMLDocument.cpp	2011-03-20 10:30:47 UTC (rev 13253)
@@ -2603,7 +2603,7 @@
           attributes.readInto(*triple, required);
           // look to see if the namespace might be a valid L3 package
           size_t pos = attributes.getURI(j).find(
-                                    "http://www.sbml.org/sbml/level3/version");
+                                    "http://www.sbml.org/sbml/level3/version1/");
           if (pos == 0)
           { // we have found a URI that could be L3 package
             mSBMLNamespaces->addPackagePrefix(attributes.getPrefix(j));
@@ -2618,8 +2618,8 @@
             }
             else
             {
-              msg << "Package '" << attributes.getPrefix(j) << 
-                "' is not a required package.";
+              msg << "Information from package '" << attributes.getPrefix(j) << 
+                "' will be lost.";
               logError(UnrequiredPackagePresent, mLevel, mVersion, msg.str());
             }
           }

Modified: trunk/libsbml/src/sbml/SBMLErrorTable.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorTable.h	2011-03-19 15:02:07 UTC (rev 13252)
+++ trunk/libsbml/src/sbml/SBMLErrorTable.h	2011-03-20 10:30:47 UTC (rev 13253)
@@ -7843,9 +7843,9 @@
     LIBSBML_SEV_WARNING,
     "Every SBML Level 3 package is identified uniquely by an XML namespace "
     "URI and defines the attribute named 'required'. LibSBML has detected "
-    "what appears to be an L3 unrequired package. The model will be correct "
-    "but the user should be aware that libSBML-4 does not attempt to read "
-    "or even store information from L3 packages(L3V1 Section 4.1.2)."
+    "what appears to be an L3 package with required=false. User should be "
+    "aware that libSBML-4 does not attempt to read "
+    "or even store information from L3 packages."
   },
 
   //99127

Added: trunk/libsbml/src/validator/test/test-data/99107-fail-01-05.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99107-fail-01-05.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99107-fail-01-05.xml	2011-03-20 10:30:47 UTC (rev 13253)
@@ -0,0 +1,195 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
+    xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+    layout:required="true">
+  <model id="TestModel_with_modifiers">
+    <listOfCompartments>
+      <compartment id="Yeast" constant="true" units="litre"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="Glucose" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="Glucose_6_phosphate" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="ATP" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="ADP" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="Pi" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+    </listOfSpecies>
+    <listOfReactions>
+      <reaction id="Hexokinase" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference id="SpeciesReference_Glucose" species="Glucose" constant="false"/>
+          <speciesReference id="SpeciesReference_ATP" species="ATP" constant="false"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference id="SpeciesReference_G6P" species="Glucose_6_phosphate" constant="false"/>
+          <speciesReference id="SpeciesReference_ADP" species="ADP" constant="false"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference id="ModifierSpeciesReference_G6P" species="Glucose_6_phosphate"/>
+          <modifierSpeciesReference id="ModifierSpeciesReference_Pi" species="Pi"/>
+        </listOfModifiers>
+      </reaction>
+    </listOfReactions>
+   <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+     <layout:layout id="Layout_1">
+       <layout:dimensions width="400" height="230"/>
+       <layout:listOfCompartmentGlyphs>
+         <layout:compartmentGlyph id="CompartmentGlyph_1" compartment="Yeast">
+           <layout:boundingBox id="bb1">
+             <layout:position x="5" y="5"/>
+             <layout:dimensions width="390" height="220"/>
+           </layout:boundingBox>
+         </layout:compartmentGlyph>
+       </layout:listOfCompartmentGlyphs>
+       <layout:listOfSpeciesGlyphs>
+         <layout:speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
+           <layout:boundingBox id="bb2">
+             <layout:position x="105" y="20"/>
+             <layout:dimensions width="130" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="SpeciesGlyph_G6P" species="Glucose_6_phosphate">
+           <layout:boundingBox id="bb5">
+             <layout:position x="50" y="190"/>
+             <layout:dimensions width="270" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="SpeciesGlyph_ATP" species="ATP">
+           <layout:boundingBox id="bb3">
+             <layout:position x="270" y="70"/>
+             <layout:dimensions width="80" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="glyph_ADP" species="ADP">
+           <layout:boundingBox id="bb4">
+             <layout:position x="270" y="140"/>
+             <layout:dimensions width="80" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="SpeciesGlyph_Pi" species="Pi">
+           <layout:boundingBox id="bb6">
+             <layout:position x="50" y="100"/>
+             <layout:dimensions width="60" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+       </layout:listOfSpeciesGlyphs>
+       <layout:listOfReactionGlyphs>
+         <layout:reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
+           <layout:curve>
+             <layout:listOfCurveSegments>
+               <layout:curveSegment xsi:type="LineSegment">
+                 <layout:start x="170" y="100"/>
+                 <layout:end x="170" y="130"/>
+               </layout:curveSegment>
+             </layout:listOfCurveSegments>
+           </layout:curve>
+           <layout:listOfSpeciesReferenceGlyphs>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_Glucose" speciesReference="SpeciesReference_Glucose" speciesGlyph="SpeciesGlyph_Glucose" role="substrate">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="LineSegment">
+                     <layout:start x="170" y="100"/>
+                     <layout:end x="170" y="50"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_ATP" speciesReference="SpeciesReference_ATP" speciesGlyph="SpeciesGlyph_ATP" role="sidesubstrate">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="170" y="100"/>
+                     <layout:end x="260" y="80"/>
+                     <layout:basePoint1 x="170" y="80"/>
+                     <layout:basePoint2 x="170" y="80"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_1" speciesReference="SpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P" role="product">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="LineSegment">
+                     <layout:start x="170" y="130"/>
+                     <layout:end x="170" y="180"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_ADP" speciesReference="SpeciesReference_ADP" speciesGlyph="glyph_ADP" role="sideproduct">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="170" y="130"/>
+                     <layout:end x="260" y="150"/>
+                     <layout:basePoint1 x="170" y="150"/>
+                     <layout:basePoint2 x="170" y="150"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_2" speciesReference="ModifierSpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P" role="inhibitor">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="45" y="200"/>
+                     <layout:end x="165" y="120"/>
+                     <layout:basePoint1 x="0" y="200"/>
+                     <layout:basePoint2 x="0" y="120"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_PI" speciesReference="ModifierSpeciesReference_Pi" speciesGlyph="SpeciesGlyph_Pi" role="activator">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="115" y="110"/>
+                     <layout:end x="165" y="110"/>
+                     <layout:basePoint1 x="140" y="110"/>
+                     <layout:basePoint2 x="140" y="110"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+           </layout:listOfSpeciesReferenceGlyphs>
+         </layout:reactionGlyph>
+       </layout:listOfReactionGlyphs>
+       <layout:listOfTextGlyphs>
+         <layout:textGlyph id="TextGlyph_Glucose" originOfText="Glucose" graphicalObject="SpeciesGlyph_Glucose">
+           <layout:boundingBox id="bbA">
+             <layout:position x="115" y="20"/>
+             <layout:dimensions width="110" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_G6P" originOfText="Glucose_6_phosphate" graphicalObject="SpeciesGlyph_G6P">
+           <layout:boundingBox id="bbD">
+             <layout:position x="60" y="190"/>
+             <layout:dimensions width="250" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_ATP" originOfText="ATP" graphicalObject="SpeciesGlyph_ATP">
+           <layout:boundingBox id="bbB">
+             <layout:position x="280" y="70"/>
+             <layout:dimensions width="60" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_ADP" originOfText="ADP" graphicalObject="glyph_ADP">
+           <layout:boundingBox id="bbC">
+             <layout:position x="280" y="140"/>
+             <layout:dimensions width="60" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_PI" originOfText="Pi" graphicalObject="SpeciesGlyph_Pi">
+           <layout:boundingBox id="bbE">
+             <layout:position x="60" y="100"/>
+             <layout:dimensions width="40" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+       </layout:listOfTextGlyphs>
+     </layout:layout>
+   </layout:listOfLayouts>
+  </model>
+</sbml>
+
+
+

Added: trunk/libsbml/src/validator/test/test-data/99108-fail-01-04.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/99108-fail-01-04.xml	                        (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/99108-fail-01-04.xml	2011-03-20 10:30:47 UTC (rev 13253)
@@ -0,0 +1,195 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
+    xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+    layout:required="false">
+  <model id="TestModel_with_modifiers">
+    <listOfCompartments>
+      <compartment id="Yeast" constant="true" units="litre"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="Glucose" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="Glucose_6_phosphate" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="ATP" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="ADP" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+      <species id="Pi" compartment="Yeast" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" substanceUnits="mole"/>
+    </listOfSpecies>
+    <listOfReactions>
+      <reaction id="Hexokinase" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference id="SpeciesReference_Glucose" species="Glucose" constant="false"/>
+          <speciesReference id="SpeciesReference_ATP" species="ATP" constant="false"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference id="SpeciesReference_G6P" species="Glucose_6_phosphate" constant="false"/>
+          <speciesReference id="SpeciesReference_ADP" species="ADP" constant="false"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference id="ModifierSpeciesReference_G6P" species="Glucose_6_phosphate"/>
+          <modifierSpeciesReference id="ModifierSpeciesReference_Pi" species="Pi"/>
+        </listOfModifiers>
+      </reaction>
+    </listOfReactions>
+   <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+     <layout:layout id="Layout_1">
+       <layout:dimensions width="400" height="230"/>
+       <layout:listOfCompartmentGlyphs>
+         <layout:compartmentGlyph id="CompartmentGlyph_1" compartment="Yeast">
+           <layout:boundingBox id="bb1">
+             <layout:position x="5" y="5"/>
+             <layout:dimensions width="390" height="220"/>
+           </layout:boundingBox>
+         </layout:compartmentGlyph>
+       </layout:listOfCompartmentGlyphs>
+       <layout:listOfSpeciesGlyphs>
+         <layout:speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
+           <layout:boundingBox id="bb2">
+             <layout:position x="105" y="20"/>
+             <layout:dimensions width="130" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="SpeciesGlyph_G6P" species="Glucose_6_phosphate">
+           <layout:boundingBox id="bb5">
+             <layout:position x="50" y="190"/>
+             <layout:dimensions width="270" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="SpeciesGlyph_ATP" species="ATP">
+           <layout:boundingBox id="bb3">
+             <layout:position x="270" y="70"/>
+             <layout:dimensions width="80" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="glyph_ADP" species="ADP">
+           <layout:boundingBox id="bb4">
+             <layout:position x="270" y="140"/>
+             <layout:dimensions width="80" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+         <layout:speciesGlyph id="SpeciesGlyph_Pi" species="Pi">
+           <layout:boundingBox id="bb6">
+             <layout:position x="50" y="100"/>
+             <layout:dimensions width="60" height="20"/>
+           </layout:boundingBox>
+         </layout:speciesGlyph>
+       </layout:listOfSpeciesGlyphs>
+       <layout:listOfReactionGlyphs>
+         <layout:reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
+           <layout:curve>
+             <layout:listOfCurveSegments>
+               <layout:curveSegment xsi:type="LineSegment">
+                 <layout:start x="170" y="100"/>
+                 <layout:end x="170" y="130"/>
+               </layout:curveSegment>
+             </layout:listOfCurveSegments>
+           </layout:curve>
+           <layout:listOfSpeciesReferenceGlyphs>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_Glucose" speciesReference="SpeciesReference_Glucose" speciesGlyph="SpeciesGlyph_Glucose" role="substrate">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="LineSegment">
+                     <layout:start x="170" y="100"/>
+                     <layout:end x="170" y="50"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_ATP" speciesReference="SpeciesReference_ATP" speciesGlyph="SpeciesGlyph_ATP" role="sidesubstrate">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="170" y="100"/>
+                     <layout:end x="260" y="80"/>
+                     <layout:basePoint1 x="170" y="80"/>
+                     <layout:basePoint2 x="170" y="80"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_1" speciesReference="SpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P" role="product">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="LineSegment">
+                     <layout:start x="170" y="130"/>
+                     <layout:end x="170" y="180"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_ADP" speciesReference="SpeciesReference_ADP" speciesGlyph="glyph_ADP" role="sideproduct">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="170" y="130"/>
+                     <layout:end x="260" y="150"/>
+                     <layout:basePoint1 x="170" y="150"/>
+                     <layout:basePoint2 x="170" y="150"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_2" speciesReference="ModifierSpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P" role="inhibitor">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="45" y="200"/>
+                     <layout:end x="165" y="120"/>
+                     <layout:basePoint1 x="0" y="200"/>
+                     <layout:basePoint2 x="0" y="120"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+             <layout:speciesReferenceGlyph id="SpeciesReferenceGlyph_PI" speciesReference="ModifierSpeciesReference_Pi" speciesGlyph="SpeciesGlyph_Pi" role="activator">
+               <layout:curve>
+                 <layout:listOfCurveSegments>
+                   <layout:curveSegment xsi:type="CubicBezier">
+                     <layout:start x="115" y="110"/>
+                     <layout:end x="165" y="110"/>
+                     <layout:basePoint1 x="140" y="110"/>
+                     <layout:basePoint2 x="140" y="110"/>
+                   </layout:curveSegment>
+                 </layout:listOfCurveSegments>
+               </layout:curve>
+             </layout:speciesReferenceGlyph>
+           </layout:listOfSpeciesReferenceGlyphs>
+         </layout:reactionGlyph>
+       </layout:listOfReactionGlyphs>
+       <layout:listOfTextGlyphs>
+         <layout:textGlyph id="TextGlyph_Glucose" originOfText="Glucose" graphicalObject="SpeciesGlyph_Glucose">
+           <layout:boundingBox id="bbA">
+             <layout:position x="115" y="20"/>
+             <layout:dimensions width="110" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_G6P" originOfText="Glucose_6_phosphate" graphicalObject="SpeciesGlyph_G6P">
+           <layout:boundingBox id="bbD">
+             <layout:position x="60" y="190"/>
+             <layout:dimensions width="250" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_ATP" originOfText="ATP" graphicalObject="SpeciesGlyph_ATP">
+           <layout:boundingBox id="bbB">
+             <layout:position x="280" y="70"/>
+             <layout:dimensions width="60" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_ADP" originOfText="ADP" graphicalObject="glyph_ADP">
+           <layout:boundingBox id="bbC">
+             <layout:position x="280" y="140"/>
+             <layout:dimensions width="60" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+         <layout:textGlyph id="TextGlyph_PI" originOfText="Pi" graphicalObject="SpeciesGlyph_Pi">
+           <layout:boundingBox id="bbE">
+             <layout:position x="60" y="100"/>
+             <layout:dimensions width="40" height="20"/>
+           </layout:boundingBox>
+         </layout:textGlyph>
+       </layout:listOfTextGlyphs>
+     </layout:layout>
+   </layout:listOfLayouts>
+  </model>
+</sbml>
+
+
+


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 13254
          http://sbml.svn.sourceforge.net/sbml/?rev=13254&view=rev
Author:   sarahkeating
Date:     2011-03-20 12:09:31 +0000 (Sun, 20 Mar 2011)

Log Message:
-----------
The isValidSBMLSId function returned true for an empty string. The reason for this was historical but it really is incorrect. The public function will now not return true and there is an internal version of the function that allows backward compatibility to be preserved.

Modified Paths:
--------------
    trunk/libsbml/src/math/ASTNode.cpp
    trunk/libsbml/src/sbml/Compartment.cpp
    trunk/libsbml/src/sbml/CompartmentType.cpp
    trunk/libsbml/src/sbml/Event.cpp
    trunk/libsbml/src/sbml/EventAssignment.cpp
    trunk/libsbml/src/sbml/FunctionDefinition.cpp
    trunk/libsbml/src/sbml/InitialAssignment.cpp
    trunk/libsbml/src/sbml/KineticLaw.cpp
    trunk/libsbml/src/sbml/Model.cpp
    trunk/libsbml/src/sbml/Parameter.cpp
    trunk/libsbml/src/sbml/Reaction.cpp
    trunk/libsbml/src/sbml/Rule.cpp
    trunk/libsbml/src/sbml/SBase.cpp
    trunk/libsbml/src/sbml/Species.cpp
    trunk/libsbml/src/sbml/SpeciesReference.cpp
    trunk/libsbml/src/sbml/SpeciesType.cpp
    trunk/libsbml/src/sbml/SyntaxChecker.cpp
    trunk/libsbml/src/sbml/SyntaxChecker.h
    trunk/libsbml/src/sbml/UnitDefinition.cpp
    trunk/libsbml/src/sbml/layout/BoundingBox.cpp
    trunk/libsbml/src/sbml/layout/GraphicalObject.cpp
    trunk/libsbml/src/sbml/layout/Layout.cpp
    trunk/libsbml/src/sbml/layout/LineSegment.cpp
    trunk/libsbml/src/sbml/test/TestSyntaxChecker.c

Modified: trunk/libsbml/src/math/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/math/ASTNode.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/math/ASTNode.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -1717,7 +1717,7 @@
   if (!isNumber())
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
 
-  if (!SyntaxChecker::isValidUnitSId(units))
+  if (!SyntaxChecker::isValidInternalUnitSId(units))
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
 
   mUnits     = units;

Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/Compartment.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -493,7 +493,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -520,7 +520,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -553,7 +553,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -669,7 +669,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -691,7 +691,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -1061,7 +1061,7 @@
   //{
   //  logEmptyString(id, level, version, "<compartment>");
   //}
-  //if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  //if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   ////
   //// volume  { use="optional" default="1" }  (L1v1, L1v2)
@@ -1078,7 +1078,7 @@
   //{
   //  logEmptyString("units", level, version, "<compartment>");
   //}
-  //if (!SyntaxChecker::isValidUnitSId(mUnits))
+  //if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   //{
   //  logError(InvalidUnitIdSyntax);
   //}
@@ -1206,7 +1206,7 @@
   {
     logEmptyString("name", level, version, "<compartment>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // volume  { use="optional" default="1" }  (L1v1, L1v2)
@@ -1221,7 +1221,7 @@
   {
     logEmptyString("units", level, version, "<compartment>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   {
     logError(InvalidUnitIdSyntax);
   }
@@ -1293,7 +1293,7 @@
   {
     logEmptyString("id", level, version, "<compartment>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // size    { use="optional" }              (L2v1 ->)
@@ -1308,7 +1308,7 @@
   {
     logEmptyString("units", level, version, "<compartment>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   {
     logError(InvalidUnitIdSyntax);
   }
@@ -1420,7 +1420,7 @@
   {
     logEmptyString("id", level, version, "<compartment>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // size    { use="optional" }              (L2v1 ->)
@@ -1435,7 +1435,7 @@
   {
     logEmptyString("units", level, version, "<compartment>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   {
     logError(InvalidUnitIdSyntax);
   }

Modified: trunk/libsbml/src/sbml/CompartmentType.cpp
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/CompartmentType.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -211,7 +211,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -238,7 +238,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -382,7 +382,7 @@
   {
     logEmptyString("id", level, version, "<compartmentType>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // name: string  { use="optional" }  (L2v2 ->)

Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/Event.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -471,7 +471,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -499,7 +499,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -654,7 +654,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -1384,7 +1384,7 @@
   {
     logEmptyString("id", level, version, "<event>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // name: string  { use="optional" }  (L2v1 ->)
@@ -1402,7 +1402,7 @@
     {
       logEmptyString("timeUnits", level, version, "<event>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mTimeUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mTimeUnits))
     {
       logError(InvalidUnitIdSyntax);
     }
@@ -1472,7 +1472,7 @@
   {
     logEmptyString("id", level, version, "<event>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // name: string  { use="optional" }  (L2v1 ->)

Modified: trunk/libsbml/src/sbml/EventAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/EventAssignment.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -222,7 +222,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -563,7 +563,7 @@
   {
     logEmptyString("variable", level, version, "<eventAssignment>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mVariable)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mVariable)) logError(InvalidIdSyntax);
 
 
   //
@@ -622,7 +622,7 @@
   {
     logEmptyString("variable", level, version, "<eventAssignment>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mVariable)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mVariable)) logError(InvalidIdSyntax);
 
 
   //

Modified: trunk/libsbml/src/sbml/FunctionDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/FunctionDefinition.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/FunctionDefinition.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -258,7 +258,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -285,7 +285,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -669,7 +669,7 @@
   {
     logEmptyString("id", level, version, "<functionDefinition>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // name: string  { use="optional" }  (L2v1 ->)

Modified: trunk/libsbml/src/sbml/InitialAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/InitialAssignment.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -222,7 +222,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -564,7 +564,7 @@
   {
     logEmptyString("symbol", level, version, "<initialAssignment>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mSymbol)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mSymbol)) logError(InvalidIdSyntax);
 
   //
   // sboTerm: SBOTerm { use="optional" }  (L2v2 ->)
@@ -623,7 +623,7 @@
   {
     logEmptyString("symbol", level, version, "<initialAssignment>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mSymbol)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mSymbol)) logError(InvalidIdSyntax);
 
   //
   // sboTerm: SBOTerm { use="optional" }  (L2v2 ->)

Modified: trunk/libsbml/src/sbml/KineticLaw.cpp
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/KineticLaw.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -409,7 +409,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -437,7 +437,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }

Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/Model.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -608,7 +608,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -635,7 +635,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -667,7 +667,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(units)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -693,7 +693,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(units)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -719,7 +719,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(units)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -745,7 +745,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(units)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -771,7 +771,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(units)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -797,7 +797,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(units)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -823,7 +823,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(id)))
+  else if (!(SyntaxChecker::isValidInternalSId(id)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -4193,7 +4193,7 @@
   {
     logEmptyString(id, level, version, "<model>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   if (level > 1)
   {
@@ -4219,7 +4219,7 @@
     {
       logEmptyString("substanceUnits", level, version, "<model>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mSubstanceUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mSubstanceUnits))
     {
       logError(InvalidUnitIdSyntax);
     }
@@ -4232,7 +4232,7 @@
     {
       logEmptyString("timeUnits", level, version, "<model>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mTimeUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mTimeUnits))
     {
       logError(InvalidUnitIdSyntax);
     }
@@ -4245,7 +4245,7 @@
     {
       logEmptyString("volumeUnits", level, version, "<model>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mVolumeUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mVolumeUnits))
     {
       logError(InvalidUnitIdSyntax);
     }
@@ -4258,7 +4258,7 @@
     {
       logEmptyString("areaUnits", level, version, "<model>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mAreaUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mAreaUnits))
     {
       logError(InvalidUnitIdSyntax);
     }
@@ -4271,7 +4271,7 @@
     {
       logEmptyString("lengthUnits", level, version, "<model>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mLengthUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mLengthUnits))
     {
       logError(InvalidUnitIdSyntax);
     }
@@ -4284,7 +4284,7 @@
     {
       logEmptyString("extentUnits", level, version, "<model>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mExtentUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mExtentUnits))
     {
       logError(InvalidUnitIdSyntax);
     }

Modified: trunk/libsbml/src/sbml/Parameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/Parameter.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/Parameter.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -338,7 +338,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -365,7 +365,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -405,7 +405,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else  if (!(SyntaxChecker::isValidUnitSId(units)))
+  else  if (!(SyntaxChecker::isValidInternalUnitSId(units)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -724,7 +724,7 @@
   //{
   //  logEmptyString(id, level, version, "<parameter>");
   //}
-  //if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  //if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   ////
   //// value: double  { use="required" }  (L1v2)
@@ -748,7 +748,7 @@
   //{
   //  logEmptyString("units", level, version, "<parameter>");
   //}
-  //if (!SyntaxChecker::isValidUnitSId(mUnits))
+  //if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   //{
   //  logError(InvalidUnitIdSyntax);
   //}
@@ -834,7 +834,7 @@
   {
     logEmptyString("name", level, version, "<parameter>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // value: double  { use="required" }  (L1v2)
@@ -857,7 +857,7 @@
   {
     logEmptyString("units", level, version, "<parameter>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   {
     logError(InvalidUnitIdSyntax);
   }
@@ -926,7 +926,7 @@
   {
     logEmptyString("id", level, version, "<parameter>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // value: double  { use="optional" }  (L1v2->)
@@ -941,7 +941,7 @@
   {
     logEmptyString("units", level, version, "<parameter>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   {
     logError(InvalidUnitIdSyntax);
   }
@@ -1035,7 +1035,7 @@
   {
     logEmptyString("id", level, version, "<parameter>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // value: double  { use="optional" }  (L1v2->)
@@ -1050,7 +1050,7 @@
   {
     logEmptyString("units", level, version, "<parameter>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mUnits))
   {
     logError(InvalidUnitIdSyntax);
   }

Modified: trunk/libsbml/src/sbml/Reaction.cpp
===================================================================
--- trunk/libsbml/src/sbml/Reaction.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/Reaction.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -489,7 +489,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -516,7 +516,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -610,7 +610,7 @@
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
 
-  if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -1548,7 +1548,7 @@
   {
     logEmptyString("name", level, version, "<reaction>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // reversible: boolean  { use="optional"  default="true" }
@@ -1615,7 +1615,7 @@
   {
     logEmptyString("id", level, version, "<reaction>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // reversible: boolean  { use="optional"  default="true" }
@@ -1695,7 +1695,7 @@
   {
     logEmptyString("id", level, version, "<reaction>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // reversible: boolean  { use="required"} (L3v1->)
@@ -1733,7 +1733,7 @@
   {
     logEmptyString("compartment", level, version, "<reaction>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mCompartment)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mCompartment)) logError(InvalidIdSyntax);
 }
 /** @endcond */
 

Modified: trunk/libsbml/src/sbml/Rule.cpp
===================================================================
--- trunk/libsbml/src/sbml/Rule.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/Rule.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -399,7 +399,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -431,7 +431,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidUnitSId(sname)))
+  else if (!(SyntaxChecker::isValidInternalUnitSId(sname)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -976,7 +976,7 @@
     {
       logEmptyString(s, level, version, "<rule>");
     }
-    if (!SyntaxChecker::isValidSBMLSId(mVariable)) 
+    if (!SyntaxChecker::isValidInternalSId(mVariable)) 
       logError(InvalidIdSyntax);
   }
   else if ( isCompartmentVolume() )
@@ -989,7 +989,7 @@
     {
       logEmptyString("compartment", level, version, "<rule>");
     }
-    if (!SyntaxChecker::isValidSBMLSId(mVariable)) 
+    if (!SyntaxChecker::isValidInternalSId(mVariable)) 
       logError(InvalidIdSyntax);
   }
   else if ( isParameter() )
@@ -1002,7 +1002,7 @@
     {
       logEmptyString("name", level, version, "<rule>");
     }
-    if (!SyntaxChecker::isValidSBMLSId(mVariable)) 
+    if (!SyntaxChecker::isValidInternalSId(mVariable)) 
       logError(InvalidIdSyntax);
 
     //
@@ -1063,7 +1063,7 @@
     {
       logEmptyString("variable", level, version, "<rule>");
     }
-    if (!SyntaxChecker::isValidSBMLSId(mVariable)) 
+    if (!SyntaxChecker::isValidInternalSId(mVariable)) 
       logError(InvalidIdSyntax);
   }
 
@@ -1138,7 +1138,7 @@
     {
       logEmptyString("variable", level, version, "<rule>");
     }
-    if (!SyntaxChecker::isValidSBMLSId(mVariable)) 
+    if (!SyntaxChecker::isValidInternalSId(mVariable)) 
       logError(InvalidIdSyntax);
   }
 

Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/SBase.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -1033,7 +1033,7 @@
     */
     if (getLevel() == 1)
     {
-      if (!(SyntaxChecker::isValidSBMLSId(name)))
+      if (!(SyntaxChecker::isValidInternalSId(name)))
       {
         return LIBSBML_INVALID_ATTRIBUTE_VALUE;
       }

Modified: trunk/libsbml/src/sbml/Species.cpp
===================================================================
--- trunk/libsbml/src/sbml/Species.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/Species.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -595,7 +595,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -622,7 +622,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -655,7 +655,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -677,7 +677,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -736,7 +736,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else  if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else  if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -763,7 +763,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -870,7 +870,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -1257,7 +1257,7 @@
   {
     logEmptyString("name", level, version, "<species>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // compartment: SName  { use="required" }  (L1v1, L2v1)
@@ -1278,7 +1278,7 @@
   {
     logEmptyString("units", level, version, "<species>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mSubstanceUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mSubstanceUnits))
   {
     logError(InvalidUnitIdSyntax);
   }
@@ -1366,7 +1366,7 @@
   {
     logEmptyString("id", level, version, "<species>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // compartment: SId    { use="required" }  (L2v1->)
@@ -1386,7 +1386,7 @@
   {
     logEmptyString("substanceUnits", level, version, "<species>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mSubstanceUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mSubstanceUnits))
   {
     logError(InvalidUnitIdSyntax);
   }
@@ -1432,7 +1432,7 @@
     {
       logEmptyString("spatialSizeUnits", level, version, "<species>");
     }
-    if (!SyntaxChecker::isValidUnitSId(mSpatialSizeUnits))
+    if (!SyntaxChecker::isValidInternalUnitSId(mSpatialSizeUnits))
     {
       logError(InvalidUnitIdSyntax);
     }
@@ -1516,7 +1516,7 @@
   {
     logEmptyString("id", level, version, "<species>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // compartment: SId    { use="required" }  (L2v1->)
@@ -1541,7 +1541,7 @@
   {
     logEmptyString("substanceUnits", level, version, "<species>");
   }
-  if (!SyntaxChecker::isValidUnitSId(mSubstanceUnits))
+  if (!SyntaxChecker::isValidInternalUnitSId(mSubstanceUnits))
   {
     logError(InvalidUnitIdSyntax);
   }
@@ -1598,7 +1598,7 @@
   {
     logEmptyString("conversionFactor", level, version, "<species>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mConversionFactor))
+  if (!SyntaxChecker::isValidInternalSId(mConversionFactor))
   {
     logError(InvalidIdSyntax);
   }

Modified: trunk/libsbml/src/sbml/SpeciesReference.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesReference.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/SpeciesReference.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -224,7 +224,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -256,7 +256,7 @@
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
 #endif
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -283,7 +283,7 @@
   {
     return LIBSBML_UNEXPECTED_ATTRIBUTE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(name)))
+  else if (!(SyntaxChecker::isValidInternalSId(name)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -491,7 +491,7 @@
     {
       logEmptyString("id", level, version, "<speciesReference>");
     }
-    if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+    if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
     //
     // name: string  { use="optional" }  (L2v2->)
@@ -567,7 +567,7 @@
   {
     logEmptyString("id", level, version, "<speciesReference>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // name: string  { use="optional" }  (L2v2->)

Modified: trunk/libsbml/src/sbml/SpeciesType.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesType.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/SpeciesType.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -211,7 +211,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -238,7 +238,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -382,7 +382,7 @@
   {
     logEmptyString("id", level, version, "<speciesType>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // name: string  { use="optional" }  (L2v2->)

Modified: trunk/libsbml/src/sbml/SyntaxChecker.cpp
===================================================================
--- trunk/libsbml/src/sbml/SyntaxChecker.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/SyntaxChecker.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -116,11 +116,6 @@
 {
   unsigned int size = sid.size();
 
-  if (size == 0)
-  {
-    return true;
-  }
-
   unsigned int n = 0;
 
   char c = sid[n];
@@ -300,7 +295,42 @@
   return correctSyntax;
 }
 /** @cond doxygen-libsbml-internal */
+bool
+SyntaxChecker::isValidInternalUnitSId(std::string units)
+{
+  return isValidInternalSId(units);
+}
 
+
+
+bool
+SyntaxChecker::isValidInternalSId(std::string sid)
+{
+  unsigned int size = sid.size();
+
+  if (size == 0)
+  {
+    return true;
+  }
+
+  unsigned int n = 0;
+
+  char c = sid[n];
+  bool okay = (isalpha(c) || (c == '_'));
+  n++;
+
+  while (okay && n < size)
+  {
+    c = sid[n];
+    okay = (isalnum(c) || c == '_');
+    n++;
+  }
+
+  return okay;
+
+}
+
+
 bool 
 SyntaxChecker::isAllowedElement(const XMLNode& node)
 {
@@ -1895,7 +1925,7 @@
 int
 SyntaxChecker_isValidSBMLSId(const char * sid)
 {
-  if (sid == NULL) return 1;
+  if (sid == NULL) return 0;
   return static_cast<int>(SyntaxChecker::isValidSBMLSId(sid));
 }
 

Modified: trunk/libsbml/src/sbml/SyntaxChecker.h
===================================================================
--- trunk/libsbml/src/sbml/SyntaxChecker.h	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/SyntaxChecker.h	2011-03-20 12:09:31 UTC (rev 13254)
@@ -229,6 +229,13 @@
 
   /** @cond doxygen-libsbml-internal */
 
+  /**
+   * Returns true @c true or @c false depending on whether the argument
+   * string conforms to the syntax of SBML identifiers or is empty.
+   */  
+  static bool isValidInternalSId(std::string sid);
+
+  static bool isValidInternalUnitSId(std::string sid);
   /*
    * return true if element is an allowed xhtml element
    */

Modified: trunk/libsbml/src/sbml/UnitDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/UnitDefinition.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/UnitDefinition.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -231,7 +231,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(sid)))
+  else if (!(SyntaxChecker::isValidInternalSId(sid)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
@@ -258,7 +258,7 @@
   }
   else if (getLevel() == 1)
   {
-    if (!(SyntaxChecker::isValidSBMLSId(name)))
+    if (!(SyntaxChecker::isValidInternalSId(name)))
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -1383,7 +1383,7 @@
   {
     logEmptyString(id, level, version, "<unitDefinition>");
   }
-  if (!SyntaxChecker::isValidSBMLSId(mId)) logError(InvalidIdSyntax);
+  if (!SyntaxChecker::isValidInternalSId(mId)) logError(InvalidIdSyntax);
 
   //
   // name: string  { use="optional" }  (L2v1->)

Modified: trunk/libsbml/src/sbml/layout/BoundingBox.cpp
===================================================================
--- trunk/libsbml/src/sbml/layout/BoundingBox.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/layout/BoundingBox.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -252,7 +252,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(id)))
+  else if (!(SyntaxChecker::isValidInternalSId(id)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }

Modified: trunk/libsbml/src/sbml/layout/GraphicalObject.cpp
===================================================================
--- trunk/libsbml/src/sbml/layout/GraphicalObject.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/layout/GraphicalObject.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -235,7 +235,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(id)))
+  else if (!(SyntaxChecker::isValidInternalSId(id)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }

Modified: trunk/libsbml/src/sbml/layout/Layout.cpp
===================================================================
--- trunk/libsbml/src/sbml/layout/Layout.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/layout/Layout.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -353,7 +353,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(id)))
+  else if (!(SyntaxChecker::isValidInternalSId(id)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }

Modified: trunk/libsbml/src/sbml/layout/LineSegment.cpp
===================================================================
--- trunk/libsbml/src/sbml/layout/LineSegment.cpp	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/layout/LineSegment.cpp	2011-03-20 12:09:31 UTC (rev 13254)
@@ -241,7 +241,7 @@
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }
-  else if (!(SyntaxChecker::isValidSBMLSId(id)))
+  else if (!(SyntaxChecker::isValidInternalSId(id)))
   {
     return LIBSBML_INVALID_ATTRIBUTE_VALUE;
   }

Modified: trunk/libsbml/src/sbml/test/TestSyntaxChecker.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestSyntaxChecker.c	2011-03-20 10:30:47 UTC (rev 13253)
+++ trunk/libsbml/src/sbml/test/TestSyntaxChecker.c	2011-03-20 12:09:31 UTC (rev 13254)
@@ -47,6 +47,7 @@
 {
   fail_unless( SyntaxChecker_isValidSBMLSId("cell")  == 1 );
   fail_unless( SyntaxChecker_isValidSBMLSId("1cell") == 0 );
+  fail_unless( SyntaxChecker_isValidSBMLSId("") == 0 );
 }
 END_TEST
 
@@ -100,8 +101,8 @@
 START_TEST (test_SyntaxChecker_accessWithNULL)
 {
   fail_unless(SyntaxChecker_hasExpectedXHTMLSyntax(NULL, NULL) == 0);
-  fail_unless(SyntaxChecker_isValidSBMLSId(NULL) == 1);
-  fail_unless(SyntaxChecker_isValidUnitSId(NULL) == 1);
+  fail_unless(SyntaxChecker_isValidSBMLSId(NULL) == 0);
+  fail_unless(SyntaxChecker_isValidUnitSId(NULL) == 0);
   fail_unless(SyntaxChecker_isValidXMLID(NULL) == 0);
 }
 END_TEST


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 13277
          http://sbml.svn.sourceforge.net/sbml/?rev=13277&view=rev
Author:   sarahkeating
Date:     2011-03-22 16:30:43 +0000 (Tue, 22 Mar 2011)

Log Message:
-----------
getting rid of more warnings

Modified Paths:
--------------
    trunk/libsbml/src/annotation/test/TestCopyAndClone.cpp
    trunk/libsbml/src/math/test/TestReadMathML.cpp
    trunk/libsbml/src/sbml/test/TestSBMLTransforms.cpp
    trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp
    trunk/libsbml/src/xml/test/TestXMLExceptions.cpp

Modified: trunk/libsbml/src/annotation/test/TestCopyAndClone.cpp
===================================================================
--- trunk/libsbml/src/annotation/test/TestCopyAndClone.cpp	2011-03-22 15:24:03 UTC (rev 13276)
+++ trunk/libsbml/src/annotation/test/TestCopyAndClone.cpp	2011-03-22 16:30:43 UTC (rev 13277)
@@ -114,10 +114,11 @@
   fail_unless(msg == "");
 
   Date *date1 = NULL;
+  Date *date2 = NULL;
   msg = "";
   try
   {
-    Date* date2=new Date(*date1);
+    date2=new Date(*date1);
   }
   catch (SBMLConstructorException &e)
   {
@@ -126,7 +127,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  Date *date2 = new Date();
+  date2 = new Date();
   try
   {
     (*date2) = *date1;
@@ -219,10 +220,11 @@
   fail_unless(msg == "");
 
   ModelCreator *mc1 = NULL;
+  ModelCreator *mc2 = NULL;
   msg = "";
   try
   {
-    ModelCreator* mc2=new ModelCreator(*mc1);
+    mc2=new ModelCreator(*mc1);
   }
   catch (SBMLConstructorException &e)
   {
@@ -231,7 +233,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  ModelCreator *mc2 = new ModelCreator();
+  mc2 = new ModelCreator();
   try
   {
     (*mc2) = *mc1;
@@ -370,10 +372,11 @@
   fail_unless(msg == "");
 
   ModelHistory *mh1 = NULL;
+  ModelHistory *mh2 = NULL;
   msg = "";
   try
   {
-    ModelHistory* mh2=new ModelHistory(*mh1);
+    mh2=new ModelHistory(*mh1);
   }
   catch (SBMLConstructorException &e)
   {
@@ -382,7 +385,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  ModelHistory *mh2 = new ModelHistory();
+  mh2 = new ModelHistory();
   try
   {
     (*mh2) = *mh1;
@@ -479,10 +482,11 @@
   fail_unless(msg == "");
 
   CVTerm *cvterm1 = NULL;
+  CVTerm *cvterm2 = NULL;
   msg = "";
   try
   {
-    CVTerm* cvterm2=new CVTerm(*cvterm1);
+    cvterm2=new CVTerm(*cvterm1);
   }
   catch (SBMLConstructorException &e)
   {
@@ -491,7 +495,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  CVTerm *cvterm2 = new CVTerm(BIOLOGICAL_QUALIFIER);
+  cvterm2 = new CVTerm(BIOLOGICAL_QUALIFIER);
   try
   {
     (*cvterm2) = *cvterm1;

Modified: trunk/libsbml/src/math/test/TestReadMathML.cpp
===================================================================
--- trunk/libsbml/src/math/test/TestReadMathML.cpp	2011-03-22 15:24:03 UTC (rev 13276)
+++ trunk/libsbml/src/math/test/TestReadMathML.cpp	2011-03-22 16:30:43 UTC (rev 13277)
@@ -1956,7 +1956,7 @@
   // this fails while default level/version is 2/4
   // but other validation fails if I change it to 3/1
   
-  // tcase_add_test( tcase, test_element_ci_definitionURL       );
+  tcase_add_test( tcase, test_element_ci_definitionURL       );
   tcase_add_test( tcase, test_element_csymbol_avogadro              );
 
   suite_add_tcase(suite, tcase);

Modified: trunk/libsbml/src/sbml/test/TestSBMLTransforms.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestSBMLTransforms.cpp	2011-03-22 15:24:03 UTC (rev 13276)
+++ trunk/libsbml/src/sbml/test/TestSBMLTransforms.cpp	2011-03-22 16:30:43 UTC (rev 13277)
@@ -476,9 +476,6 @@
   SBMLReader        reader;
   SBMLDocument*     d;
   Model*            m;
-  const ASTNode*          ast;
-  FunctionDefinition*     fd;
-  ListOfFunctionDefinitions * lofd;
 
   std::string filename(TestDataDirectory);
   filename += "initialAssignments.xml";
@@ -515,9 +512,6 @@
   SBMLReader        reader;
   SBMLDocument*     d;
   Model*            m;
-  const ASTNode*          ast;
-  FunctionDefinition*     fd;
-  ListOfFunctionDefinitions * lofd;
 
   std::string filename(TestDataDirectory);
   filename += "initialAssignments_species.xml";

Modified: trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp	2011-03-22 15:24:03 UTC (rev 13276)
+++ trunk/libsbml/src/sbml/test/TestWriteL3SBML.cpp	2011-03-22 16:30:43 UTC (rev 13277)
@@ -183,7 +183,7 @@
   const char* expected = wrapSBML_L3v1(
     "  <model/>\n"
     );
-  Model * m = D->createModel("");
+  D->createModel("");
 
   S = writeSBMLToString(D);
 

Modified: trunk/libsbml/src/xml/test/TestXMLExceptions.cpp
===================================================================
--- trunk/libsbml/src/xml/test/TestXMLExceptions.cpp	2011-03-22 15:24:03 UTC (rev 13276)
+++ trunk/libsbml/src/xml/test/TestXMLExceptions.cpp	2011-03-22 16:30:43 UTC (rev 13277)
@@ -71,11 +71,12 @@
   fail_unless(msg == "");
 
   XMLAttributes *att1 = NULL;
+  XMLAttributes *att2 = NULL;
   msg = "";
   // copy constructor
   try
   {
-    XMLAttributes* att2=new XMLAttributes(*att1);
+    att2=new XMLAttributes(*att1);
   }
   catch (XMLConstructorException &e)
   {
@@ -84,7 +85,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  XMLAttributes *att2 = new XMLAttributes();
+  att2 = new XMLAttributes();
   // assignment
   try
   {
@@ -115,11 +116,12 @@
   fail_unless(msg == "");
 
   XMLError *err1 = NULL;
+  XMLError *err2 = NULL;
   msg = "";
   // copy constructor
   try
   {
-    XMLError* err2=new XMLError(*err1);
+    err2=new XMLError(*err1);
   }
   catch (XMLConstructorException &e)
   {
@@ -128,7 +130,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  XMLError *err2 = new XMLError(MissingXMLDecl);
+  err2 = new XMLError(MissingXMLDecl);
   // assignment
   try
   {
@@ -159,11 +161,12 @@
   fail_unless(msg == "");
 
   XMLNamespaces *ns1 = NULL;
+  XMLNamespaces *ns2 = NULL;
   msg = "";
   // copy constructor
   try
   {
-    XMLNamespaces* ns2=new XMLNamespaces(*ns1);
+    ns2=new XMLNamespaces(*ns1);
   }
   catch (XMLConstructorException &e)
   {
@@ -172,7 +175,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  XMLNamespaces *ns2 = new XMLNamespaces();
+  ns2 = new XMLNamespaces();
   // assignment
   try
   {
@@ -203,11 +206,12 @@
   fail_unless(msg == "");
 
   XMLNode *node1 = NULL;
+  XMLNode *node2 = NULL;
   msg = "";
   // copy constructor
   try
   {
-    XMLNode* node2=new XMLNode(*node1);
+    node2=new XMLNode(*node1);
   }
   catch (XMLConstructorException &e)
   {
@@ -216,7 +220,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  XMLNode *node2 = new XMLNode();
+  node2 = new XMLNode();
   // assignment
   try
   {
@@ -248,10 +252,11 @@
 
   msg = "";
   XMLTriple *triple = NULL;
+  XMLToken * token3 = NULL;
   // ctor from triple
   try 
   {
-    XMLToken * token3 = new XMLToken(*(triple));
+    token3 = new XMLToken(*(triple));
   }
   catch (XMLConstructorException &e)
   {
@@ -265,7 +270,7 @@
   // ctor from triple and attributes
   try 
   {
-    XMLToken * token3 = new XMLToken(*(triple1), *(att));
+    token3 = new XMLToken(*(triple1), *(att));
   }
   catch (XMLConstructorException &e)
   {
@@ -279,7 +284,7 @@
   // ctor from triple, attributes & namespaces
   try 
   {
-    XMLToken * token3 = new XMLToken(*(triple1), *(att1), *(ns));
+    token3 = new XMLToken(*(triple1), *(att1), *(ns));
   }
   catch (XMLConstructorException &e)
   {
@@ -292,7 +297,7 @@
   // ctor from string
   try 
   {
-    XMLToken * token3 = new XMLToken(*(mess));
+    token3 = new XMLToken(*(mess));
   }
   catch (XMLConstructorException &e)
   {
@@ -301,11 +306,12 @@
   fail_unless(msg == errMsg);
 
   XMLToken *token1 = NULL;
+  XMLToken *token2 = NULL;
   msg = "";
   // copy ctor
   try
   {
-    XMLToken* token2=new XMLToken(*token1);
+    token2=new XMLToken(*token1);
   }
   catch (XMLConstructorException &e)
   {
@@ -314,7 +320,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  XMLToken *token2 = new XMLToken();
+  token2 = new XMLToken();
   // assignment
   try
   {
@@ -348,11 +354,12 @@
   fail_unless(msg == "");
 
   XMLTriple *triple1 = NULL;
+  XMLTriple *triple2 = NULL;
   msg = "";
   // copy constructor
   try
   {
-    XMLTriple* triple2=new XMLTriple(*triple1);
+    triple2=new XMLTriple(*triple1);
   }
   catch (XMLConstructorException &e)
   {
@@ -361,7 +368,7 @@
   fail_unless(msg == errMsg1);
 
   msg = "";
-  XMLTriple *triple2 = new XMLTriple();
+  triple2 = new XMLTriple();
   // assignment
   try
   {
@@ -380,7 +387,7 @@
     std::string *name = NULL;
     std::string uri = "uri";
     std::string prefix = "prefix";
-    XMLTriple *triple2 = new XMLTriple (*(name), uri, prefix);
+    triple2 = new XMLTriple (*(name), uri, prefix);
   }
   catch (XMLConstructorException &e)
   {
@@ -395,7 +402,7 @@
     std::string name = "name";
     std::string *uri = NULL;
     std::string prefix = "prefix";
-    XMLTriple *triple2 = new XMLTriple (name, *(uri), prefix);
+    triple2 = new XMLTriple (name, *(uri), prefix);
   }
   catch (XMLConstructorException &e)
   {
@@ -411,7 +418,7 @@
     std::string name = "name";
     std::string uri = "uri";
     std::string *prefix = NULL;
-    XMLTriple *triple2 = new XMLTriple (name, uri, *(prefix));
+    triple2 = new XMLTriple (name, uri, *(prefix));
   }
   catch (XMLConstructorException &e)
   {
@@ -424,7 +431,7 @@
   std::string *triplet = NULL;
   try
   {
-    XMLTriple *triple2 = new XMLTriple (*(triplet));
+    triple2 = new XMLTriple (*(triplet));
   }
   catch (XMLConstructorException &e)
   {
@@ -441,11 +448,12 @@
 {
   string msg;
   std::ostream *stream = NULL;
+  XMLOutputStream* opstream2 = NULL;
   msg = "";
   // ctor from stream
   try
   {
-    XMLOutputStream* opstream2=new XMLOutputStream(*(stream));
+    opstream2=new XMLOutputStream(*(stream));
   }
   catch (XMLConstructorException &e)
   {


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 13287
          http://sbml.svn.sourceforge.net/sbml/?rev=13287&view=rev
Author:   sarahkeating
Date:     2011-03-23 15:22:55 +0000 (Wed, 23 Mar 2011)

Log Message:
-----------
added tests for relaxation of xthml rules

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestSyntaxChecker.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSyntaxChecker.java
    trunk/libsbml/src/bindings/python/test/sbml/TestSyntaxChecker.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestSyntaxChecker.rb
    trunk/libsbml/src/sbml/test/TestSyntaxChecker.c

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestSyntaxChecker.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestSyntaxChecker.cs	2011-03-23 13:31:21 UTC (rev 13286)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestSyntaxChecker.cs	2011-03-23 15:22:55 UTC (rev 13287)
@@ -1,176 +1,199 @@
-///  @file    TestSyntaxChecker.cs
-///  @brief   SyntaxChecker unit tests
-///  @author  Frank Bergmann (Csharp conversion)
-///  @author  Akiya Jouraku (Csharp conversion)
-///  @author  Sarah Keating 
-/// 
-///  $Id$
-///  $HeadURL$
-/// 
-///  ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-/// 
-///  DO NOT EDIT THIS FILE.
-/// 
-///  This file was generated automatically by converting the file located at
-///  src/sbml/test/TestSyntaxChecker.c
-///  using the conversion program dev/utilities/translateTests/translateTests.pl.
-///  Any changes made here will be lost the next time the file is regenerated.
-/// 
-///  -----------------------------------------------------------------------------
-///  This file is part of libSBML.  Please visit http://sbml.org for more
-///  information about SBML, and the latest version of libSBML.
-/// 
-///  Copyright 2005-2010 California Institute of Technology.
-///  Copyright 2002-2005 California Institute of Technology and
-///                      Japan Science and Technology Corporation.
-///  
-///  This library is free software; you can redistribute it and/or modify it
-///  under the terms of the GNU Lesser General Public License as published by
-///  the Free Software Foundation.  A copy of the license agreement is provided
-///  in the file named "LICENSE.txt" included with this software distribution
-///  and also available online as http://sbml.org/software/libsbml/license.html
-///  -----------------------------------------------------------------------------
-
-
-namespace LibSBMLCSTest {
-
-  using libsbml;
-
-  using System;
-
-  using System.IO;
-
-  public class TestSyntaxChecker {
-    public class AssertionError : System.Exception 
-    {
-      public AssertionError() : base()
-      {
-        
-      }
-    }
-
-
-    static void assertTrue(bool condition)
-    {
-      if (condition == true)
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertEquals(object a, object b)
-    {
-      if ( (a == null) && (b == null) )
-      {
-        return;
-      }
-      else if ( (a == null) || (b == null) )
-      {
-        throw new AssertionError();
-      }
-      else if (a.Equals(b))
-      {
-        return;
-      }
-  
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(object a, object b)
-    {
-      if ( (a == null) && (b == null) )
-      {
-        throw new AssertionError();
-      }
-      else if ( (a == null) || (b == null) )
-      {
-        return;
-      }
-      else if (a.Equals(b))
-      {
-        throw new AssertionError();
-      }
-    }
-
-    static void assertEquals(bool a, bool b)
-    {
-      if ( a == b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(bool a, bool b)
-    {
-      if ( a != b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertEquals(int a, int b)
-    {
-      if ( a == b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-    static void assertNotEquals(int a, int b)
-    {
-      if ( a != b )
-      {
-        return;
-      }
-      throw new AssertionError();
-    }
-
-
-    public void test_SyntaxChecker_validID()
-    {
-      assertTrue( SyntaxChecker.isValidXMLID("cell") == true );
-      assertTrue( SyntaxChecker.isValidXMLID("1cell") == false );
-      assertTrue( SyntaxChecker.isValidXMLID("_cell") == true );
-    }
-
-    public void test_SyntaxChecker_validId()
-    {
-      assertTrue( SyntaxChecker.isValidSBMLSId("cell") == true );
+///  @file    TestSyntaxChecker.cs
+///  @brief   SyntaxChecker unit tests
+///  @author  Frank Bergmann (Csharp conversion)
+///  @author  Akiya Jouraku (Csharp conversion)
+///  @author  Sarah Keating 
+/// 
+///  $Id$
+///  $HeadURL$
+/// 
+///  ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+/// 
+///  DO NOT EDIT THIS FILE.
+/// 
+///  This file was generated automatically by converting the file located at
+///  src/sbml/test/TestSyntaxChecker.c
+///  using the conversion program dev/utilities/translateTests/translateTests.pl.
+///  Any changes made here will be lost the next time the file is regenerated.
+/// 
+///  -----------------------------------------------------------------------------
+///  This file is part of libSBML.  Please visit http://sbml.org for more
+///  information about SBML, and the latest version of libSBML.
+/// 
+///  Copyright 2005-2010 California Institute of Technology.
+///  Copyright 2002-2005 California Institute of Technology and
+///                      Japan Science and Technology Corporation.
+///  
+///  This library is free software; you can redistribute it and/or modify it
+///  under the terms of the GNU Lesser General Public License as published by
+///  the Free Software Foundation.  A copy of the license agreement is provided
+///  in the file named "LICENSE.txt" included with this software distribution
+///  and also available online as http://sbml.org/software/libsbml/license.html
+///  -----------------------------------------------------------------------------
+
+
+namespace LibSBMLCSTest {
+
+  using libsbml;
+
+  using System;
+
+  using System.IO;
+
+  public class TestSyntaxChecker {
+    public class AssertionError : System.Exception 
+    {
+      public AssertionError() : base()
+      {
+        
+      }
+    }
+
+
+    static void assertTrue(bool condition)
+    {
+      if (condition == true)
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertEquals(object a, object b)
+    {
+      if ( (a == null) && (b == null) )
+      {
+        return;
+      }
+      else if ( (a == null) || (b == null) )
+      {
+        throw new AssertionError();
+      }
+      else if (a.Equals(b))
+      {
+        return;
+      }
+  
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(object a, object b)
+    {
+      if ( (a == null) && (b == null) )
+      {
+        throw new AssertionError();
+      }
+      else if ( (a == null) || (b == null) )
+      {
+        return;
+      }
+      else if (a.Equals(b))
+      {
+        throw new AssertionError();
+      }
+    }
+
+    static void assertEquals(bool a, bool b)
+    {
+      if ( a == b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(bool a, bool b)
+    {
+      if ( a != b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertEquals(int a, int b)
+    {
+      if ( a == b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+    static void assertNotEquals(int a, int b)
+    {
+      if ( a != b )
+      {
+        return;
+      }
+      throw new AssertionError();
+    }
+
+
+    public void test_SyntaxChecker_validID()
+    {
+      assertTrue( SyntaxChecker.isValidXMLID("cell") == true );
+      assertTrue( SyntaxChecker.isValidXMLID("1cell") == false );
+      assertTrue( SyntaxChecker.isValidXMLID("_cell") == true );
+    }
+
+    public void test_SyntaxChecker_validId()
+    {
+      assertTrue( SyntaxChecker.isValidSBMLSId("cell") == true );
       assertTrue( SyntaxChecker.isValidSBMLSId("1cell") == false );
-      assertTrue( SyntaxChecker.isValidSBMLSId("") == false);
-    }
-
-    public void test_SyntaxChecker_validUnitId()
-    {
-      assertTrue( SyntaxChecker.isValidUnitSId("cell") == true );
-      assertTrue( SyntaxChecker.isValidUnitSId("1cell") == false );
-    }
-
-    public void test_SyntaxChecker_validXHTML()
-    {
-      XMLToken token;
-      XMLNode node;
-      XMLTriple triple = new  XMLTriple("p", "", "");
-      XMLAttributes att = new  XMLAttributes();
-      XMLNamespaces ns = new  XMLNamespaces();
-      ns.add( "http://www.w3.org/1999/xhtml", "");
-      XMLToken tt = new  XMLToken("This is my text");
-      XMLNode n1 = new XMLNode(tt);
-      token = new  XMLToken(triple,att,ns);
-      node = new XMLNode(token);
-      node.addChild(n1);
-      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(node,null) == false );
-      triple = new  XMLTriple("html", "", "");
-      ns.clear();
-      token = new  XMLToken(triple,att,ns);
-      node = new XMLNode(token);
-      node.addChild(n1);
-      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(node,null) == false );
-    }
-
-  }
-}
+      assertTrue( SyntaxChecker.isValidSBMLSId("") == false );
+    }
+
+    public void test_SyntaxChecker_validUnitId()
+    {
+      assertTrue( SyntaxChecker.isValidUnitSId("cell") == true );
+      assertTrue( SyntaxChecker.isValidUnitSId("1cell") == false );
+    }
+
+    public void test_SyntaxChecker_validXHTML()
+    {
+      SBMLNamespaces NS24 = new  SBMLNamespaces(2,4);
+      SBMLNamespaces NS31 = new  SBMLNamespaces(3,1);
+      XMLToken toptoken;
+      XMLNode topnode;
+      XMLTriple toptriple = new  XMLTriple("notes", "", "");
+      XMLToken token;
+      XMLNode node;
+      XMLTriple triple = new  XMLTriple("p", "", "");
+      XMLAttributes att = new  XMLAttributes();
+      XMLNamespaces ns = new  XMLNamespaces();
+      ns.add( "http://www.w3.org/1999/xhtml", "");
+      XMLToken tt = new  XMLToken("This is my text");
+      XMLNode n1 = new XMLNode(tt);
+      toptoken = new  XMLToken(toptriple,att);
+      topnode = new XMLNode(toptoken);
+      token = new  XMLToken(triple,att,ns);
+      node = new XMLNode(token);
+      node.addChild(n1);
+      topnode.addChild(node);
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == true );
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
+      triple = new  XMLTriple("html", "", "");
+      token = new  XMLToken(triple,att,ns);
+      node = new XMLNode(token);
+      node.addChild(n1);
+      topnode.removeChild(0);
+      topnode.addChild(node);
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
+      triple = new  XMLTriple("html", "", "");
+      ns.clear();
+      token = new  XMLToken(triple,att,ns);
+      node = new XMLNode(token);
+      node.addChild(n1);
+      topnode.removeChild(0);
+      topnode.addChild(node);
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == false );
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
+      assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == false );
+    }
+
+  }
+}

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSyntaxChecker.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSyntaxChecker.java	2011-03-23 13:31:21 UTC (rev 13286)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSyntaxChecker.java	2011-03-23 15:22:55 UTC (rev 13287)
@@ -1,218 +1,241 @@
-/*
- * @file    TestSyntaxChecker.java
- * @brief   SyntaxChecker unit tests
- *
- * @author  Akiya Jouraku (Java conversion)
- * @author  Sarah Keating 
- *
- * $Id$
- * $HeadURL$
- *
- * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
- *
- * DO NOT EDIT THIS FILE.
- *
- * This file was generated automatically by converting the file located at
- * src/sbml/test/TestSyntaxChecker.c
- * using the conversion program dev/utilities/translateTests/translateTests.pl.
- * Any changes made here will be lost the next time the file is regenerated.
- *
- * -----------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright 2005-2010 California Institute of Technology.
- * Copyright 2002-2005 California Institute of Technology and
- *                     Japan Science and Technology Corporation.
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * -----------------------------------------------------------------------------
- */
-
-package org.sbml.libsbml.test.sbml;
-
-import org.sbml.libsbml.*;
-
-import java.io.File;
-import java.lang.AssertionError;
-
-public class TestSyntaxChecker {
-
-  static void assertTrue(boolean condition) throws AssertionError
-  {
-    if (condition == true)
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertEquals(Object a, Object b) throws AssertionError
-  {
-    if ( (a == null) && (b == null) )
-    {
-      return;
-    }
-    else if ( (a == null) || (b == null) )
-    {
-      throw new AssertionError();
-    }
-    else if (a.equals(b))
-    {
-      return;
-    }
-
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(Object a, Object b) throws AssertionError
-  {
-    if ( (a == null) && (b == null) )
-    {
-      throw new AssertionError();
-    }
-    else if ( (a == null) || (b == null) )
-    {
-      return;
-    }
-    else if (a.equals(b))
-    {
-      throw new AssertionError();
-    }
-  }
-
-  static void assertEquals(boolean a, boolean b) throws AssertionError
-  {
-    if ( a == b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(boolean a, boolean b) throws AssertionError
-  {
-    if ( a != b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertEquals(int a, int b) throws AssertionError
-  {
-    if ( a == b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  static void assertNotEquals(int a, int b) throws AssertionError
-  {
-    if ( a != b )
-    {
-      return;
-    }
-    throw new AssertionError();
-  }
-
-  public void test_SyntaxChecker_validID()
-  {
-    assertTrue( SyntaxChecker.isValidXMLID("cell") == true );
-    assertTrue( SyntaxChecker.isValidXMLID("1cell") == false );
-    assertTrue( SyntaxChecker.isValidXMLID("_cell") == true );
-  }
-
-  public void test_SyntaxChecker_validId()
-  {
-    assertTrue( SyntaxChecker.isValidSBMLSId("cell") == true );
-    assertTrue( SyntaxChecker.isValidSBMLSId("1cell") == false );
-    assertTrue( SyntaxChecker.isValidSBMLSId("") == false );
-  }
-
-  public void test_SyntaxChecker_validUnitId()
-  {
-    assertTrue( SyntaxChecker.isValidUnitSId("cell") == true );
-    assertTrue( SyntaxChecker.isValidUnitSId("1cell") == false );
-  }
-
-  public void test_SyntaxChecker_validXHTML()
-  {
-    XMLToken token;
-    XMLNode node;
-    XMLTriple triple = new  XMLTriple("p", "", "");
-    XMLAttributes att = new  XMLAttributes();
-    XMLNamespaces ns = new  XMLNamespaces();
-    ns.add( "http://www.w3.org/1999/xhtml", "");
-    XMLToken tt = new  XMLToken("This is my text");
-    XMLNode n1 = new XMLNode(tt);
-    token = new  XMLToken(triple,att,ns);
-    node = new XMLNode(token);
-    node.addChild(n1);
-    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(node,null) == false );
-    triple = new  XMLTriple("html", "", "");
-    ns.clear();
-    token = new  XMLToken(triple,att,ns);
-    node = new XMLNode(token);
-    node.addChild(n1);
-    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(node,null) == false );
-  }
-
-  /**
-   * Loads the SWIG-generated libSBML Java module when this class is
-   * loaded, or reports a sensible diagnostic message about why it failed.
-   */
-  static
-  {
-    String varname;
-    String shlibname;
-
-    if (System.getProperty("mrj.version") != null)
-    {
-      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
-      shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
-    }
-    else
-    {
-      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
-      shlibname = "libsbmlj.so and/or libsbml.so";
-    }
-
-    try
-    {
-      System.loadLibrary("sbmlj");
-      // For extra safety, check that the jar file is in the classpath.
-      Class.forName("org.sbml.libsbml.libsbml");
-    }
-    catch (SecurityException e)
-    {
-      e.printStackTrace();
-      System.err.println("Could not load the libSBML library files due to a"+
-                         " security exception.\n");
-      System.exit(1);
-    }
-    catch (UnsatisfiedLinkError e)
-    {
-      e.printStackTrace();
-      System.err.println("Error: could not link with the libSBML library files."+
-                         " It is likely\nyour " + varname +
-                         " environment variable does not include the directories\n"+
-                         "containing the " + shlibname + " library files.\n");
-      System.exit(1);
-    }
-    catch (ClassNotFoundException e)
-    {
-      e.printStackTrace();
-      System.err.println("Error: unable to load the file libsbmlj.jar."+
-                         " It is likely\nyour -classpath option and CLASSPATH" +
-                         " environment variable\n"+
-                         "do not include the path to libsbmlj.jar.\n");
-      System.exit(1);
-    }
-  }
-}
+/*
+ * @file    TestSyntaxChecker.java
+ * @brief   SyntaxChecker unit tests
+ *
+ * @author  Akiya Jouraku (Java conversion)
+ * @author  Sarah Keating 
+ *
+ * $Id$
+ * $HeadURL$
+ *
+ * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+ *
+ * DO NOT EDIT THIS FILE.
+ *
+ * This file was generated automatically by converting the file located at
+ * src/sbml/test/TestSyntaxChecker.c
+ * using the conversion program dev/utilities/translateTests/translateTests.pl.
+ * Any changes made here will be lost the next time the file is regenerated.
+ *
+ * -----------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright 2005-2010 California Institute of Technology.
+ * Copyright 2002-2005 California Institute of Technology and
+ *                     Japan Science and Technology Corporation.
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * -----------------------------------------------------------------------------
+ */
+
+package org.sbml.libsbml.test.0;
+
+import org.sbml.libsbml.*;
+
+import java.io.File;
+import java.lang.AssertionError;
+
+public class TestSyntaxChecker {
+
+  static void assertTrue(boolean condition) throws AssertionError
+  {
+    if (condition == true)
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertEquals(Object a, Object b) throws AssertionError
+  {
+    if ( (a == null) && (b == null) )
+    {
+      return;
+    }
+    else if ( (a == null) || (b == null) )
+    {
+      throw new AssertionError();
+    }
+    else if (a.equals(b))
+    {
+      return;
+    }
+
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(Object a, Object b) throws AssertionError
+  {
+    if ( (a == null) && (b == null) )
+    {
+      throw new AssertionError();
+    }
+    else if ( (a == null) || (b == null) )
+    {
+      return;
+    }
+    else if (a.equals(b))
+    {
+      throw new AssertionError();
+    }
+  }
+
+  static void assertEquals(boolean a, boolean b) throws AssertionError
+  {
+    if ( a == b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(boolean a, boolean b) throws AssertionError
+  {
+    if ( a != b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertEquals(int a, int b) throws AssertionError
+  {
+    if ( a == b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  static void assertNotEquals(int a, int b) throws AssertionError
+  {
+    if ( a != b )
+    {
+      return;
+    }
+    throw new AssertionError();
+  }
+
+  public void test_SyntaxChecker_validID()
+  {
+    assertTrue( SyntaxChecker.isValidXMLID("cell") == true );
+    assertTrue( SyntaxChecker.isValidXMLID("1cell") == false );
+    assertTrue( SyntaxChecker.isValidXMLID("_cell") == true );
+  }
+
+  public void test_SyntaxChecker_validId()
+  {
+    assertTrue( SyntaxChecker.isValidSBMLSId("cell") == true );
+    assertTrue( SyntaxChecker.isValidSBMLSId("1cell") == false );
+    assertTrue( SyntaxChecker.isValidSBMLSId("") == false );
+  }
+
+  public void test_SyntaxChecker_validUnitId()
+  {
+    assertTrue( SyntaxChecker.isValidUnitSId("cell") == true );
+    assertTrue( SyntaxChecker.isValidUnitSId("1cell") == false );
+  }
+
+  public void test_SyntaxChecker_validXHTML()
+  {
+    SBMLNamespaces NS24 = new  SBMLNamespaces(2,4);
+    SBMLNamespaces NS31 = new  SBMLNamespaces(3,1);
+    XMLToken toptoken;
+    XMLNode topnode;
+    XMLTriple toptriple = new  XMLTriple("notes", "", "");
+    XMLToken token;
+    XMLNode node;
+    XMLTriple triple = new  XMLTriple("p", "", "");
+    XMLAttributes att = new  XMLAttributes();
+    XMLNamespaces ns = new  XMLNamespaces();
+    ns.add( "http://www.w3.org/1999/xhtml", "");
+    XMLToken tt = new  XMLToken("This is my text");
+    XMLNode n1 = new XMLNode(tt);
+    toptoken = new  XMLToken(toptriple,att);
+    topnode = new XMLNode(toptoken);
+    token = new  XMLToken(triple,att,ns);
+    node = new XMLNode(token);
+    node.addChild(n1);
+    topnode.addChild(node);
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == true );
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
+    triple = new  XMLTriple("html", "", "");
+    token = new  XMLToken(triple,att,ns);
+    node = new XMLNode(token);
+    node.addChild(n1);
+    topnode.removeChild(0);
+    topnode.addChild(node);
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
+    triple = new  XMLTriple("html", "", "");
+    ns.clear();
+    token = new  XMLToken(triple,att,ns);
+    node = new XMLNode(token);
+    node.addChild(n1);
+    topnode.removeChild(0);
+    topnode.addChild(node);
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == false );
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
+    assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == false );
+  }
+
+  /**
+   * Loads the SWIG-generated libSBML Java module when this class is
+   * loaded, or reports a sensible diagnostic message about why it failed.
+   */
+  static
+  {
+    String varname;
+    String shlibname;
+
+    if (System.getProperty("mrj.version") != null)
+    {
+      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
+      shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
+    }
+    else
+    {
+      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
+      shlibname = "libsbmlj.so and/or libsbml.so";
+    }
+
+    try
+    {
+      System.loadLibrary("sbmlj");
+      // For extra safety, check that the jar file is in the classpath.
+      Class.forName("org.sbml.libsbml.libsbml");
+    }
+    catch (SecurityException e)
+    {
+      e.printStackTrace();
+      System.err.println("Could not load the libSBML library files due to a"+
+                         " security exception.\n");
+      System.exit(1);
+    }
+    catch (UnsatisfiedLinkError e)
+    {
+      e.printStackTrace();
+      System.err.println("Error: could not link with the libSBML library files."+
+                         " It is likely\nyour " + varname +
+                         " environment variable does not include the directories\n"+
+                         "containing the " + shlibname + " library files.\n");
+      System.exit(1);
+    }
+    catch (ClassNotFoundException e)
+    {
+      e.printStackTrace();
+      System.err.println("Error: unable to load the file libsbmlj.jar."+
+                         " It is likely\nyour -classpath option and CLASSPATH" +
+                         " environment variable\n"+
+                         "do not include the path to libsbmlj.jar.\n");
+      System.exit(1);
+    }
+  }
+}

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestSyntaxChecker.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestSyntaxChecker.py	2011-03-23 13:31:21 UTC (rev 13286)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestSyntaxChecker.py	2011-03-23 15:22:55 UTC (rev 13287)
@@ -1,89 +1,110 @@
-#
-# @file    TestSyntaxChecker.py
-# @brief   SyntaxChecker unit tests
-#
-# @author  Akiya Jouraku (Python conversion)
-# @author  Sarah Keating 
-#
-# $Id$
-# $HeadURL$
-#
-# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-#
-# DO NOT EDIT THIS FILE.
-#
-# This file was generated automatically by converting the file located at
-# src/sbml/test/TestSyntaxChecker.c
-# using the conversion program dev/utilities/translateTests/translateTests.pl.
-# Any changes made here will be lost the next time the file is regenerated.
-#
-# -----------------------------------------------------------------------------
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright 2005-2010 California Institute of Technology.
-# Copyright 2002-2005 California Institute of Technology and
-#                     Japan Science and Technology Corporation.
-# 
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation.  A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-# -----------------------------------------------------------------------------
-
-import sys
-import unittest
-import libsbml
-
-
-class TestSyntaxChecker(unittest.TestCase):
-
-
-  def test_SyntaxChecker_validID(self):
-    self.assert_( libsbml.SyntaxChecker.isValidXMLID("cell") == True )
-    self.assert_( libsbml.SyntaxChecker.isValidXMLID("1cell") == False )
-    self.assert_( libsbml.SyntaxChecker.isValidXMLID("_cell") == True )
-    pass  
-
-  def test_SyntaxChecker_validId(self):
-    self.assert_( libsbml.SyntaxChecker.isValidSBMLSId("cell") == True )
-    self.assert_( libsbml.SyntaxChecker.isValidSBMLSId("1cell") == False )
-    self.assert_( libsbml.SyntaxChecker.isValidSBMLSId("") == False )
-    pass  
-
-  def test_SyntaxChecker_validUnitId(self):
-    self.assert_( libsbml.SyntaxChecker.isValidUnitSId("cell") == True )
-    self.assert_( libsbml.SyntaxChecker.isValidUnitSId("1cell") == False )
-    pass  
-
-  def test_SyntaxChecker_validXHTML(self):
-    triple = libsbml.XMLTriple("p", "", "")
-    att = libsbml.XMLAttributes()
-    ns = libsbml.XMLNamespaces()
-    ns.add( "http://www.w3.org/1999/xhtml", "")
-    tt = libsbml.XMLToken("This is my text")
-    n1 = libsbml.XMLNode(tt)
-    token = libsbml.XMLToken(triple,att,ns)
-    node = libsbml.XMLNode(token)
-    node.addChild(n1)
-    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(node,None) == False )
-    triple = libsbml.XMLTriple("html", "", "")
-    ns.clear()
-    token = libsbml.XMLToken(triple,att,ns)
-    node = libsbml.XMLNode(token)
-    node.addChild(n1)
-    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(node,None) == False )
-    pass  
-
-def suite():
-  suite = unittest.TestSuite()
-  suite.addTest(unittest.makeSuite(TestSyntaxChecker))
-
-  return suite
-
-if __name__ == "__main__":
-  if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
-    sys.exit(0)
-  else:
-    sys.exit(1)
+#
+# @file    TestSyntaxChecker.py
+# @brief   SyntaxChecker unit tests
+#
+# @author  Akiya Jouraku (Python conversion)
+# @author  Sarah Keating 
+#
+# $Id$
+# $HeadURL$
+#
+# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+#
+# DO NOT EDIT THIS FILE.
+#
+# This file was generated automatically by converting the file located at
+# src/sbml/test/TestSyntaxChecker.c
+# using the conversion program dev/utilities/translateTests/translateTests.pl.
+# Any changes made here will be lost the next time the file is regenerated.
+#
+# -----------------------------------------------------------------------------
+# This file is part of libSBML.  Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright 2005-2010 California Institute of Technology.
+# Copyright 2002-2005 California Institute of Technology and
+#                     Japan Science and Technology Corporation.
+# 
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation.  A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+# -----------------------------------------------------------------------------
+
+import sys
+import unittest
+import libsbml
+
+
+class TestSyntaxChecker(unittest.TestCase):
+
+
+  def test_SyntaxChecker_validID(self):
+    self.assert_( libsbml.SyntaxChecker.isValidXMLID("cell") == True )
+    self.assert_( libsbml.SyntaxChecker.isValidXMLID("1cell") == False )
+    self.assert_( libsbml.SyntaxChecker.isValidXMLID("_cell") == True )
+    pass  
+
+  def test_SyntaxChecker_validId(self):
+    self.assert_( libsbml.SyntaxChecker.isValidSBMLSId("cell") == True )
+    self.assert_( libsbml.SyntaxChecker.isValidSBMLSId("1cell") == False )
+    self.assert_( libsbml.SyntaxChecker.isValidSBMLSId("") == False )
+    pass  
+
+  def test_SyntaxChecker_validUnitId(self):
+    self.assert_( libsbml.SyntaxChecker.isValidUnitSId("cell") == True )
+    self.assert_( libsbml.SyntaxChecker.isValidUnitSId("1cell") == False )
+    pass  
+
+  def test_SyntaxChecker_validXHTML(self):
+    NS24 = libsbml.SBMLNamespaces(2,4)
+    NS31 = libsbml.SBMLNamespaces(3,1)
+    toptriple = libsbml.XMLTriple("notes", "", "")
+    triple = libsbml.XMLTriple("p", "", "")
+    att = libsbml.XMLAttributes()
+    ns = libsbml.XMLNamespaces()
+    ns.add( "http://www.w3.org/1999/xhtml", "")
+    tt = libsbml.XMLToken("This is my text")
+    n1 = libsbml.XMLNode(tt)
+    toptoken = libsbml.XMLToken(toptriple,att)
+    topnode = libsbml.XMLNode(toptoken)
+    token = libsbml.XMLToken(triple,att,ns)
+    node = libsbml.XMLNode(token)
+    node.addChild(n1)
+    topnode.addChild(node)
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == True )
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == True )
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == True )
+    triple = libsbml.XMLTriple("html", "", "")
+    token = libsbml.XMLToken(triple,att,ns)
+    node = libsbml.XMLNode(token)
+    node.addChild(n1)
+    topnode.removeChild(0)
+    topnode.addChild(node)
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == True )
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == False )
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == True )
+    triple = libsbml.XMLTriple("html", "", "")
+    ns.clear()
+    token = libsbml.XMLToken(triple,att,ns)
+    node = libsbml.XMLNode(token)
+    node.addChild(n1)
+    topnode.removeChild(0)
+    topnode.addChild(node)
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == False )
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == False )
+    self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == False )
+    pass  
+
+def suite():
+  suite = unittest.TestSuite()
+  suite.addTest(unittest.makeSuite(TestSyntaxChecker))
+
+  return suite
+
+if __name__ == "__main__":
+  if unittest.TextTestRunner(verbosity=1).run(suite()).wasSuccessful() :
+    sys.exit(0)
+  else:
+    sys.exit(1)

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestSyntaxChecker.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestSyntaxChecker.rb	2011-03-23 13:31:21 UTC (rev 13286)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestSyntaxChecker.rb	2011-03-23 15:22:55 UTC (rev 13287)
@@ -1,74 +1,95 @@
-# @file    TestSyntaxChecker.rb
-# @brief   SyntaxChecker unit tests
-#
-# @author  Akiya Jouraku (Ruby conversion)
-# @author  Sarah Keating 
-#
-# $Id$
-# $HeadURL$
-#
-# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
-#
-# DO NOT EDIT THIS FILE.
-#
-# This file was generated automatically by converting the file located at
-# src/sbml/test/TestSyntaxChecker.c
-# using the conversion program dev/utilities/translateTests/translateTests.pl.
-# Any changes made here will be lost the next time the file is regenerated.
-#
-# -----------------------------------------------------------------------------
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright 2005-2010 California Institute of Technology.
-# Copyright 2002-2005 California Institute of Technology and
-#                     Japan Science and Technology Corporation.
-# 
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation.  A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-# -----------------------------------------------------------------------------
-require 'test/unit'
-require 'libSBML'
-
-class TestSyntaxChecker < Test::Unit::TestCase
-
-  def test_SyntaxChecker_validID
-    assert( LibSBML::SyntaxChecker.isValidXMLID("cell") == true )
-    assert( LibSBML::SyntaxChecker.isValidXMLID("1cell") == false )
-    assert( LibSBML::SyntaxChecker.isValidXMLID("_cell") == true )
-  end
-
-  def test_SyntaxChecker_validId
-    assert( LibSBML::SyntaxChecker.isValidSBMLSId("cell") == true )
-    assert( LibSBML::SyntaxChecker.isValidSBMLSId("1cell") == false )
-    assert( LibSBML::SyntaxChecker.isValidSBMLSId("") == false )
-  end
-
-  def test_SyntaxChecker_validUnitId
-    assert( LibSBML::SyntaxChecker.isValidUnitSId("cell") == true )
-    assert( LibSBML::SyntaxChecker.isValidUnitSId("1cell") == false )
-  end
-
-  def test_SyntaxChecker_validXHTML
-    triple = LibSBML::XMLTriple.new("p", "", "")
-    att = LibSBML::XMLAttributes.new()
-    ns = LibSBML::XMLNamespaces.new()
-    ns.add( "http://www.w3.org/1999/xhtml", "")
-    tt = LibSBML::XMLToken.new("This is my text")
-    n1 = LibSBML::XMLNode.new(tt)
-    token = LibSBML::XMLToken.new(triple,att,ns)
-    node = LibSBML::XMLNode.new(token)
-    node.addChild(n1)
-    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(node,nil) == false )
-    triple = LibSBML::XMLTriple.new("html", "", "")
-    ns.clear()
-    token = LibSBML::XMLToken.new(triple,att,ns)
-    node = LibSBML::XMLNode.new(token)
-    node.addChild(n1)
-    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(node,nil) == false )
-  end
-
-end
+# @file    TestSyntaxChecker.rb
+# @brief   SyntaxChecker unit tests
+#
+# @author  Akiya Jouraku (Ruby conversion)
+# @author  Sarah Keating 
+#
+# $Id$
+# $HeadURL$
+#
+# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
+#
+# DO NOT EDIT THIS FILE.
+#
+# This file was generated automatically by converting the file located at
+# src/sbml/test/TestSyntaxChecker.c
+# using the conversion program dev/utilities/translateTests/translateTests.pl.
+# Any changes made here will be lost the next time the file is regenerated.
+#
+# -----------------------------------------------------------------------------
+# This file is part of libSBML.  Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright 2005-2010 California Institute of Technology.
+# Copyright 2002-2005 California Institute of Technology and
+#                     Japan Science and Technology Corporation.
+# 
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation.  A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+# -----------------------------------------------------------------------------
+require 'test/unit'
+require 'libSBML'
+
+class TestSyntaxChecker < Test::Unit::TestCase
+
+  def test_SyntaxChecker_validID
+    assert( LibSBML::SyntaxChecker.isValidXMLID("cell") == true )
+    assert( LibSBML::SyntaxChecker.isValidXMLID("1cell") == false )
+    assert( LibSBML::SyntaxChecker.isValidXMLID("_cell") == true )
+  end
+
+  def test_SyntaxChecker_validId
+    assert( LibSBML::SyntaxChecker.isValidSBMLSId("cell") == true )
+    assert( LibSBML::SyntaxChecker.isValidSBMLSId("1cell") == false )
+    assert( LibSBML::SyntaxChecker.isValidSBMLSId("") == false )
+  end
+
+  def test_SyntaxChecker_validUnitId
+    assert( LibSBML::SyntaxChecker.isValidUnitSId("cell") == true )
+    assert( LibSBML::SyntaxChecker.isValidUnitSId("1cell") == false )
+  end
+
+  def test_SyntaxChecker_validXHTML
+    ns24 = LibSBML::SBMLNamespaces.new(2,4)
+    ns31 = LibSBML::SBMLNamespaces.new(3,1)
+    toptriple = LibSBML::XMLTriple.new("notes", "", "")
+    triple = LibSBML::XMLTriple.new("p", "", "")
+    att = LibSBML::XMLAttributes.new()
+    ns = LibSBML::XMLNamespaces.new()
+    ns.add( "http://www.w3.org/1999/xhtml", "")
+    tt = LibSBML::XMLToken.new("This is my text")
+    n1 = LibSBML::XMLNode.new(tt)
+    toptoken = LibSBML::XMLToken.new(toptriple,att)
+    topnode = LibSBML::XMLNode.new(toptoken)
+    token = LibSBML::XMLToken.new(triple,att,ns)
+    node = LibSBML::XMLNode.new(token)
+    node.addChild(n1)
+    topnode.addChild(node)
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,nil) == true )
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,ns24) == true )
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,ns31) == true )
+    triple = LibSBML::XMLTriple.new("html", "", "")
+    token = LibSBML::XMLToken.new(triple,att,ns)
+    node = LibSBML::XMLNode.new(token)
+    node.addChild(n1)
+    topnode.removeChild(0)
+    topnode.addChild(node)
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,nil) == true )
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,ns24) == false )
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,ns31) == true )
+    triple = LibSBML::XMLTriple.new("html", "", "")
+    ns.clear()
+    token = LibSBML::XMLToken.new(triple,att,ns)
+    node = LibSBML::XMLNode.new(token)
+    node.addChild(n1)
+    topnode.removeChild(0)
+    topnode.addChild(node)
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,nil) == false )
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,ns24) == false )
+    assert( LibSBML::SyntaxChecker.hasExpectedXHTMLSyntax(topnode,ns31) == false )
+  end
+
+end

Modified: trunk/libsbml/src/sbml/test/TestSyntaxChecker.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestSyntaxChecker.c	2011-03-23 13:31:21 UTC (rev 13286)
+++ trunk/libsbml/src/sbml/test/TestSyntaxChecker.c	2011-03-23 15:22:55 UTC (rev 13287)
@@ -32,6 +32,7 @@
 
 #include <sbml/SBase.h>
 #include <sbml/SyntaxChecker.h>
+#include <sbml/SBMLNamespaces.h>
 #include <sbml/xml/XMLNamespaces.h>
 #include <sbml/xml/XMLAttributes.h>
 #include <sbml/xml/XMLTriple.h>
@@ -71,6 +72,13 @@
 
 START_TEST (test_SyntaxChecker_validXHTML)
 {
+  SBMLNamespaces_t *NS24 = SBMLNamespaces_create(2,4);
+  SBMLNamespaces_t *NS31 = SBMLNamespaces_create(3,1);
+
+  XMLToken_t *toptoken;
+  XMLNode_t *topnode;
+  XMLTriple_t * toptriple = XMLTriple_createWith("notes", "", "");
+
   XMLToken_t *token;
   XMLNode_t *node;
   XMLTriple_t * triple = XMLTriple_createWith("p", "", "");
@@ -81,20 +89,41 @@
   XMLNode_t *n1 = XMLNode_createFromToken(tt);
 
 
+  toptoken = XMLToken_createWithTripleAttr(toptriple, att);
+  topnode = XMLNode_createFromToken(toptoken);
+
   token = XMLToken_createWithTripleAttrNS(triple, att, ns);
   node = XMLNode_createFromToken(token);
   XMLNode_addChild(node, n1);
+  XMLNode_addChild(topnode, node);
 
-  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(node, NULL) == 0 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NULL) == 1 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS24) == 1 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS31) == 1 );
 
   triple = XMLTriple_createWith("html", "", "");
+  token = XMLToken_createWithTripleAttrNS(triple, att, ns);
+  node = XMLNode_createFromToken(token);
+  XMLNode_addChild(node, n1);
+  XMLNode_removeChild(topnode, 0);
+  XMLNode_addChild(topnode, node);
+
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NULL) == 1 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS24) == 0 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS31) == 1 );
+
+  triple = XMLTriple_createWith("html", "", "");
   XMLNamespaces_clear(ns);
 
   token = XMLToken_createWithTripleAttrNS(triple, att, ns);
   node = XMLNode_createFromToken(token);
   XMLNode_addChild(node, n1);
+  XMLNode_removeChild(topnode, 0);
+  XMLNode_addChild(topnode, node);
 
-  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(node, NULL) == 0 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NULL) == 0 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS24) == 0 );
+  fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS31) == 0 );
 }
 END_TEST
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 14561
          http://sbml.svn.sourceforge.net/sbml/?rev=14561&view=rev
Author:   sarahkeating
Date:     2011-10-27 09:02:24 +0000 (Thu, 27 Oct 2011)
Log Message:
-----------
changed the name of the test file to clearly show it is invalid

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile1.cs
    trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile2.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile1.java
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile2.java
    trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile1.py
    trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile2.py
    trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile1.rb
    trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile2.rb
    trunk/libsbml/src/sbml/math/test/TestReadFromFile1.cpp
    trunk/libsbml/src/sbml/math/test/TestReadFromFile2.cpp

Added Paths:
-----------
    trunk/libsbml/src/sbml/math/test/test-data/mathML_1-invalid.xml
    trunk/libsbml/src/sbml/math/test/test-data/mathML_2-invalid.xml

Removed Paths:
-------------
    trunk/libsbml/src/sbml/math/test/test-data/mathML_1.xml
    trunk/libsbml/src/sbml/math/test/test-data/mathML_2.xml

Modified: trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile1.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile1.cs	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile1.cs	2011-10-27 09:02:24 UTC (rev 14561)
@@ -138,7 +138,7 @@
       Rule r;
       KineticLaw kl;
       string filename =  "../../sbml/math/test/test-data/";
-      filename += "mathML_1.xml";
+      filename += "mathML_1-invalid.xml";
       d = reader.readSBML(filename);
       if (d == null);
       {

Modified: trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile2.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile2.cs	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/csharp/test/math/TestReadFromFile2.cs	2011-10-27 09:02:24 UTC (rev 14561)
@@ -137,7 +137,7 @@
       InitialAssignment ia;
       Rule r;
       string filename =  "../../sbml/math/test/test-data/";
-      filename += "mathML_2.xml";
+      filename += "mathML_2-invalid.xml";
       d = reader.readSBML(filename);
       if (d == null);
       {

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile1.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile1.java	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile1.java	2011-10-27 09:02:24 UTC (rev 14561)
@@ -128,7 +128,7 @@
     Rule r;
     KineticLaw kl;
     String filename = new String( "../../sbml/math/test/test-data/" );
-    filename += "mathML_1.xml";
+    filename += "mathML_1-invalid.xml";
     d = reader.readSBML(filename);
     if (d == null);
     {

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile2.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile2.java	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile2.java	2011-10-27 09:02:24 UTC (rev 14561)
@@ -127,7 +127,7 @@
     InitialAssignment ia;
     Rule r;
     String filename = new String( "../../sbml/math/test/test-data/" );
-    filename += "mathML_2.xml";
+    filename += "mathML_2-invalid.xml";
     d = reader.readSBML(filename);
     if (d == null);
     {

Modified: trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile1.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile1.py	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile1.py	2011-10-27 09:02:24 UTC (rev 14561)
@@ -40,7 +40,7 @@
   def test_read_MathML_1(self):
     reader = libsbml.SBMLReader()
     filename = "../../sbml/math/test/test-data/"
-    filename += "mathML_1.xml"
+    filename += "mathML_1-invalid.xml"
     d = reader.readSBML(filename)
     if (d == None):
       pass    

Modified: trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile2.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile2.py	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/python/test/math/TestMathReadFromFile2.py	2011-10-27 09:02:24 UTC (rev 14561)
@@ -40,7 +40,7 @@
   def test_read_MathML_2(self):
     reader = libsbml.SBMLReader()
     filename = "../../sbml/math/test/test-data/"
-    filename += "mathML_2.xml"
+    filename += "mathML_2-invalid.xml"
     d = reader.readSBML(filename)
     if (d == None):
       pass    

Modified: trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile1.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile1.rb	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile1.rb	2011-10-27 09:02:24 UTC (rev 14561)
@@ -36,7 +36,7 @@
   def test_read_MathML_1
     reader = LibSBML::SBMLReader.new()
     filename = "../../sbml/math/test/test-data/"
-    filename += "mathML_1.xml"
+    filename += "mathML_1-invalid.xml"
     d = reader.readSBML(filename)
     if (d == nil)
     end

Modified: trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile2.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile2.rb	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/bindings/ruby/test/math/TestMathReadFromFile2.rb	2011-10-27 09:02:24 UTC (rev 14561)
@@ -36,7 +36,7 @@
   def test_read_MathML_2
     reader = LibSBML::SBMLReader.new()
     filename = "../../sbml/math/test/test-data/"
-    filename += "mathML_2.xml"
+    filename += "mathML_2-invalid.xml"
     d = reader.readSBML(filename)
     if (d == nil)
     end

Modified: trunk/libsbml/src/sbml/math/test/TestReadFromFile1.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestReadFromFile1.cpp	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/sbml/math/test/TestReadFromFile1.cpp	2011-10-27 09:02:24 UTC (rev 14561)
@@ -58,14 +58,14 @@
 
 
   std::string filename(TestDataDirectory);
-  filename += "mathML_1.xml";
+  filename += "mathML_1-invalid.xml";
 
 
   d = reader.readSBML(filename);
 
   if (d == NULL)
   {
-    fail("readSBML(\"mathML_1.xml\") returned a NULL pointer.");
+    fail("readSBML(\"mathML_1-invalid.xml\") returned a NULL pointer.");
   }
 
   m = d->getModel();

Modified: trunk/libsbml/src/sbml/math/test/TestReadFromFile2.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestReadFromFile2.cpp	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/sbml/math/test/TestReadFromFile2.cpp	2011-10-27 09:02:24 UTC (rev 14561)
@@ -58,14 +58,14 @@
 
 
   std::string filename(TestDataDirectory);
-  filename += "mathML_2.xml";
+  filename += "mathML_2-invalid.xml";
 
 
   d = reader.readSBML(filename);
 
   if (d == NULL)
   {
-    fail("readSBML(\"mathML_2.xml\") returned a NULL pointer.");
+    fail("readSBML(\"mathML_2-invalid.xml\") returned a NULL pointer.");
   }
 
   m = d->getModel();

Copied: trunk/libsbml/src/sbml/math/test/test-data/mathML_1-invalid.xml (from rev 14560, trunk/libsbml/src/sbml/math/test/test-data/mathML_1.xml)
===================================================================
--- trunk/libsbml/src/sbml/math/test/test-data/mathML_1-invalid.xml	                        (rev 0)
+++ trunk/libsbml/src/sbml/math/test/test-data/mathML_1-invalid.xml	2011-10-27 09:02:24 UTC (rev 14561)
@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+  <model id="l2v3_all">
+    <listOfFunctionDefinitions>
+      <functionDefinition id="fd">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply/>
+          </lambda>
+        </math>
+      </functionDefinition>
+      <functionDefinition id="fd1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+             <true/>
+          </lambda>
+        </math>
+      </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfCompartments>
+      <compartment id="a" size="1" constant="false"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="s" compartment="a" initialAmount="0"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="p" value="2" units="second" constant="false"/>
+      <parameter id="p1" value="2" units="litre" constant="false"/>
+      <parameter id="p2" value="2" units="litre" constant="false"/>
+      <parameter id="p3" value="2" units="litre" constant="false"/>
+      <parameter id="x" value="2" units="dimensionless" constant="false"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="p1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply/>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfRules>
+      <algebraicRule>
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <true/>
+        </math>
+      </algebraicRule>
+      <assignmentRule variable="p2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <infinity/>
+        </math>
+      </assignmentRule>
+    </listOfRules>
+    <listOfReactions>
+      <reaction id="r">
+        <listOfReactants>
+          <speciesReference species="s"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <cn> 4.5 </cn>
+            </apply>
+          </math>
+          <listOfParameters>
+            <parameter id="k" value="9" units="litre"/>
+          </listOfParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

Deleted: trunk/libsbml/src/sbml/math/test/test-data/mathML_1.xml
===================================================================
--- trunk/libsbml/src/sbml/math/test/test-data/mathML_1.xml	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/sbml/math/test/test-data/mathML_1.xml	2011-10-27 09:02:24 UTC (rev 14561)
@@ -1,76 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
-  <model id="l2v3_all">
-    <listOfFunctionDefinitions>
-      <functionDefinition id="fd">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <apply/>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="fd1">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-             <true/>
-          </lambda>
-        </math>
-      </functionDefinition>
-    </listOfFunctionDefinitions>
-    <listOfCompartments>
-      <compartment id="a" size="1" constant="false"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="s" compartment="a" initialAmount="0"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="p" value="2" units="second" constant="false"/>
-      <parameter id="p1" value="2" units="litre" constant="false"/>
-      <parameter id="p2" value="2" units="litre" constant="false"/>
-      <parameter id="p3" value="2" units="litre" constant="false"/>
-      <parameter id="x" value="2" units="dimensionless" constant="false"/>
-    </listOfParameters>
-    <listOfInitialAssignments>
-      <initialAssignment symbol="p1">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply/>
-        </math>
-      </initialAssignment>
-    </listOfInitialAssignments>
-    <listOfRules>
-      <algebraicRule>
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <true/>
-        </math>
-      </algebraicRule>
-      <assignmentRule variable="p2">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <infinity/>
-        </math>
-      </assignmentRule>
-    </listOfRules>
-    <listOfReactions>
-      <reaction id="r">
-        <listOfReactants>
-          <speciesReference species="s"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <cn> 4.5 </cn>
-            </apply>
-          </math>
-          <listOfParameters>
-            <parameter id="k" value="9" units="litre"/>
-          </listOfParameters>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>

Copied: trunk/libsbml/src/sbml/math/test/test-data/mathML_2-invalid.xml (from rev 14560, trunk/libsbml/src/sbml/math/test/test-data/mathML_2.xml)
===================================================================
--- trunk/libsbml/src/sbml/math/test/test-data/mathML_2-invalid.xml	                        (rev 0)
+++ trunk/libsbml/src/sbml/math/test/test-data/mathML_2-invalid.xml	2011-10-27 09:02:24 UTC (rev 14561)
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+  <model id="l2v3_all">
+    <listOfFunctionDefinitions>
+      <functionDefinition id="fd">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <apply/>
+          </lambda>
+        </math>
+      </functionDefinition>
+      <functionDefinition id="fd1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <piecewise>
+              <piece>
+                <ci> p </ci>
+                <apply>
+                  <leq/>
+                  <ci> x </ci>
+                  <cn type="integer"> 4 </cn>
+                </apply>
+              </piece>
+            </piecewise>
+          </lambda>
+        </math>
+      </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfCompartments>
+      <compartment id="a" size="1" constant="false"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="s" compartment="a" initialAmount="0"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="p" value="2" units="second" constant="false"/>
+      <parameter id="p1" value="2" units="litre" constant="false"/>
+      <parameter id="p2" value="2" units="litre" constant="false"/>
+      <parameter id="p3" value="2" units="litre" constant="false"/>
+      <parameter id="x" value="2" units="dimensionless" constant="false"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="p1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <piecewise>
+              <piece>
+                  <apply><minus/><ci> x </ci></apply>
+                  <apply><lt/><ci> x </ci> <cn> 0 </cn></apply>
+              </piece>
+              <piece>
+                  <cn> 0 </cn>
+                  <apply><eq/><ci> x </ci> <cn> 0 </cn></apply>
+              </piece>
+            </piecewise>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfRules>
+      <algebraicRule>
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+          <true/>
+          </apply>
+        </math>
+      </algebraicRule>
+      <assignmentRule variable="p2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <log/>
+            <logbase>
+              <cn> 3 </cn>
+            </logbase>
+            <ci> x </ci>
+          </apply>
+        </math>
+      </assignmentRule>
+    </listOfRules>
+  </model>
+</sbml>

Deleted: trunk/libsbml/src/sbml/math/test/test-data/mathML_2.xml
===================================================================
--- trunk/libsbml/src/sbml/math/test/test-data/mathML_2.xml	2011-10-27 05:26:16 UTC (rev 14560)
+++ trunk/libsbml/src/sbml/math/test/test-data/mathML_2.xml	2011-10-27 09:02:24 UTC (rev 14561)
@@ -1,82 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
-  <model id="l2v3_all">
-    <listOfFunctionDefinitions>
-      <functionDefinition id="fd">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <apply/>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="fd1">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <piecewise>
-              <piece>
-                <ci> p </ci>
-                <apply>
-                  <leq/>
-                  <ci> x </ci>
-                  <cn type="integer"> 4 </cn>
-                </apply>
-              </piece>
-            </piecewise>
-          </lambda>
-        </math>
-      </functionDefinition>
-    </listOfFunctionDefinitions>
-    <listOfCompartments>
-      <compartment id="a" size="1" constant="false"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="s" compartment="a" initialAmount="0"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="p" value="2" units="second" constant="false"/>
-      <parameter id="p1" value="2" units="litre" constant="false"/>
-      <parameter id="p2" value="2" units="litre" constant="false"/>
-      <parameter id="p3" value="2" units="litre" constant="false"/>
-      <parameter id="x" value="2" units="dimensionless" constant="false"/>
-    </listOfParameters>
-    <listOfInitialAssignments>
-      <initialAssignment symbol="p1">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <piecewise>
-              <piece>
-                  <apply><minus/><ci> x </ci></apply>
-                  <apply><lt/><ci> x </ci> <cn> 0 </cn></apply>
-              </piece>
-              <piece>
-                  <cn> 0 </cn>
-                  <apply><eq/><ci> x </ci> <cn> 0 </cn></apply>
-              </piece>
-            </piecewise>
-        </math>
-      </initialAssignment>
-    </listOfInitialAssignments>
-    <listOfRules>
-      <algebraicRule>
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-          <true/>
-          </apply>
-        </math>
-      </algebraicRule>
-      <assignmentRule variable="p2">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <log/>
-            <logbase>
-              <cn> 3 </cn>
-            </logbase>
-            <ci> x </ci>
-          </apply>
-        </math>
-      </assignmentRule>
-    </listOfRules>
-  </model>
-</sbml>

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 14563
          http://sbml.svn.sourceforge.net/sbml/?rev=14563&view=rev
Author:   sarahkeating
Date:     2011-10-27 09:51:23 +0000 (Thu, 27 Oct 2011)
Log Message:
-----------
changed the name of the test file to clearly show it is invalid

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestReadFromFile9.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile9.java
    trunk/libsbml/src/bindings/perl/t/02__ReadFromFileL3.t
    trunk/libsbml/src/bindings/python/test/sbml/TestReadFromFile9.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestReadFromFile9.rb
    trunk/libsbml/src/sbml/test/TestReadFromFile9.cpp

Added Paths:
-----------
    trunk/libsbml/src/sbml/test/test-data/l3v1-new-invalid.xml

Removed Paths:
-------------
    trunk/libsbml/src/sbml/test/test-data/l3v1-new.xml

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestReadFromFile9.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestReadFromFile9.cs	2011-10-27 09:44:46 UTC (rev 14562)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestReadFromFile9.cs	2011-10-27 09:51:23 UTC (rev 14563)
@@ -1,8 +1,8 @@
 ///  @file    TestReadFromFile9.cs
-///  @brief   Reads tests/l3v1-new.xml into memory and tests it.
+///  @brief   Reads tests/l3v1-new.xml into memory and tests it.
 ///  @author  Frank Bergmann (Csharp conversion)
 ///  @author  Akiya Jouraku (Csharp conversion)
-///  @author  Sarah Keating
+///  @author  Sarah Keating
  
 /// 
 /// 
@@ -153,7 +153,7 @@
       Trigger t;
       Priority pr;
       string filename =  "../../sbml/test/test-data/";
-      filename += "l3v1-new.xml";
+      filename += "l3v1-new-invalid.xml";
       d = reader.readSBML(filename);
       if (d == null);
       {

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile9.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile9.java	2011-10-27 09:44:46 UTC (rev 14562)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile9.java	2011-10-27 09:51:23 UTC (rev 14563)
@@ -1,9 +1,9 @@
 /*
  * @file    TestReadFromFile9.java
- * @brief   Reads tests/l3v1-new.xml into memory and tests it.
+ * @brief   Reads tests/l3v1-new.xml into memory and tests it.
  *
  * @author  Akiya Jouraku (Java conversion)
- * @author  Sarah Keating
+ * @author  Sarah Keating
  
  * 
  * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
@@ -143,7 +143,7 @@
     Trigger t;
     Priority pr;
     String filename = new String( "../../sbml/test/test-data/" );
-    filename += "l3v1-new.xml";
+    filename += "l3v1-new-invalid.xml";
     d = reader.readSBML(filename);
     if (d == null);
     {

Modified: trunk/libsbml/src/bindings/perl/t/02__ReadFromFileL3.t
===================================================================
--- trunk/libsbml/src/bindings/perl/t/02__ReadFromFileL3.t	2011-10-27 09:44:46 UTC (rev 14562)
+++ trunk/libsbml/src/bindings/perl/t/02__ReadFromFileL3.t	2011-10-27 09:51:23 UTC (rev 14563)
@@ -15,7 +15,7 @@
 $level = 1;
 $version = 1;
 $rd = new LibSBML::SBMLReader;
-@... = qw/l3v1-new.xml/;
+@files = qw/l3v1-new-invalid.xml/;
 
 foreach (@files) {
   $level = 3;

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestReadFromFile9.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestReadFromFile9.py	2011-10-27 09:44:46 UTC (rev 14562)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestReadFromFile9.py	2011-10-27 09:51:23 UTC (rev 14563)
@@ -1,9 +1,9 @@
 #
 # @file    TestReadFromFile9.py
-# @brief   Reads tests/l3v1-new.xml into memory and tests it.
+# @brief   Reads tests/l3v1-new.xml into memory and tests it.
 #
 # @author  Akiya Jouraku (Python conversion)
-# @author  Sarah Keating
+# @author  Sarah Keating
  
 # 
 # ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
@@ -45,7 +45,7 @@
   def test_read_l3v1_new(self):
     reader = libsbml.SBMLReader()
     filename = "../../sbml/test/test-data/"
-    filename += "l3v1-new.xml"
+    filename += "l3v1-new-invalid.xml"
     d = reader.readSBML(filename)
     if (d == None):
       pass    

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestReadFromFile9.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestReadFromFile9.rb	2011-10-27 09:44:46 UTC (rev 14562)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestReadFromFile9.rb	2011-10-27 09:51:23 UTC (rev 14563)
@@ -1,8 +1,8 @@
 # @file    TestReadFromFile9.rb
-# @brief   Reads tests/l3v1-new.xml into memory and tests it.
+# @brief   Reads tests/l3v1-new.xml into memory and tests it.
 #
 # @author  Akiya Jouraku (Ruby conversion)
-# @author  Sarah Keating
+# @author  Sarah Keating
  
 #
 #
@@ -41,7 +41,7 @@
   def test_read_l3v1_new
     reader = LibSBML::SBMLReader.new()
     filename = "../../sbml/test/test-data/"
-    filename += "l3v1-new.xml"
+    filename += "l3v1-new-invalid.xml"
     d = reader.readSBML(filename)
     if (d == nil)
     end

Modified: trunk/libsbml/src/sbml/test/TestReadFromFile9.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestReadFromFile9.cpp	2011-10-27 09:44:46 UTC (rev 14562)
+++ trunk/libsbml/src/sbml/test/TestReadFromFile9.cpp	2011-10-27 09:51:23 UTC (rev 14563)
@@ -75,14 +75,14 @@
   Priority*         pr;
 
   std::string filename(TestDataDirectory);
-  filename += "l3v1-new.xml";
+  filename += "l3v1-new-invalid.xml";
 
 
   d = reader.readSBML(filename);
 
   if (d == NULL)
   {
-    fail("readSBML(\"l3v1-new.xml\") returned a NULL pointer.");
+    fail("readSBML(\"l3v1-new-invalid.xml\") returned a NULL pointer.");
   }
 
 

Copied: trunk/libsbml/src/sbml/test/test-data/l3v1-new-invalid.xml (from rev 14560, trunk/libsbml/src/sbml/test/test-data/l3v1-new.xml)
===================================================================
--- trunk/libsbml/src/sbml/test/test-data/l3v1-new-invalid.xml	                        (rev 0)
+++ trunk/libsbml/src/sbml/test/test-data/l3v1-new-invalid.xml	2011-10-27 09:51:23 UTC (rev 14563)
@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model timeUnits="second" extentUnits="mole"
+         volumeUnits="litre" areaUnits="metre" lengthUnits="metre"
+         conversionFactor="p" substanceUnits="mole">
+     <listOfUnitDefinitions>
+       <unitDefinition id="per_second">
+          <listOfUnits>
+             <unit kind="second"/>
+          </listOfUnits>
+       </unitDefinition>
+       <unitDefinition id="nonsense">
+          <listOfUnits>
+             <unit kind="mole"   exponent="-1" scale="2" multiplier="1.3"/>
+             <unit kind="litre"  exponent="1.5"  scale="10" multiplier="0.5"/>
+             <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+          </listOfUnits>
+       </unitDefinition>
+     </listOfUnitDefinitions>
+     <listOfCompartments>
+       <compartment id="comp" size="1e-14" spatialDimensions="3" units="litre" constant="true"/>
+      <compartment id="comp1" constant="false"/>
+      <compartment id="comp2" spatialDimensions="4.6"/>
+     </listOfCompartments>
+     <listOfSpecies>
+       <species compartment="comp" id="ES" initialAmount="0"     boundaryCondition="false"
+                hasOnlySubstanceUnits="false" substanceUnits="mole" constant="false" conversionFactor="p"/>
+       <species compartment="comp" id="P"/>
+     </listOfSpecies>
+     <listOfParameters>
+        <parameter id="Keq" value="2.5" units="dimensionless" constant="true"/>
+        <parameter id="Keq1" constant="false"/>
+        <parameter id="Keq2"/>
+     </listOfParameters>
+     <listOfReactions>
+        <reaction id="in" reversible="false" fast="false" compartment="comp">
+            <listOfReactants>
+                <speciesReference species="X0" stoichiometry="1" constant="true"/>
+            </listOfReactants>
+            <listOfProducts>
+                <speciesReference species="T" constant="false"/>
+            </listOfProducts>
+            <kineticLaw>
+                <math xmlns="http://www.w3.org/1998/Math/MathML">
+                    <apply>
+                        <times/>
+                        <ci> k1 </ci>
+                        <ci> X0 </ci>
+                        <ci> cell </ci>
+                    </apply>
+                </math>
+                <listOfLocalParameters>
+                    <localParameter id="k1" value="0.1" units="per_second"/>
+                    <localParameter id="k2"/>
+                </listOfLocalParameters>
+            </kineticLaw>
+        </reaction>
+        <reaction id="out1" reversible="true" fast="true">
+            <listOfReactants>
+                <speciesReference species="T" stoichiometry="1"/>
+            </listOfReactants>
+            <listOfProducts>
+                <speciesReference species="X1" stoichiometry="1" constant="true"/>
+            </listOfProducts>
+            <listOfModifiers>
+                    <modifierSpeciesReference species="S2"/>
+            </listOfModifiers>
+            <kineticLaw>
+                <math xmlns="http://www.w3.org/1998/Math/MathML">
+                    <apply>
+                        <times/>
+                        <ci> k2 </ci>
+                        <ci> S2 </ci>
+                        <ci> cell </ci>
+                    </apply>
+                </math>
+                <listOfLocalParameters>
+                    <localParameter id="k2" value="0.15" units="per_second"/>
+                </listOfLocalParameters>
+            </kineticLaw>
+        </reaction>
+        <reaction id="out">
+            <listOfReactants>
+                <speciesReference species="T" stoichiometry="1" constant="true"/>
+            </listOfReactants>
+            <listOfProducts>
+                <speciesReference species="X1" stoichiometry="1" constant="true"/>
+            </listOfProducts>
+            <listOfModifiers>
+                    <modifierSpeciesReference species="S2"/>
+            </listOfModifiers>
+            <kineticLaw>
+                <math xmlns="http://www.w3.org/1998/Math/MathML">
+                    <apply>
+                        <times/>
+                        <ci> k2 </ci>
+                        <ci> S2 </ci>
+                        <ci> cell </ci>
+                    </apply>
+                </math>
+                <listOfLocalParameters>
+                    <localParameter id="k2" value="0.15" units="per_second"/>
+                </listOfLocalParameters>
+            </kineticLaw>
+        </reaction>
+     </listOfReactions>
+     <listOfEvents>
+       <event useValuesFromTriggerTime="true">
+         <trigger initialValue="false" persistent="false">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <true/>
+            </math>
+         </trigger>
+         <priority>
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn> 1 </cn>
+            </math>
+         </priority>
+       </event>
+       <event>
+         <trigger>
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <true/>
+            </math>
+         </trigger>
+       </event>
+     </listOfEvents>
+  </model>
+</sbml>

Deleted: trunk/libsbml/src/sbml/test/test-data/l3v1-new.xml
===================================================================
--- trunk/libsbml/src/sbml/test/test-data/l3v1-new.xml	2011-10-27 09:44:46 UTC (rev 14562)
+++ trunk/libsbml/src/sbml/test/test-data/l3v1-new.xml	2011-10-27 09:51:23 UTC (rev 14563)
@@ -1,129 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
-  <model timeUnits="second" extentUnits="mole"
-         volumeUnits="litre" areaUnits="metre" lengthUnits="metre"
-         conversionFactor="p" substanceUnits="mole">
-     <listOfUnitDefinitions>
-       <unitDefinition id="per_second">
-          <listOfUnits>
-             <unit kind="second"/>
-          </listOfUnits>
-       </unitDefinition>
-       <unitDefinition id="nonsense">
-          <listOfUnits>
-             <unit kind="mole"   exponent="-1" scale="2" multiplier="1.3"/>
-             <unit kind="litre"  exponent="1.5"  scale="10" multiplier="0.5"/>
-             <unit kind="second" exponent="1" scale="0" multiplier="1"/>
-          </listOfUnits>
-       </unitDefinition>
-     </listOfUnitDefinitions>
-     <listOfCompartments>
-       <compartment id="comp" size="1e-14" spatialDimensions="3" units="litre" constant="true"/>
-      <compartment id="comp1" constant="false"/>
-      <compartment id="comp2" spatialDimensions="4.6"/>
-     </listOfCompartments>
-     <listOfSpecies>
-       <species compartment="comp" id="ES" initialAmount="0"     boundaryCondition="false"
-                hasOnlySubstanceUnits="false" substanceUnits="mole" constant="false" conversionFactor="p"/>
-       <species compartment="comp" id="P"/>
-     </listOfSpecies>
-     <listOfParameters>
-        <parameter id="Keq" value="2.5" units="dimensionless" constant="true"/>
-        <parameter id="Keq1" constant="false"/>
-        <parameter id="Keq2"/>
-     </listOfParameters>
-     <listOfReactions>
-        <reaction id="in" reversible="false" fast="false" compartment="comp">
-            <listOfReactants>
-                <speciesReference species="X0" stoichiometry="1" constant="true"/>
-            </listOfReactants>
-            <listOfProducts>
-                <speciesReference species="T" constant="false"/>
-            </listOfProducts>
-            <kineticLaw>
-                <math xmlns="http://www.w3.org/1998/Math/MathML">
-                    <apply>
-                        <times/>
-                        <ci> k1 </ci>
-                        <ci> X0 </ci>
-                        <ci> cell </ci>
-                    </apply>
-                </math>
-                <listOfLocalParameters>
-                    <localParameter id="k1" value="0.1" units="per_second"/>
-                    <localParameter id="k2"/>
-                </listOfLocalParameters>
-            </kineticLaw>
-        </reaction>
-        <reaction id="out1" reversible="true" fast="true">
-            <listOfReactants>
-                <speciesReference species="T" stoichiometry="1"/>
-            </listOfReactants>
-            <listOfProducts>
-                <speciesReference species="X1" stoichiometry="1" constant="true"/>
-            </listOfProducts>
-            <listOfModifiers>
-                    <modifierSpeciesReference species="S2"/>
-            </listOfModifiers>
-            <kineticLaw>
-                <math xmlns="http://www.w3.org/1998/Math/MathML">
-                    <apply>
-                        <times/>
-                        <ci> k2 </ci>
-                        <ci> S2 </ci>
-                        <ci> cell </ci>
-                    </apply>
-                </math>
-                <listOfLocalParameters>
-                    <localParameter id="k2" value="0.15" units="per_second"/>
-                </listOfLocalParameters>
-            </kineticLaw>
-        </reaction>
-        <reaction id="out">
-            <listOfReactants>
-                <speciesReference species="T" stoichiometry="1" constant="true"/>
-            </listOfReactants>
-            <listOfProducts>
-                <speciesReference species="X1" stoichiometry="1" constant="true"/>
-            </listOfProducts>
-            <listOfModifiers>
-                    <modifierSpeciesReference species="S2"/>
-            </listOfModifiers>
-            <kineticLaw>
-                <math xmlns="http://www.w3.org/1998/Math/MathML">
-                    <apply>
-                        <times/>
-                        <ci> k2 </ci>
-                        <ci> S2 </ci>
-                        <ci> cell </ci>
-                    </apply>
-                </math>
-                <listOfLocalParameters>
-                    <localParameter id="k2" value="0.15" units="per_second"/>
-                </listOfLocalParameters>
-            </kineticLaw>
-        </reaction>
-     </listOfReactions>
-     <listOfEvents>
-       <event useValuesFromTriggerTime="true">
-         <trigger initialValue="false" persistent="false">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-                <true/>
-            </math>
-         </trigger>
-         <priority>
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-                <cn> 1 </cn>
-            </math>
-         </priority>
-       </event>
-       <event>
-         <trigger>
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-                <true/>
-            </math>
-         </trigger>
-       </event>
-     </listOfEvents>
-  </model>
-</sbml>

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 14653
          http://sbml.svn.sourceforge.net/sbml/?rev=14653&view=rev
Author:   fbergmann
Date:     2011-10-31 19:08:54 +0000 (Mon, 31 Oct 2011)
Log Message:
-----------
Make it easier to access arguments and failures from language bindings 
- SBMLValidator returns number of failures and allows to get them by index 
- SBMLExternalValidator returns arguments by index

Modified Paths:
--------------
    trunk/libsbml/src/bindings/swig/libsbml.i
    trunk/libsbml/src/sbml/SBMLErrorLog.cpp
    trunk/libsbml/src/sbml/SBMLErrorLog.h
    trunk/libsbml/src/sbml/validator/SBMLExternalValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLExternalValidator.h
    trunk/libsbml/src/sbml/validator/SBMLValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLValidator.h

Modified: trunk/libsbml/src/bindings/swig/libsbml.i
===================================================================
--- trunk/libsbml/src/bindings/swig/libsbml.i	2011-10-31 18:07:29 UTC (rev 14652)
+++ trunk/libsbml/src/bindings/swig/libsbml.i	2011-10-31 19:08:54 UTC (rev 14653)
@@ -173,6 +173,14 @@
 %ignore XMLErrorLog::add(const std::list<XMLError>& errors);
 %ignore SBMLErrorLog::add(const std::list<SBMLError>& errors);
 
+/** 
+ * Ignore methods from SBML Validator that can't be wrapped
+ */
+%ignore SBMLValidator::getFailures;
+%ignore SBMLExternalValidator::getArguments;
+%ignore SBMLExternalValidator::setArguments;
+
+
 /**
  * Ignore 'static ParentMap mParent;' in SBO.h
  */

Modified: trunk/libsbml/src/sbml/SBMLErrorLog.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorLog.cpp	2011-10-31 18:07:29 UTC (rev 14652)
+++ trunk/libsbml/src/sbml/SBMLErrorLog.cpp	2011-10-31 19:08:54 UTC (rev 14653)
@@ -140,7 +140,22 @@
     XMLErrorLog::add( *iter );
 }
 
+/*
+ * Logs (copies) the SBMLErrors in the given SBMLError vector to this
+ * SBMLErrorLog.
+ *
+ * @param errors vector, a vector of SBMLError to be added to the log.
+ */
+void
+SBMLErrorLog::add (const std::vector<SBMLError>& errors)
+{
+  vector<SBMLError>::const_iterator end = errors.end();
+  vector<SBMLError>::const_iterator iter;
 
+  for (iter = errors.begin(); iter != end; ++iter)
+    XMLErrorLog::add( *iter );
+}
+
 /*
  * Helper class used by SBMLErrorLog::remove.
  */

Modified: trunk/libsbml/src/sbml/SBMLErrorLog.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorLog.h	2011-10-31 18:07:29 UTC (rev 14652)
+++ trunk/libsbml/src/sbml/SBMLErrorLog.h	2011-10-31 19:08:54 UTC (rev 14653)
@@ -77,6 +77,8 @@
 
 #ifdef __cplusplus
 
+#include <vector>
+
 LIBSBML_CPP_NAMESPACE_BEGIN
 
 class LIBSBML_EXTERN SBMLErrorLog : public XMLErrorLog
@@ -199,6 +201,13 @@
    */
   void add (const std::list<SBMLError>& errors);
 
+  /**
+   * Adds (copies) the SBMLErrors in the given SBMLError vector to this
+   * SBMLErrorLog.
+   *
+   * @param errors vector, a vector of SBMLError to be added to the log.
+   */
+  void add (const std::vector<SBMLError>& errors);
 
   /**
    * Removes an error having errorId from the SBMLError list.

Modified: trunk/libsbml/src/sbml/validator/SBMLExternalValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/validator/SBMLExternalValidator.cpp	2011-10-31 18:07:29 UTC (rev 14652)
+++ trunk/libsbml/src/sbml/validator/SBMLExternalValidator.cpp	2011-10-31 19:08:54 UTC (rev 14653)
@@ -236,7 +236,7 @@
   return LIBSBML_SEV_NOT_APPLICABLE;
 }
 
-void parseResultFile(std::string &mOutputFileName, std::list<SBMLError>& errors)
+void parseResultFile(std::string &mOutputFileName, std::vector<SBMLError>& errors)
 {
   XMLInputStream stream (mOutputFileName.c_str());  
 
@@ -333,6 +333,20 @@
   return (unsigned int)mFailures.size();
 }
 
+unsigned int 
+SBMLExternalValidator::getNumArguments() const
+{
+  return (unsigned int)mArguments.size();
+}
+
+std::string 
+SBMLExternalValidator::getArgument(unsigned int n) const
+{
+  return (n < mArguments.size()) ? mArguments[n] : "";
+}
+
+
+
 /** @cond doxygen-c-only */
 
 

Modified: trunk/libsbml/src/sbml/validator/SBMLExternalValidator.h
===================================================================
--- trunk/libsbml/src/sbml/validator/SBMLExternalValidator.h	2011-10-31 18:07:29 UTC (rev 14652)
+++ trunk/libsbml/src/sbml/validator/SBMLExternalValidator.h	2011-10-31 19:08:54 UTC (rev 14653)
@@ -133,7 +133,20 @@
    */
   void addArgument(std::string arg);
 
+  /** 
+   * @return the number of arguments. 
+   */
+  unsigned int getNumArguments() const;
 
+  /** 
+   * Returns the argument for the given index. 
+   * 
+   * @param n the zero based index of the argument. 
+   *
+   * @return the argument at the given index. 
+   */
+  std::string getArgument(unsigned int n) const;
+
   /**
    * @return all arguments
    */

Modified: trunk/libsbml/src/sbml/validator/SBMLValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/validator/SBMLValidator.cpp	2011-10-31 18:07:29 UTC (rev 14652)
+++ trunk/libsbml/src/sbml/validator/SBMLValidator.cpp	2011-10-31 19:08:54 UTC (rev 14653)
@@ -143,7 +143,7 @@
 /*
  * @return a list of failures logged during validation.
  */
-const std::list<SBMLError>&
+const std::vector<SBMLError>&
 SBMLValidator::getFailures () const
 {
   return mFailures;
@@ -233,6 +233,17 @@
 }
   
 
+SBMLError*
+SBMLValidator::getFailure (unsigned int n) const
+{
+  return (n < mFailures.size()) ? mFailures[n].clone() : NULL;
+}
+
+unsigned int
+SBMLValidator::getNumFailures() const
+{
+  return (unsigned int) mFailures.size();
+}
   
 /** @cond doxygen-c-only */
 

Modified: trunk/libsbml/src/sbml/validator/SBMLValidator.h
===================================================================
--- trunk/libsbml/src/sbml/validator/SBMLValidator.h	2011-10-31 18:07:29 UTC (rev 14652)
+++ trunk/libsbml/src/sbml/validator/SBMLValidator.h	2011-10-31 19:08:54 UTC (rev 14653)
@@ -112,7 +112,7 @@
    * 
    * @return a list of failures logged during validation.
    */
-  const std::list<SBMLError>& getFailures () const;
+  const std::vector<SBMLError>& getFailures () const;
 
 
   /**
@@ -176,6 +176,26 @@
    */
   Model* getModel ();
 
+  /** 
+   * Returns the local number of failures
+   * 
+   * This method returns the number of failures logged by this validator 
+   * (that is it does not include the number of the documents error log).
+   *
+   * @return the number of errors logged by this validator. 
+   */
+  unsigned int getNumFailures() const;
+
+  /** 
+   * Returns the failure at the given index. 
+   *
+   * @param n the zero based index of failures
+   * 
+   * @return the failure at the given index
+   */
+  SBMLError* getFailure (unsigned int n) const;
+
+
 #ifndef SWIG
 
 #endif // SWIG
@@ -184,7 +204,7 @@
 
 protected:
   /** @cond doxygen-libsbml-internal */
-  std::list<SBMLError>  mFailures;
+  std::vector<SBMLError>  mFailures;
   SBMLDocument *   mDocument;
   friend class SBMLDocument;
   /** @endcond doxygen-libsbml-internal */

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Revision: 15293
          http://sbml.svn.sourceforge.net/sbml/?rev=15293&view=rev
Author:   sarahkeating
Date:     2012-01-23 10:50:18 +0000 (Mon, 23 Jan 2012)
Log Message:
-----------
stopped events with priority being down converted

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBMLConvert.java
    trunk/libsbml/src/bindings/python/test/sbml/TestSBMLConvert.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestSBMLConvert.rb
    trunk/libsbml/src/sbml/SBMLErrorTable.h
    trunk/libsbml/src/sbml/test/TestRunner.c
    trunk/libsbml/src/sbml/test/TestSBMLConvert.c
    trunk/libsbml/src/sbml/test/TestSBMLConvertStrict.c

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestSBMLConvert.cs	2012-01-23 10:50:18 UTC (rev 15293)
@@ -257,11 +257,11 @@
       Event e = m.createEvent();
       Priority p = e.createPriority();
       assertTrue( d.setLevelAndVersion(1,1,false) == false );
-      assertTrue( d.setLevelAndVersion(1,2,false) == false );
-      assertTrue( d.setLevelAndVersion(2,1,false) == true );
-      assertTrue( d.setLevelAndVersion(2,2,false) == true );
-      assertTrue( d.setLevelAndVersion(2,3,false) == true );
-      assertTrue( d.setLevelAndVersion(2,4,false) == true );
+      assertTrue( d.setLevelAndVersion(1,2,false) == false );
+      assertTrue(d.setLevelAndVersion(2, 1, false) == false);
+      assertTrue(d.setLevelAndVersion(2, 2, false) == false);
+      assertTrue(d.setLevelAndVersion(2, 3, false) == false);
+      assertTrue(d.setLevelAndVersion(2, 4, false) == false);
       assertTrue( d.setLevelAndVersion(3,1,false) == true );
     }
 

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBMLConvert.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBMLConvert.java	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBMLConvert.java	2012-01-23 10:50:18 UTC (rev 15293)
@@ -248,10 +248,10 @@
     Priority p = e.createPriority();
     assertTrue( d.setLevelAndVersion(1,1,false) == false );
     assertTrue( d.setLevelAndVersion(1,2,false) == false );
-    assertTrue( d.setLevelAndVersion(2,1,false) == true );
-    assertTrue( d.setLevelAndVersion(2,2,false) == true );
-    assertTrue( d.setLevelAndVersion(2,3,false) == true );
-    assertTrue( d.setLevelAndVersion(2,4,false) == true );
+    assertTrue( d.setLevelAndVersion(2,1,false) == false );
+    assertTrue( d.setLevelAndVersion(2,2,false) == false );
+    assertTrue( d.setLevelAndVersion(2,3,false) == false );
+    assertTrue( d.setLevelAndVersion(2,4,false) == false );
     assertTrue( d.setLevelAndVersion(3,1,false) == true );
   }
 

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestSBMLConvert.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestSBMLConvert.py	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestSBMLConvert.py	2012-01-23 10:50:18 UTC (rev 15293)
@@ -157,10 +157,10 @@
     p = e.createPriority()
     self.assert_( d.setLevelAndVersion(1,1,False) == False )
     self.assert_( d.setLevelAndVersion(1,2,False) == False )
-    self.assert_( d.setLevelAndVersion(2,1,False) == True )
-    self.assert_( d.setLevelAndVersion(2,2,False) == True )
-    self.assert_( d.setLevelAndVersion(2,3,False) == True )
-    self.assert_( d.setLevelAndVersion(2,4,False) == True )
+    self.assert_( d.setLevelAndVersion(2,1,False) == False )
+    self.assert_( d.setLevelAndVersion(2,2,False) == False )
+    self.assert_( d.setLevelAndVersion(2,3,False) == False )
+    self.assert_( d.setLevelAndVersion(2,4,False) == False )
     self.assert_( d.setLevelAndVersion(3,1,False) == True )
     pass  
 

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestSBMLConvert.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestSBMLConvert.rb	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestSBMLConvert.rb	2012-01-23 10:50:18 UTC (rev 15293)
@@ -153,10 +153,10 @@
     p = e.createPriority()
     assert( d.setLevelAndVersion(1,1,false) == false )
     assert( d.setLevelAndVersion(1,2,false) == false )
-    assert( d.setLevelAndVersion(2,1,false) == true )
-    assert( d.setLevelAndVersion(2,2,false) == true )
-    assert( d.setLevelAndVersion(2,3,false) == true )
-    assert( d.setLevelAndVersion(2,4,false) == true )
+    assert( d.setLevelAndVersion(2,1,false) == false )
+    assert( d.setLevelAndVersion(2,2,false) == false )
+    assert( d.setLevelAndVersion(2,3,false) == false )
+    assert( d.setLevelAndVersion(2,4,false) == false )
     assert( d.setLevelAndVersion(3,1,false) == true )
   end
 

Modified: trunk/libsbml/src/sbml/SBMLErrorTable.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorTable.h	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/sbml/SBMLErrorTable.h	2012-01-23 10:50:18 UTC (rev 15293)
@@ -7175,9 +7175,8 @@
     LIBSBML_SEV_NOT_APPLICABLE,
     LIBSBML_SEV_NOT_APPLICABLE,
     LIBSBML_SEV_NOT_APPLICABLE,
-    LIBSBML_SEV_WARNING,
-    "Prioirty is not supported in SBML Level 2.  This information will be "
-    "lost during conversion."
+    LIBSBML_SEV_ERROR,
+    "Event priority is not supported in SBML Level 2."
   },
 
   //92012

Modified: trunk/libsbml/src/sbml/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestRunner.c	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/sbml/test/TestRunner.c	2012-01-23 10:50:18 UTC (rev 15293)
@@ -266,8 +266,8 @@
   srunner_add_suite( runner, create_suite_UnitDefinition_newSetters     () );
   srunner_add_suite( runner, create_suite_UnitKind                      () );
   srunner_add_suite( runner, create_suite_CopyAndClone                  () );
-  //srunner_add_suite( runner, create_suite_SBMLConvert                   () );
-  //srunner_add_suite( runner, create_suite_SBMLConvertStrict             () );
+  srunner_add_suite( runner, create_suite_SBMLConvert                   () );
+  srunner_add_suite( runner, create_suite_SBMLConvertStrict             () );
   srunner_add_suite( runner, create_suite_SBMLDocument                  () );
   srunner_add_suite( runner, create_suite_SBMLError                     () );
   srunner_add_suite( runner, create_suite_TestReadFromFile1             () );

Modified: trunk/libsbml/src/sbml/test/TestSBMLConvert.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestSBMLConvert.c	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/sbml/test/TestSBMLConvert.c	2012-01-23 10:50:18 UTC (rev 15293)
@@ -764,77 +764,16 @@
 
   fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 1, 1) == 0);
   fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 1, 2) == 0);
-  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 1) == 1);
+  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 1) == 0);
+  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 2) == 0);
+  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 3) == 0);
+  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 4) == 0);
 
   SBMLDocument_free(d);
 }
 END_TEST
 
 
-START_TEST (test_SBMLConvert_convertFromL3_priority2)
-{
-  SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
-  Model_t        *m = SBMLDocument_createModel(d);
-
-  Event_t * e = Model_createEvent(m);
-  Priority_t * p = Event_createPriority(e);
-  (void) p;
-
-  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 2) == 1);
-
-  SBMLDocument_free(d);
-}
-END_TEST
-
-
-START_TEST (test_SBMLConvert_convertFromL3_priority3)
-{
-  SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
-  Model_t        *m = SBMLDocument_createModel(d);
-
-  Event_t * e = Model_createEvent(m);
-  Priority_t * p = Event_createPriority(e);
-  (void) p;
-
-  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 3) == 1);
-
-  SBMLDocument_free(d);
-}
-END_TEST
-
-
-START_TEST (test_SBMLConvert_convertFromL3_priority4)
-{
-  SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
-  Model_t        *m = SBMLDocument_createModel(d);
-
-  Event_t * e = Model_createEvent(m);
-  Priority_t * p = Event_createPriority(e);
-  (void) p;
-
-  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 2, 4) == 1);
-
-  SBMLDocument_free(d);
-}
-END_TEST
-
-
-START_TEST (test_SBMLConvert_convertFromL3_priority5)
-{
-  SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
-  Model_t        *m = SBMLDocument_createModel(d);
-
-  Event_t * e = Model_createEvent(m);
-  Priority_t * p = Event_createPriority(e);
-  (void) p;
-
-  fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1);
-
-  SBMLDocument_free(d);
-}
-END_TEST
-
-
 START_TEST (test_SBMLConvert_convertFromL3_persistent)
 {
   SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
@@ -1276,10 +1215,6 @@
   tcase_add_test( tcase, test_SBMLConvert_convertFromL3_modelUnits );
   tcase_add_test( tcase, test_SBMLConvert_convertFromL3_conversionFactor );
   tcase_add_test( tcase, test_SBMLConvert_convertFromL3_priority1 );
-  tcase_add_test( tcase, test_SBMLConvert_convertFromL3_priority2 );
-  tcase_add_test( tcase, test_SBMLConvert_convertFromL3_priority3 );
-  tcase_add_test( tcase, test_SBMLConvert_convertFromL3_priority4 );
-  tcase_add_test( tcase, test_SBMLConvert_convertFromL3_priority5 );
   tcase_add_test( tcase, test_SBMLConvert_convertFromL3_persistent );
   tcase_add_test( tcase, test_SBMLConvert_convertFromL3_initialValue );
   tcase_add_test( tcase, test_SBMLConvert_convertFromL3_stoichMath1 );

Modified: trunk/libsbml/src/sbml/test/TestSBMLConvertStrict.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestSBMLConvertStrict.c	2012-01-22 12:27:12 UTC (rev 15292)
+++ trunk/libsbml/src/sbml/test/TestSBMLConvertStrict.c	2012-01-23 10:50:18 UTC (rev 15293)
@@ -266,57 +266,6 @@
 END_TEST
 
 
-START_TEST (test_SBMLConvertStrict_convertL3Priority)
-{
-  SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
-  Model_t * m = SBMLDocument_createModel(d);
-  
-  /* create a compartment */
-  Compartment_t * c = Model_createCompartment(m);
-  Compartment_setId(c, "c");
-  Compartment_setConstant(c, 0);
-  Compartment_setSpatialDimensions(c, 3);
-
-  /* create  a parameter */
-  Parameter_t * p = Model_createParameter(m);
-  Parameter_setId(p, "p");
-  Parameter_setConstant(p, 0);
-
-  /* create a math element */
-  ASTNode_t *math = SBML_parseFormula("3");
-  ASTNode_t *math1 = SBML_parseFormula("lt(p,2)");
-
-  /* create an event */
-  Event_t *ar = Model_createEvent(m);
-  Event_setUseValuesFromTriggerTime(ar, 1);
-
-  Trigger_t *t = Event_createTrigger(ar);
-  Trigger_setInitialValue(t, 1);
-  Trigger_setPersistent(t, 1);
-  Trigger_setMath(t, math1);
-
-  EventAssignment_t *ea = Event_createEventAssignment(ar);
-  EventAssignment_setVariable(ea, "c");
-  EventAssignment_setMath(ea, math);
-
-  Priority_t *pr = Event_createPriority(ar);
-  Priority_setMath(pr, math);
-
-  fail_unless( Event_isSetPriority(ar) == 1);
-
-  fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 4) == 1 );
-  fail_unless( SBMLDocument_getLevel  (d) == 2, NULL );
-  fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
-
-  Event_t * r1 = Model_getEvent(SBMLDocument_getModel(d), 0);
-
-  fail_unless (Event_isSetPriority(r1) == 0 );
-
-  SBMLDocument_free(d);
-}
-END_TEST
-
-
 START_TEST (test_SBMLConvertStrict_convertFromL3_stoichMath1)
 {
   SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
@@ -903,7 +852,6 @@
   tcase_add_test( tcase, test_SBMLConvertStrict_convertSBO1                 );
   tcase_add_test( tcase, test_SBMLConvertStrict_convertSBO2                 );
   tcase_add_test( tcase, test_SBMLConvertStrict_convertL1ParamRule          );
-  tcase_add_test( tcase, test_SBMLConvertStrict_convertL3Priority          );
   tcase_add_test( tcase, test_SBMLConvertStrict_convertFromL3_stoichMath1 );
   tcase_add_test( tcase, test_SBMLConvertStrict_convertFromL3_stoichMath2 );
   tcase_add_test( tcase, test_SBMLConvertStrict_convertFromL3_stoichMath3 );

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Revision: 15472
          http://sbml.svn.sourceforge.net/sbml/?rev=15472&view=rev
Author:   fbergmann
Date:     2012-02-21 02:45:27 +0000 (Tue, 21 Feb 2012)
Log Message:
-----------
- commit changes to package build so libsbml will automatically register all enabled packages 

Modified Paths:
--------------
    trunk/libsbml/src/CMakeLists.txt
    trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.cpp
    trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.h

Added Paths:
-----------
    trunk/libsbml/src/sbml/extension/RegisterExtensions.cxx
    trunk/libsbml/src/sbml/extension/RegisterExtensions.h
    trunk/libsbml/src/sbml/packages/layout-register.cxx
    trunk/libsbml/src/sbml/packages/layout-register.h

Modified: trunk/libsbml/src/CMakeLists.txt
===================================================================
--- trunk/libsbml/src/CMakeLists.txt	2012-02-21 02:32:37 UTC (rev 15471)
+++ trunk/libsbml/src/CMakeLists.txt	2012-02-21 02:45:27 UTC (rev 15472)
@@ -44,6 +44,29 @@
 
 ###############################################################################
 #
+# Register all packagess
+#
+
+file(GLOB REGISTER_EXTENSIONS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}/ "${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/*-register.h")
+file(WRITE "${CMAKE_CURRENT_SOURCE_DIR}/sbml/extension/RegisterExtensions.h" "// This file is autogenerated and will be overwritten by the configuration process\n\n")
+file(APPEND "${CMAKE_CURRENT_SOURCE_DIR}/sbml/extension/RegisterExtensions.h" "#include <sbml/extension/SBMLExtension.h>\n")
+foreach(package ${REGISTER_EXTENSIONS})
+	file(APPEND "${CMAKE_CURRENT_SOURCE_DIR}/sbml/extension/RegisterExtensions.h" "#include <${package}>\n")
+endforeach()
+file(APPEND "${CMAKE_CURRENT_SOURCE_DIR}/sbml/extension/RegisterExtensions.h" "\n")
+
+file(GLOB REGISTER_EXTENSIONS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}/ "${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/*-register.cxx")
+file(WRITE "${CMAKE_CURRENT_SOURCE_DIR}/sbml/extension/RegisterExtensions.cxx" "// This file is autogenerated and will be overwritten by the configuration process\n\n")
+foreach(package ${REGISTER_EXTENSIONS})
+	file(APPEND "${CMAKE_CURRENT_SOURCE_DIR}/sbml/extension/RegisterExtensions.cxx" "#include <${package}>\n")
+endforeach()
+file(APPEND "${CMAKE_CURRENT_SOURCE_DIR}/sbml/extension/RegisterExtensions.cxx" "\n")
+
+
+
+
+###############################################################################
+#
 # create libsbml-config-common.h
 # 
 include(CheckIncludeFiles)

Added: trunk/libsbml/src/sbml/extension/RegisterExtensions.cxx
===================================================================
--- trunk/libsbml/src/sbml/extension/RegisterExtensions.cxx	                        (rev 0)
+++ trunk/libsbml/src/sbml/extension/RegisterExtensions.cxx	2012-02-21 02:45:27 UTC (rev 15472)
@@ -0,0 +1,3 @@
+// This file is autogenerated and will be overwritten by the configuration process
+
+#include <sbml/packages/layout-register.cxx>

Added: trunk/libsbml/src/sbml/extension/RegisterExtensions.h
===================================================================
--- trunk/libsbml/src/sbml/extension/RegisterExtensions.h	                        (rev 0)
+++ trunk/libsbml/src/sbml/extension/RegisterExtensions.h	2012-02-21 02:45:27 UTC (rev 15472)
@@ -0,0 +1,4 @@
+// This file is autogenerated and will be overwritten by the configuration process
+
+#include <sbml/extension/SBMLExtension.h>
+#include <sbml/packages/layout-register.h>

Modified: trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.cpp
===================================================================
--- trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.cpp	2012-02-21 02:32:37 UTC (rev 15471)
+++ trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.cpp	2012-02-21 02:45:27 UTC (rev 15472)
@@ -35,6 +35,9 @@
 #include <iostream>
 #include <string>
 
+#include "RegisterExtensions.h"
+
+
 #ifdef __cplusplus
 
 #include <sbml/validator/constraints/IdList.h>
@@ -43,6 +46,7 @@
 
 LIBSBML_CPP_NAMESPACE_BEGIN
 
+bool SBMLExtensionRegistry::registered = false;
 
 /*
  *
@@ -51,9 +55,19 @@
 SBMLExtensionRegistry::getInstance()
 {
   static SBMLExtensionRegistry singletonObj;
+  if (!registered)
+  {
+    registered = true;
+    #include "RegisterExtensions.cxx"
+  }
   return singletonObj;
 }
 
+SBMLExtensionRegistry::SBMLExtensionRegistry()
+{
+}
+
+
 SBMLExtensionRegistry::SBMLExtensionRegistry(const SBMLExtensionRegistry& orig)
 {
   if (&orig != NULL)

Modified: trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.h
===================================================================
--- trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.h	2012-02-21 02:32:37 UTC (rev 15471)
+++ trunk/libsbml/src/sbml/extension/SBMLExtensionRegistry.h	2012-02-21 02:45:27 UTC (rev 15472)
@@ -251,8 +251,10 @@
   //
   // Constructor and Copy constructor must not be overridden.
   //
-  SBMLExtensionRegistry() {};
+  SBMLExtensionRegistry();
   SBMLExtensionRegistry(const SBMLExtensionRegistry& orig);
+  
+  static bool registered;
 
   /** @cond doxygen-libsbml-internal */
  

Added: trunk/libsbml/src/sbml/packages/layout-register.cxx
===================================================================
--- trunk/libsbml/src/sbml/packages/layout-register.cxx	                        (rev 0)
+++ trunk/libsbml/src/sbml/packages/layout-register.cxx	2012-02-21 02:45:27 UTC (rev 15472)
@@ -0,0 +1,5 @@
+
+#ifdef USE_LAYOUT
+LayoutExtension::init();
+#endif	
+

Added: trunk/libsbml/src/sbml/packages/layout-register.h
===================================================================
--- trunk/libsbml/src/sbml/packages/layout-register.h	                        (rev 0)
+++ trunk/libsbml/src/sbml/packages/layout-register.h	2012-02-21 02:45:27 UTC (rev 15472)
@@ -0,0 +1,5 @@
+
+#ifdef USE_LAYOUT
+#include <sbml/packages/layout/extension/LayoutExtension.h>
+#endif	
+

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Revision: 15499
          http://sbml.svn.sourceforge.net/sbml/?rev=15499&view=rev
Author:   fbergmann
Date:     2012-02-22 17:22:12 +0000 (Wed, 22 Feb 2012)
Log Message:
-----------
- added new generated files to distribution list 

Modified Paths:
--------------
    trunk/libsbml/src/bindings/Makefile.in
    trunk/libsbml/src/bindings/csharp/Makefile.in
    trunk/libsbml/src/bindings/java/Makefile.in
    trunk/libsbml/src/bindings/perl/Makefile.in
    trunk/libsbml/src/bindings/python/Makefile.in
    trunk/libsbml/src/bindings/ruby/Makefile.in
    trunk/libsbml/src/sbml/common/libsbml-package.h
    trunk/libsbml/src/sbml/common/libsbml-version.h
    trunk/libsbml/src/sbml/extension/Makefile.in
    trunk/libsbml/src/sbml/packages/Makefile.in

Modified: trunk/libsbml/src/bindings/Makefile.in
===================================================================
--- trunk/libsbml/src/bindings/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/bindings/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -76,18 +76,18 @@
   subdirs = java matlab octave python perl ruby csharp
 endif
 
-swig_extras =             \
-  swig/layout-package.h   \
-  swig/layout-package.i   \
-  swig/libsbml.h          \
-  swig/libsbml.i          \
-  swig/libsbml-packages.h \
-  swig/libsbml-packages.i \
-  swig/swigdoc.py         \
-  swig/ListWrapper.h      \
-  swig/OStream.cpp        \
-  swig/OStream.h          \
-  swig/std_set.i          \
+swig_extras =                \
+  swig/layout-package.h      \
+  swig/layout-package.i      \
+  swig/libsbml.h             \
+  swig/libsbml.i             \
+  swig/libsbml-packages.h.in \
+  swig/libsbml-packages.i.in \
+  swig/swigdoc.py            \
+  swig/ListWrapper.h         \
+  swig/OStream.cpp           \
+  swig/OStream.h             \
+  swig/std_set.i             \
   CMakeLists.txt
   
 

Modified: trunk/libsbml/src/bindings/csharp/Makefile.in
===================================================================
--- trunk/libsbml/src/bindings/csharp/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/bindings/csharp/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -85,11 +85,11 @@
                      local.cpp \
                      local.i \
 					 local-downcast-extension-layout.i \
-					 local-downcast-extension.i \
+					 local-downcast-extension.i.in \
 					 local-downcast-namespaces-layout.i \
-					 local-downcast-namespaces.i \
+					 local-downcast-namespaces.i.in \
 					 local-packages-layout.i \
-					 local-packages.i
+					 local-packages.i.in
 
 test_dir          = test
 test_source_path  = $(test_dir)

Modified: trunk/libsbml/src/bindings/java/Makefile.in
===================================================================
--- trunk/libsbml/src/bindings/java/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/bindings/java/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -58,11 +58,11 @@
                     local.i                            \
                     local-doc-extras.i                 \
                     local-downcast-extension-layout.i  \
-                    local-downcast-extension.i         \
+                    local-downcast-extension.i.in      \
                     local-downcast-namespaces-layout.i \
-                    local-downcast-namespaces.i        \
+                    local-downcast-namespaces.i.in     \
                     local-packages-layout.i            \
-                    local-packages.i
+                    local-packages.i.in
 
 # The SWIG interface files should not need to be regenerated for recipients
 # of the libSBML distributions; only developers should need to regenerate

Modified: trunk/libsbml/src/bindings/perl/Makefile.in
===================================================================
--- trunk/libsbml/src/bindings/perl/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/bindings/perl/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -85,15 +85,15 @@
   local.cpp                            \
   local.i                              \
   local-layout.i                       \
-  local-packages.i                     \
+  local-packages.i.in                  \
   local-downcast-extension-layout.cpp  \
-  local-downcast-extension.cpp         \
+  local-downcast-extension.cpp.in      \
   local-downcast-namespaces-layout.cpp \
-  local-downcast-namespaces.cpp        \
+  local-downcast-namespaces.cpp.in     \
   local-downcast-plugins-layout.cpp    \
-  local-downcast-plugins.cpp           \
+  local-downcast-plugins.cpp.in        \
   local-downcast-packages-layout.cpp   \
-  local-downcast.cpp                   \
+  local-downcast.cpp.in                \
   Makefile.in                          \
   Makefile.PL.in                       \
   MANIFEST                             \

Modified: trunk/libsbml/src/bindings/python/Makefile.in
===================================================================
--- trunk/libsbml/src/bindings/python/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/bindings/python/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -58,13 +58,13 @@
                 local.cpp                            \
                 local.i                              \
                 local-downcast-extension-layout.cpp  \
-                local-downcast-extension.cpp         \
+                local-downcast-extension.cpp.in      \
                 local-downcast-namespaces-layout.cpp \
-                local-downcast-namespaces.cpp        \
+                local-downcast-namespaces.cpp.in     \
                 local-downcast-plugins-layout.cpp    \
-                local-downcast-plugins.cpp           \
+                local-downcast-plugins.cpp.in        \
                 local-downcast-packages-layout.cpp   \
-                local-downcast.cpp                   \
+                local-downcast.cpp.in                \
                 pydoc-normal.i                       \
                 pydoc-doxygen.i
 
@@ -162,7 +162,7 @@
             Makefile.in                    \
             CMakeLists.txt                 \
             test.py                        \
-            local-packages.i               \
+            local-packages.i.in            \
             local-layout.i                 \
             setup.cfg                      \
             setup.py.in                    \

Modified: trunk/libsbml/src/bindings/ruby/Makefile.in
===================================================================
--- trunk/libsbml/src/bindings/ruby/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/bindings/ruby/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -51,18 +51,18 @@
 
 sources       =  libsbml_wrap.cpp libsbml_wrap.h
 extra_sources =  libsbml.i \
-                 local-packages.i \
+                 local-packages.i.in \
 				 local-layout.i \
                  local.cpp \
 				 local.i \
 				 local-downcast-extension-layout.cpp \
-				 local-downcast-extension.cpp \
+				 local-downcast-extension.cpp.in \
 				 local-downcast-namespaces-layout.cpp \
-				 local-downcast-namespaces.cpp \
+				 local-downcast-namespaces.cpp.in \
 				 local-downcast-plugins-layout.cpp \
-				 local-downcast-plugins.cpp \
+				 local-downcast-plugins.cpp.in \
 				 local-downcast-packages-layout.cpp \
-				 local-downcast.cpp
+				 local-downcast.cpp.in
 
 # The SWIG interface files should not need to be regenerated for recipients
 # of the libSBML distributions; only developers should need to regenerate

Modified: trunk/libsbml/src/sbml/common/libsbml-package.h
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-package.h	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/sbml/common/libsbml-package.h	2012-02-22 17:22:12 UTC (rev 15499)
@@ -52,11 +52,11 @@
 #define PACKAGE_NAME "libSBML"
 
 /* Define to the full name and version of this package. */
-#define PACKAGE_STRING "libSBML 5.4.1"
+#define PACKAGE_STRING "libSBML 5.4.0"
 
 /* Define to the one symbol short name of this package. */
 #define PACKAGE_TARNAME "libsbml"
 
 /* Define to the version of this package. */
-#define PACKAGE_VERSION "5.4.1"
+#define PACKAGE_VERSION "5.4.0"
 

Modified: trunk/libsbml/src/sbml/common/libsbml-version.h
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-version.h	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/sbml/common/libsbml-version.h	2012-02-22 17:22:12 UTC (rev 15499)
@@ -37,7 +37,7 @@
  *
  * A version string of the form "1.2.3".
  */
-#define LIBSBML_DOTTED_VERSION	"5.4.1"
+#define LIBSBML_DOTTED_VERSION	"5.4.0"
 
 
 /**
@@ -48,7 +48,7 @@
  * libSBML is released, making it easy to use less-than and greater-than
  * comparisons when testing versions numbers.
  */
-#define LIBSBML_VERSION		50401
+#define LIBSBML_VERSION		50400
 
 
 /**
@@ -56,7 +56,7 @@
  *
  * The numeric version as a string: version 1.2.3 becomes "10203".
  */
-#define LIBSBML_VERSION_STRING	"50401"
+#define LIBSBML_VERSION_STRING	"50400"
 
 
 LIBSBML_CPP_NAMESPACE_BEGIN

Modified: trunk/libsbml/src/sbml/extension/Makefile.in
===================================================================
--- trunk/libsbml/src/sbml/extension/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/sbml/extension/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -99,7 +99,7 @@
 # `distfiles_exclude' is used to filter out specific items, so that even if
 # they appear in `distfiles', they will not be copied in the distribution.
 
-distfiles = $(sources) $(headers) Makefile.in
+distfiles = $(sources) $(headers) Makefile.in RegisterExtensions.cxx.in RegisterExtensions.h.in
 
 
 # -----------------------------------------------------------------------------

Modified: trunk/libsbml/src/sbml/packages/Makefile.in
===================================================================
--- trunk/libsbml/src/sbml/packages/Makefile.in	2012-02-22 16:58:54 UTC (rev 15498)
+++ trunk/libsbml/src/sbml/packages/Makefile.in	2012-02-22 17:22:12 UTC (rev 15499)
@@ -61,7 +61,7 @@
 # `extra_CXXFLAGS', `extra_LDFLAGS' and `distfiles' are used by the default
 # rules in `makefile-common-actions.mk' included at the end.
 
-distfiles = Makefile.in 
+distfiles = Makefile.in layout-register.h layout-register.cxx
 
 
 # -----------------------------------------------------------------------------

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15582
          http://sbml.svn.sourceforge.net/sbml/?rev=15582&view=rev
Author:   sarahkeating
Date:     2012-04-15 14:31:41 +0000 (Sun, 15 Apr 2012)
Log Message:
-----------
changed appendAnnotation to not work if there is already an annotation with the same toplevel ns

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
    trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
    trunk/libsbml/src/sbml/Model.cpp
    trunk/libsbml/src/sbml/SBase.cpp
    trunk/libsbml/src/sbml/annotation/test/Makefile.in
    trunk/libsbml/src/sbml/common/operationReturnValues.h
    trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs	2012-04-15 14:31:41 UTC (rev 15582)
@@ -174,17 +174,34 @@
       XMLNode node;
       XMLToken token1;
       XMLNode node1;
-      token = new  XMLToken("This is a test note");
+      XMLToken token_top;
+      XMLNode node_top;
+      XMLTriple triple = new XMLTriple("any", "", "pr");
+      XMLAttributes att = new XMLAttributes();
+      XMLNamespaces ns = new XMLNamespaces();
+      ns.add("http://www.any", "pr");
+      XMLToken token_top1;
+      XMLNode node_top1;
+      XMLTriple triple1 = new XMLTriple("anyOther", "", "prOther");
+      XMLNamespaces ns1 = new XMLNamespaces();
+      ns1.add("http://www.any.other", "prOther");
+      token = new XMLToken("This is a test note");
       node = new XMLNode(token);
       token1 = new  XMLToken("This is additional");
       node1 = new XMLNode(token1);
-      int i = S.setAnnotation(node);
+      token_top = new XMLToken(triple, att, ns);
+      node_top = new XMLNode(token_top);
+      node_top.addChild(node);
+      token_top1 = new XMLToken(triple1, att, ns1);
+      node_top1 = new XMLNode(token_top1);
+      node_top1.addChild(node1);
+      int i = S.setAnnotation(node_top);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
-      i = S.appendAnnotation(node1);
+      i = S.appendAnnotation(node_top1);
       XMLNode t1 = S.getAnnotation();
       assertTrue( t1.getNumChildren() == 2 );
-      assertTrue((     "This is a test note" == t1.getChild(0).getCharacters() ));
-      assertTrue((     "This is additional" == t1.getChild(1).getCharacters() ));
+      assertTrue((     "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ));
+      assertTrue((     "This is additional" == t1.getChild(1).getChild(0).getCharacters() ));
     }
 
     public void test_SBase_appendAnnotationString()
@@ -193,15 +210,24 @@
       XMLNode node;
       token = new  XMLToken("This is a test note");
       node = new XMLNode(token);
-      int i = S.setAnnotation(node);
+      XMLToken token_top;
+      XMLNode node_top;
+      XMLTriple triple = new XMLTriple("any", "", "pr");
+      XMLAttributes att = new XMLAttributes();
+      XMLNamespaces ns = new XMLNamespaces();
+      ns.add("http://www.any", "pr");
+      token_top = new XMLToken(triple, att, ns);
+      node_top = new XMLNode(token_top);
+      node_top.addChild(node);
+      int i = S.setAnnotation(node_top);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
-      i = S.appendAnnotation( "This is additional");
+      i = S.appendAnnotation("<prA:other xmlns:prA=\"http://some\">This is additional</prA:other>");
       XMLNode t1 = S.getAnnotation();
       assertTrue( t1.getNumChildren() == 2 );
-      assertTrue((     "This is a test note" == t1.getChild(0).getCharacters() ));
+      assertTrue((     "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ));
       XMLNode c1 = t1.getChild(1);
-      assertTrue( c1.getNumChildren() == 0 );
-      assertTrue((  "This is additional" == c1.getCharacters() ));
+      assertTrue( c1.getNumChildren() == 1 );
+      assertTrue((  "This is additional" == c1.getChild(0).getCharacters() ));
     }
 
     public void test_SBase_appendNotes()

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java	2012-04-15 14:31:41 UTC (rev 15582)
@@ -164,17 +164,34 @@
     XMLNode node;
     XMLToken token1;
     XMLNode node1;
+    XMLToken token_top;
+    XMLNode node_top;
+    XMLTriple triple = new XMLTriple("any", "", "pr");
+    XMLAttributes att = new XMLAttributes();
+    XMLNamespaces ns = new XMLNamespaces();
+    ns.add("http://www.any", "pr");
+    XMLToken token_top1;
+    XMLNode node_top1;
+    XMLTriple triple1 = new XMLTriple("anyOther", "", "prOther");
+    XMLNamespaces ns1 = new XMLNamespaces();
+    ns1.add("http://www.any.other", "prOther");
     token = new  XMLToken("This is a test note");
     node = new XMLNode(token);
     token1 = new  XMLToken("This is additional");
     node1 = new XMLNode(token1);
-    int i = S.setAnnotation(node);
+    token_top = new XMLToken(triple, att, ns);
+    node_top = new XMLNode(token_top);
+    node_top.addChild(node);
+    token_top1 = new XMLToken(triple1, att, ns1);
+    node_top1 = new XMLNode(token_top1);
+    node_top1.addChild(node1);
+    int i = S.setAnnotation(node_top);
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
-    i = S.appendAnnotation(node1);
+    i = S.appendAnnotation(node_top1);
     XMLNode t1 = S.getAnnotation();
     assertTrue( t1.getNumChildren() == 2 );
-    assertTrue(t1.getChild(0).getCharacters().equals(    "This is a test note"));
-    assertTrue(t1.getChild(1).getCharacters().equals(    "This is additional"));
+    assertTrue(t1.getChild(0).getChild(0).getCharacters().equals(    "This is a test note"));
+    assertTrue(t1.getChild(1).getChild(0).getCharacters().equals(    "This is additional"));
   }
 
   public void test_SBase_appendAnnotationString()
@@ -183,15 +200,24 @@
     XMLNode node;
     token = new  XMLToken("This is a test note");
     node = new XMLNode(token);
-    int i = S.setAnnotation(node);
+    XMLToken token_top;
+    XMLNode node_top;
+    XMLTriple triple = new XMLTriple("any", "", "pr");
+    XMLAttributes att = new XMLAttributes();
+    XMLNamespaces ns = new XMLNamespaces();
+    ns.add("http://www.any", "pr");
+    token_top = new XMLToken(triple, att, ns);
+    node_top = new XMLNode(token_top);
+    node_top.addChild(node);
+    int i = S.setAnnotation(node_top);
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
-    i = S.appendAnnotation( "This is additional");
+    i = S.appendAnnotation("<prA:other xmlns:prA=\"http://some\">This is additional</prA:other>");
     XMLNode t1 = S.getAnnotation();
     assertTrue( t1.getNumChildren() == 2 );
-    assertTrue(t1.getChild(0).getCharacters().equals(    "This is a test note"));
+    assertTrue(t1.getChild(0)..getChild(0).getCharacters().equals(    "This is a test note"));
     XMLNode c1 = t1.getChild(1);
-    assertTrue( c1.getNumChildren() == 0 );
-    assertTrue(c1.getCharacters().equals( "This is additional"));
+    assertTrue( c1.getNumChildren() == 1 );
+    assertTrue(c1.getChild(0).getCharacters().equals( "This is additional"));
   }
 
   public void test_SBase_appendNotes()

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py	2012-04-15 14:31:41 UTC (rev 15582)
@@ -80,31 +80,51 @@
     pass  
 
   def test_SBase_appendAnnotation(self):
+    triple = libsbml.XMLTriple("any", "", "pr");
+    att = libsbml.XMLAttributes();
+    ns = libsbml.XMLNamespaces();
+    ns.add("http://www.any", "pr");
+    triple1 = libsbml.XMLTriple("anyOther", "", "prOther");
+    ns1 = libsbml.XMLNamespaces();
+    ns1.add("http://www.any.other", "prOther");
     token = libsbml.XMLToken("This is a test note")
     node = libsbml.XMLNode(token)
     token1 = libsbml.XMLToken("This is additional")
     node1 = libsbml.XMLNode(token1)
-    i = self.S.setAnnotation(node)
+    token_top = libsbml.XMLToken(triple, att, ns);
+    node_top = libsbml.XMLNode(token_top);
+    node_top.addChild(node);
+    token_top1 = libsbml.XMLToken(triple1, att, ns1);
+    node_top1 = libsbml.XMLNode(token_top1);
+    node_top1.addChild(node1);
+    i = self.S.setAnnotation(node_top)
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
-    i = self.S.appendAnnotation(node1)
+    i = self.S.appendAnnotation(node_top1)
     t1 = self.S.getAnnotation()
     self.assert_( t1.getNumChildren() == 2 )
-    self.assert_((     "This is a test note" == t1.getChild(0).getCharacters() ))
-    self.assert_((     "This is additional" == t1.getChild(1).getCharacters() ))
+    self.assert_((     "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ))
+    self.assert_((     "This is additional" == t1.getChild(1).getChild(0).getCharacters() ))
     pass  
 
   def test_SBase_appendAnnotationString(self):
     token = libsbml.XMLToken("This is a test note")
     node = libsbml.XMLNode(token)
-    i = self.S.setAnnotation(node)
+    triple = libsbml.XMLTriple("any", "", "pr");
+    att = libsbml.XMLAttributes();
+    ns = libsbml.XMLNamespaces();
+    ns.add("http://www.any", "pr");
+    token_top = libsbml.XMLToken(triple, att, ns);
+    node_top = libsbml.XMLNode(token_top);
+    node_top.addChild(node);
+    i = self.S.setAnnotation(node_top)
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
-    i = self.S.appendAnnotation( "This is additional")
+    i = self.S.appendAnnotation("<prA:other xmlns:prA=\"http://some\">This is additional</prA:other>");
     t1 = self.S.getAnnotation()
     self.assert_( t1.getNumChildren() == 2 )
-    self.assert_((     "This is a test note" == t1.getChild(0).getCharacters() ))
+    self.assert_((     "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ))
     c1 = t1.getChild(1)
-    self.assert_( c1.getNumChildren() == 0 )
-    self.assert_((  "This is additional" == c1.getCharacters() ))
+    self.assert_( c1.getNumChildren() == 1 )
+    self.assert_((  "This is additional" == c1.getChild(0).getCharacters() ))
     pass  
 
   def test_SBase_appendNotes(self):

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb	2012-04-15 14:31:41 UTC (rev 15582)
@@ -70,31 +70,51 @@
   end
 
   def test_SBase_appendAnnotation
+    triple = LibSBML::XMLTriple.new("any", "", "pr");
+    att = LibSBML::XMLAttributes.new();
+    ns = LibSBML::XMLNamespaces.new();
+    ns.add("http://www.any", "pr");
+    triple1 = LibSBML::XMLTriple.new("anyOther", "", "prOther");
+    ns1 = LibSBML::XMLNamespaces.new();
+    ns1.add("http://www.any.other", "prOther");
     token = LibSBML::XMLToken.new("This is a test note")
     node = LibSBML::XMLNode.new(token)
     token1 = LibSBML::XMLToken.new("This is additional")
     node1 = LibSBML::XMLNode.new(token1)
-    i = @@s.setAnnotation(node)
+    token_top = LibSBML::XMLToken.new(triple, att, ns);
+    node_top = LibSBML::XMLNode.new(token_top);
+    node_top.addChild(node);
+    token_top1 = LibSBML::XMLToken.new(triple1, att, ns1);
+    node_top1 = LibSBML::XMLNode.new(token_top1);
+    node_top1.addChild(node1);
+    i = @@s.setAnnotation(node_top)
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
-    i = @@s.appendAnnotation(node1)
+    i = @@s.appendAnnotation(nodeTop1)
     t1 = @@s.getAnnotation()
     assert( t1.getNumChildren() == 2 )
-    assert ((     "This is a test note" == t1.getChild(0).getCharacters() ))
-    assert ((     "This is additional" == t1.getChild(1).getCharacters() ))
+    assert ((     "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ))
+    assert ((     "This is additional" == t1.getChild(1).getChild(0).getCharacters() ))
   end
 
   def test_SBase_appendAnnotationString
     token = LibSBML::XMLToken.new("This is a test note")
     node = LibSBML::XMLNode.new(token)
-    i = @@s.setAnnotation(node)
+    triple = LibSBML::XMLTriple.new("any", "", "pr");
+    att = LibSBML::XMLAttributes.new();
+    ns = LibSBML::XMLNamespaces.new();
+    ns.add("http://www.any", "pr");
+    token_top = LibSBML::XMLToken.new(triple, att, ns);
+    node_top = LibSBML::XMLNode.new(token_top);
+    node_top.addChild(node);
+    i = @@s.setAnnotation(node_top)
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
-    i = @@s.appendAnnotation( "This is additional")
+    i = @@s.appendAnnotation("<prA:other xmlns:prA=\"http://some\">This is additional</prA:other>");
     t1 = @@s.getAnnotation()
     assert( t1.getNumChildren() == 2 )
-    assert ((     "This is a test note" == t1.getChild(0).getCharacters() ))
+    assert ((     "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ))
     c1 = t1.getChild(1)
-    assert( c1.getNumChildren() == 0 )
-    assert ((  "This is additional" == c1.getCharacters() ))
+    assert( c1.getNumChildren() == 1 )
+    assert ((  "This is additional" == c1.getChild(0).getCharacters() ))
   end
 
   def test_SBase_appendNotes

Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/sbml/Model.cpp	2012-04-15 14:31:41 UTC (rev 15582)
@@ -2230,41 +2230,45 @@
 int
 Model::appendAnnotation (const XMLNode* annotation)
 {
-  int success = LIBSBML_OPERATION_FAILED;
-  if(annotation == NULL) return LIBSBML_OPERATION_SUCCESS;
+  // take out any attempt to merge RDF
 
-  XMLNode* new_annotation = NULL;
-  const string&  name = annotation->getName();
+  return SBase::appendAnnotation(annotation);
 
-  // check for annotation tags and add if necessary
-  if (name != "annotation")
-  {
-    XMLToken ann_t = XMLToken(XMLTriple("annotation", "", ""), XMLAttributes());
-    new_annotation = new XMLNode(ann_t);
-    new_annotation->addChild(*annotation);
-  }
-  else
-  {
-    new_annotation = annotation->clone();
-  }
-
-  // parse new_annotation and reset mHistory 
-  if (RDFAnnotationParser::hasHistoryRDFAnnotation(new_annotation))
-  {
-    ModelHistory* new_mhistory = RDFAnnotationParser::parseRDFAnnotation(new_annotation);
-    if(new_mhistory != NULL)
-    {
-      delete mHistory;
-      mHistory = new_mhistory;
-//      mHistoryChanged = true;
-    }
-  }
-
-  success = SBase::appendAnnotation(new_annotation);
-
-  delete new_annotation;
-
-  return success;
+//  int success = LIBSBML_OPERATION_FAILED;
+//  if(annotation == NULL) return LIBSBML_OPERATION_SUCCESS;
+//
+//  XMLNode* new_annotation = NULL;
+//  const string&  name = annotation->getName();
+//
+//  // check for annotation tags and add if necessary
+//  if (name != "annotation")
+//  {
+//    XMLToken ann_t = XMLToken(XMLTriple("annotation", "", ""), XMLAttributes());
+//    new_annotation = new XMLNode(ann_t);
+//    new_annotation->addChild(*annotation);
+//  }
+//  else
+//  {
+//    new_annotation = annotation->clone();
+//  }
+//
+//  // parse new_annotation and reset mHistory 
+//  if (RDFAnnotationParser::hasHistoryRDFAnnotation(new_annotation))
+//  {
+//    ModelHistory* new_mhistory = RDFAnnotationParser::parseRDFAnnotation(new_annotation);
+//    if(new_mhistory != NULL)
+//    {
+//      delete mHistory;
+//      mHistory = new_mhistory;
+////      mHistoryChanged = true;
+//    }
+//  }
+//
+//  success = SBase::appendAnnotation(new_annotation);
+//
+//  delete new_annotation;
+//
+//  return success;
 }
 
 

Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/sbml/SBase.cpp	2012-04-15 14:31:41 UTC (rev 15582)
@@ -46,6 +46,7 @@
 #include <sbml/ListOf.h>
 #include <sbml/SBase.h>
 
+#include <sbml/validator/constraints/IdList.h>
 #include <sbml/extension/SBasePlugin.h>
 #include <sbml/extension/ISBMLExtensionNamespaces.h>
 #include <sbml/extension/SBMLExtensionRegistry.h>
@@ -1232,6 +1233,7 @@
 SBase::appendAnnotation (const XMLNode* annotation)
 {
   int success = LIBSBML_OPERATION_FAILED;
+  unsigned int duplicates = 0;
 
   //
   // (*NOTICE*)
@@ -1240,7 +1242,8 @@
   // existing mCVTerm objects are properly merged in the following code.
   //
 
-  if(annotation == NULL) return LIBSBML_OPERATION_SUCCESS;
+  if(annotation == NULL) 
+    return LIBSBML_OPERATION_SUCCESS;
 
   XMLNode* new_annotation = NULL;
   const string&  name = annotation->getName();
@@ -1257,12 +1260,14 @@
     new_annotation = annotation->clone();
   }
 
-  // parse new_annotation and add mCVTerms (if any) 
-  if (RDFAnnotationParser::hasCVTermRDFAnnotation(new_annotation))
-  {
-    RDFAnnotationParser::parseRDFAnnotation(new_annotation,mCVTerms);
-//    mCVTermsChanged = true;
-  }
+  // take out an attempt to merge rdf
+//
+//  // parse new_annotation and add mCVTerms (if any) 
+//  if (RDFAnnotationParser::hasCVTermRDFAnnotation(new_annotation))
+//  {
+//    RDFAnnotationParser::parseRDFAnnotation(new_annotation,mCVTerms);
+////    mCVTermsChanged = true;
+//  }
 
   // delete RDFAnnotation (CVTerm and ModelHistory) from new_annotation 
 //  XMLNode* tmp_annotation = RDFAnnotationParser::deleteRDFAnnotation(new_annotation);
@@ -1278,34 +1283,57 @@
       mAnnotation->unsetEnd();
     }
 
-    for(unsigned int i=0; i < new_annotation->getNumChildren(); i++)
+    //for(unsigned int i=0; i < new_annotation->getNumChildren(); i++)
+    //{
+    //  if (new_annotation->getChild(i).getName() == "RDF")
+    //  {
+    //    if (RDFAnnotationParser::hasRDFAnnotation(mAnnotation))
+    //    {
+    //      unsigned int n = 0;
+    //      while(n < mAnnotation->getNumChildren())
+    //      {
+    //        if (mAnnotation->getChild(n).getName() == "RDF")
+    //        {
+    //          break;
+    //        }
+    //        n++;
+    //      }
+    //      success = mAnnotation->getChild(n).addChild(
+    //                                new_annotation->getChild(i).getChild(0));
+    //    }
+    //    else
+    //    {
+    //      success = mAnnotation->addChild(new_annotation->getChild(i));
+    //    }
+    //  }
+    //  else
+    //  {
+    //    success = mAnnotation->addChild(new_annotation->getChild(i));
+    //  }
+    //}
+
+    // create a list of existing top level ns
+    IdList topLevelNs;
+    unsigned int i = 0;
+    for(i = 0; i < mAnnotation->getNumChildren(); i++)
     {
-      if (new_annotation->getChild(i).getName() == "RDF")
+      topLevelNs.append(mAnnotation->getChild(i).getName());
+    }
+
+
+
+    for(i = 0; i < new_annotation->getNumChildren(); i++)
+    {
+      if (topLevelNs.contains(new_annotation->getChild(i).getName()) == false)
       {
-        if (RDFAnnotationParser::hasRDFAnnotation(mAnnotation))
-        {
-          unsigned int n = 0;
-          while(n < mAnnotation->getNumChildren())
-          {
-            if (mAnnotation->getChild(n).getName() == "RDF")
-            {
-              break;
-            }
-            n++;
-          }
-          success = mAnnotation->getChild(n).addChild(
-                                    new_annotation->getChild(i).getChild(0));
-        }
-        else
-        {
-          success = mAnnotation->addChild(new_annotation->getChild(i));
-        }
+        success = mAnnotation->addChild(new_annotation->getChild(i));
       }
       else
       {
-        success = mAnnotation->addChild(new_annotation->getChild(i));
+        duplicates++;
       }
     }
+
   }
   else
   {
@@ -1314,6 +1342,11 @@
 
   delete new_annotation;
 
+  if (duplicates > 0)
+  {
+    success = LIBSBML_DUPLICATE_ANNOTATION_NS;
+  }
+
   return success;
 }
 

Modified: trunk/libsbml/src/sbml/annotation/test/Makefile.in
===================================================================
--- trunk/libsbml/src/sbml/annotation/test/Makefile.in	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/sbml/annotation/test/Makefile.in	2012-04-15 14:31:41 UTC (rev 15582)
@@ -61,6 +61,7 @@
   TestRDFAnnotationC.c           \
   TestValidation.cpp             \
   TestL3ModelHistory.cpp         \
+  TestSyncAnnotation.cpp         \
   TestRunner.c
 
 test_data_files = \

Modified: trunk/libsbml/src/sbml/common/operationReturnValues.h
===================================================================
--- trunk/libsbml/src/sbml/common/operationReturnValues.h	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/sbml/common/operationReturnValues.h	2012-04-15 14:31:41 UTC (rev 15582)
@@ -109,11 +109,20 @@
      * XML in an invalid way.  */
 
   , LIBSBML_NAMESPACES_MISMATCH   = -10
-    /*!< The XML operation attempted is not valid for the object or context
-     * involved.  This error is typically returned by the XML interface layer
-     * of libSBML, when a calling program attempts to construct or manipulate
-     * XML in an invalid way.  */
+    /*!< The SBML Namespaces associated with the object
+     * do not match the SBML Namespaces of the parent object.  This error can
+     * happen when an SBML component such as a species or compartment object
+     * is created outside of a model and a calling program then attempts to
+     * add the object to a model that has a different SBML Namespaces
+     * combination. */
 
+  , LIBSBML_DUPLICATE_ANNOTATION_NS   = -11
+    /*!< There already exists a top level annotation with the same namespace as
+     * annoation being appended.  This error is
+     * typically returned in situations where the appendAnnotation function
+     * is being used to add an annotation that has a namespace that is already
+     * present in the existing annotation. */
+
    /* ---------------------------------------------------------------------------
     *   
     *              Return codes for package extension

Modified: trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp	2012-04-13 22:07:38 UTC (rev 15581)
+++ trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp	2012-04-15 14:31:41 UTC (rev 15582)
@@ -403,29 +403,216 @@
   XMLNode_t *node;
   XMLToken_t *token1;
   XMLNode_t *node1;
+  XMLToken_t *token_top;
+  XMLNode_t *node_top;
+  XMLTriple_t *triple = XMLTriple_createWith("any", "", "pr");
+  XMLAttributes_t * att = XMLAttributes_create ();
+  XMLNamespaces_t *ns = XMLNamespaces_create();
+  XMLNamespaces_add(ns, "http://www.any", "pr");
+  token_top = XMLToken_createWithTripleAttrNS(triple, att, ns);
+  node_top = XMLNode_createFromToken(token_top);
+  XMLToken_t *token_top1;
+  XMLNode_t *node_top1;
+  XMLTriple_t *triple1 = XMLTriple_createWith("anyOther", "", "prOther");
+  XMLNamespaces_t *ns1 = XMLNamespaces_create();
+  XMLNamespaces_add(ns1, "http://www.any.other", "prOther");
+  token_top1 = XMLToken_createWithTripleAttrNS(triple1, att, ns1);
+  node_top1 = XMLNode_createFromToken(token_top1);
 
   token = XMLToken_createWithText("This is a test note");
   node = XMLNode_createFromToken(token);
+  XMLNode_addChild(node_top, node);
 
+ 
+  int i = SBase_setAnnotation(S, node_top);
+  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
+
   token1 = XMLToken_createWithText("This is additional");
   node1 = XMLNode_createFromToken(token1);
+  XMLNode_addChild(node_top1, node1);
+
+  i = SBase_appendAnnotation(S, node_top1);
+  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
+
+  XMLNode_t *t1 = SBase_getAnnotation(S);
+
+  fail_unless(XMLNode_getNumChildren(t1) == 2);
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 0),0)),
+    "This is a test note"));
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 1),0)),
+    "This is additional"));
+
+  i = SBase_appendAnnotation(S, NULL);
+  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
+
+  t1 = SBase_getAnnotation(S);
+
+  fail_unless(XMLNode_getNumChildren(t1) == 2);
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 0),0)),
+    "This is a test note"));
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 1),0)),
+    "This is additional"));
+
+}
+END_TEST
+
+
+START_TEST (test_SBase_appendAnnotation1)
+{
+  XMLToken_t *token;
+  XMLNode_t *node;
+  XMLToken_t *token1;
+  XMLNode_t *node1;
+  XMLToken_t *token_top;
+  XMLNode_t *node_top;
+  XMLTriple_t *triple = XMLTriple_createWith("any", "", "pr");
+  XMLAttributes_t * att = XMLAttributes_create ();
+  XMLNamespaces_t *ns = XMLNamespaces_create();
+  XMLNamespaces_add(ns, "http://www.any", "pr");
+  token_top = XMLToken_createWithTripleAttrNS(triple, att, ns);
+  node_top = XMLNode_createFromToken(token_top);
+  XMLToken_t *token_top1;
+  XMLNode_t *node_top1;
+  XMLTriple_t *triple1 = XMLTriple_createWith("anyOther", "", "prOther");
+  XMLNamespaces_t *ns1 = XMLNamespaces_create();
+  XMLNamespaces_add(ns1, "http://www.any.other", "prOther");
+  token_top1 = XMLToken_createWithTripleAttrNS(triple1, att, ns1);
+  node_top1 = XMLNode_createFromToken(token_top1);
+
+  token = XMLToken_createWithText("This is a test note");
+  node = XMLNode_createFromToken(token);
+  XMLNode_addChild(node_top, node);
+
  
-  int i = SBase_setAnnotation(S, node);
+  int i = SBase_setAnnotation(S, NULL);
   fail_unless( i == LIBSBML_OPERATION_SUCCESS);
 
-  i = SBase_appendAnnotation(S, node1);
+  token1 = XMLToken_createWithText("This is additional");
+  node1 = XMLNode_createFromToken(token1);
+  XMLNode_addChild(node_top1, node1);
 
+  i = SBase_appendAnnotation(S, node_top1);
+  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
+
   XMLNode_t *t1 = SBase_getAnnotation(S);
 
+  fail_unless(XMLNode_getNumChildren(t1) == 1);
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 0),0)),
+    "This is additional"));
+
+  token1 = XMLToken_createWithText("This is a repeat");
+  node1 = XMLNode_createFromToken(token1);
+  node_top1 = XMLNode_createFromToken(token_top1);
+  XMLNode_addChild(node_top1, node1);
+
+  i = SBase_appendAnnotation(S, node_top1);
+  fail_unless( i == LIBSBML_DUPLICATE_ANNOTATION_NS);
+
+  t1 = SBase_getAnnotation(S);
+
+  fail_unless(XMLNode_getNumChildren(t1) == 1);
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 0),0)),
+    "This is additional"));
+
+}
+END_TEST
+
+
+START_TEST (test_SBase_appendAnnotation2)
+{
+  XMLToken_t *token;
+  XMLNode_t *node;
+  XMLToken_t *token_top;
+  XMLNode_t *node_top;
+  XMLTriple_t *triple = XMLTriple_createWith("any", "", "pr");
+  XMLAttributes_t * att = XMLAttributes_create ();
+  XMLNamespaces_t *ns = XMLNamespaces_create();
+  XMLNamespaces_add(ns, "http://www.any", "pr");
+  token_top = XMLToken_createWithTripleAttrNS(triple, att, ns);
+  node_top = XMLNode_createFromToken(token_top);
+
+  token = XMLToken_createWithText("This is a test note");
+  node = XMLNode_createFromToken(token);
+  XMLNode_addChild(node_top, node);
+
+ 
+  int i = SBase_setAnnotation(S, node_top);
+  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
+
+  i = SBase_appendAnnotationString(S, "<prA:other xmlns:prA=\"http://some\">This is additional</prA:other>");
+
+  XMLNode_t *t1 = SBase_getAnnotation(S);
+
   fail_unless(XMLNode_getNumChildren(t1) == 2);
-  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(t1,0)),
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 0),0)),
     "This is a test note"));
-  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(t1,1)),
+
+  const XMLNode_t *c1 = XMLNode_getChild(XMLNode_getChild(t1, 1), 0);
+
+  fail_unless(XMLNode_getNumChildren(c1) == 0);
+  fail_unless(!strcmp(XMLNode_getCharacters(c1), "This is additional"));
+
+  char * newann =
+    "<annotation>"
+    "<prA:other xmlns:prA=\"http://some\">This is additional repeat</prA:other>"
+    "<rdf:RDF xmlns:rdf=\"http://rdf\">This is a new annotation</rdf:RDF>"
+    "</annotation>";
+
+  i = SBase_appendAnnotationString(S, newann);
+
+  fail_unless( i == LIBSBML_DUPLICATE_ANNOTATION_NS);
+
+  t1 = SBase_getAnnotation(S);
+
+  fail_unless(XMLNode_getNumChildren(t1) == 3);
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 0),0)),
+    "This is a test note"));
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 1),0)),
     "This is additional"));
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 2),0)),
+    "This is a new annotation"));
+
 }
 END_TEST
 
 
+START_TEST (test_SBase_appendAnnotationString)
+{
+  XMLToken_t *token;
+  XMLNode_t *node;
+  XMLToken_t *token_top;
+  XMLNode_t *node_top;
+  XMLTriple_t *triple = XMLTriple_createWith("any", "", "pr");
+  XMLAttributes_t * att = XMLAttributes_create ();
+  XMLNamespaces_t *ns = XMLNamespaces_create();
+  XMLNamespaces_add(ns, "http://www.any", "pr");
+  token_top = XMLToken_createWithTripleAttrNS(triple, att, ns);
+  node_top = XMLNode_createFromToken(token_top);
+
+  token = XMLToken_createWithText("This is a test note");
+  node = XMLNode_createFromToken(token);
+  XMLNode_addChild(node_top, node);
+
+ 
+  int i = SBase_setAnnotation(S, node_top);
+  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
+
+  i = SBase_appendAnnotationString(S, "<prA:other xmlns:prA=\"http://some\">This is additional</prA:other>");
+
+  XMLNode_t *t1 = SBase_getAnnotation(S);
+
+  fail_unless(XMLNode_getNumChildren(t1) == 2);
+  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(XMLNode_getChild(t1, 0),0)),
+    "This is a test note"));
+
+  const XMLNode_t *c1 = XMLNode_getChild(XMLNode_getChild(t1, 1), 0);
+
+  fail_unless(XMLNode_getNumChildren(c1) == 0);
+  fail_unless(!strcmp(XMLNode_getCharacters(c1), "This is additional"));
+}
+END_TEST
+
+
 START_TEST (test_SBase_appendNotes)
 { // add a p tag to a p tag
   XMLToken_t *token;
@@ -1254,33 +1441,6 @@
 END_TEST
 
 
-START_TEST (test_SBase_appendAnnotationString)
-{
-  XMLToken_t *token;
-  XMLNode_t *node;
-
-  token = XMLToken_createWithText("This is a test note");
-  node = XMLNode_createFromToken(token);
-
-  int i = SBase_setAnnotation(S, node);
-  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
-
-  i = SBase_appendAnnotationString(S, "This is additional");
-
-  XMLNode_t *t1 = SBase_getAnnotation(S);
-
-  fail_unless(XMLNode_getNumChildren(t1) == 2);
-  fail_unless(!strcmp(XMLNode_getCharacters(XMLNode_getChild(t1,0)),
-    "This is a test note"));
-
-  const XMLNode_t *c1 = XMLNode_getChild(t1, 1);
-
-  fail_unless(XMLNode_getNumChildren(c1) == 0);
-  fail_unless(!strcmp(XMLNode_getCharacters(c1), "This is additional"));
-}
-END_TEST
-
-
 START_TEST (test_SBase_appendNotesString)
 {
   char * notes = "<p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note </p>";
@@ -2000,6 +2160,9 @@
   tcase_add_test(tcase, test_SBase_setNotesString);
   tcase_add_test(tcase, test_SBase_setAnnotationString);
   tcase_add_test(tcase, test_SBase_appendAnnotation );
+  tcase_add_test(tcase, test_SBase_appendAnnotation1 );
+  tcase_add_test(tcase, test_SBase_appendAnnotation2 );
+  tcase_add_test(tcase, test_SBase_appendAnnotationString );
   tcase_add_test(tcase, test_SBase_appendNotes );
   tcase_add_test(tcase, test_SBase_appendNotes1 );
   tcase_add_test(tcase, test_SBase_appendNotes2 );
@@ -2009,7 +2172,6 @@
   tcase_add_test(tcase, test_SBase_appendNotes6 );
   tcase_add_test(tcase, test_SBase_appendNotes7 );
   tcase_add_test(tcase, test_SBase_appendNotes8 );
-  tcase_add_test(tcase, test_SBase_appendAnnotationString );
   tcase_add_test(tcase, test_SBase_appendNotesString );
   tcase_add_test(tcase, test_SBase_appendNotesString1);
   tcase_add_test(tcase, test_SBase_appendNotesString2);

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15622
          http://sbml.svn.sourceforge.net/sbml/?rev=15622&view=rev
Author:   sarahkeating
Date:     2012-04-20 12:14:41 +0000 (Fri, 20 Apr 2012)
Log Message:
-----------
updated tests

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestL3Species.cs
    trunk/libsbml/src/bindings/csharp/test/sbml/TestModel.cs
    trunk/libsbml/src/bindings/csharp/test/sbml/TestModel_newSetters.cs
    trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3Species.java
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel.java
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel_newSetters.java
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
    trunk/libsbml/src/bindings/python/test/sbml/TestL3Species.py
    trunk/libsbml/src/bindings/python/test/sbml/TestModel.py
    trunk/libsbml/src/bindings/python/test/sbml/TestModel_newSetters.py
    trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestL3Species.rb
    trunk/libsbml/src/bindings/ruby/test/sbml/TestModel.rb
    trunk/libsbml/src/bindings/ruby/test/sbml/TestModel_newSetters.rb
    trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
    trunk/libsbml/src/sbml/test/TestL3Species.c
    trunk/libsbml/src/sbml/test/TestModel.c
    trunk/libsbml/src/sbml/test/TestModel_newSetters.c

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestL3Species.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestL3Species.cs	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestL3Species.cs	2012-04-20 12:14:41 UTC (rev 15622)
@@ -148,7 +148,8 @@
     }
 
     public void test_L3_Species_ModelHistory()
-    {
+    {
+      (S).setMetaId("_3");
       ModelHistory history = new  ModelHistory();
       int i = (S).setModelHistory(history);
       assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestModel.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestModel.cs	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestModel.cs	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1101,7 +1101,8 @@
     }
 
     public void test_Model_setgetModelHistory()
-    {
+    {
+      M.setMetaId("_001");
       ModelHistory history = new  ModelHistory();
       ModelCreator mc = new  ModelCreator();
       Date date = new  Date(2005,12,30,12,15,45,1,2,0);

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestModel_newSetters.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestModel_newSetters.cs	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestModel_newSetters.cs	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1122,7 +1122,8 @@
     }
 
     public void test_Model_setModelHistory1()
-    {
+    {
+      M.setMetaId("_001");
       ModelHistory mh = new  ModelHistory();
       int i = M.setModelHistory(mh);
       assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
@@ -1134,7 +1135,8 @@
     }
 
     public void test_Model_setModelHistory2()
-    {
+    {
+      M.setMetaId("_001");
       int i = M.setModelHistory(null);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertEquals( false, M.isSetModelHistory() );

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1178,7 +1178,8 @@
 
     public void test_SBase_setModelHistoryL3()
     {
-      SBase sb = new Species(3,1);
+      SBase sb = new Species(3,1);
+      sb.setMetaId("_s");
       ModelHistory mh = new  ModelHistory();
       ModelCreator mc = new  ModelCreator();
       Date date = new  Date(2005,12,30,12,15,45,1,2,0);
@@ -1202,7 +1203,8 @@
     }
 
     public void test_SBase_setModelHistory_Model()
-    {
+    {
+      S.setMetaId("_001");
       ModelHistory history = new  ModelHistory();
       ModelCreator mc = new  ModelCreator();
       Date date = new  Date(2005,12,30,12,15,45,1,2,0);

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3Species.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3Species.java	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3Species.java	2012-04-20 12:14:41 UTC (rev 15622)
@@ -139,6 +139,7 @@
 
   public void test_L3_Species_ModelHistory()
   {
+    (S).setMetaId("_3");
     ModelHistory history = new  ModelHistory();
     int i = (S).setModelHistory(history);
     assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel.java	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel.java	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1085,6 +1085,7 @@
 
   public void test_Model_setgetModelHistory()
   {
+    M.setMetaId("_001");
     ModelHistory history = new  ModelHistory();
     ModelCreator mc = new  ModelCreator();
     Date date = new  Date(2005,12,30,12,15,45,1,2,0);

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel_newSetters.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel_newSetters.java	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel_newSetters.java	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1113,6 +1113,7 @@
 
   public void test_Model_setModelHistory1()
   {
+    M.setMetaId("_001");
     ModelHistory mh = new  ModelHistory();
     int i = M.setModelHistory(mh);
     assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
@@ -1125,6 +1126,7 @@
 
   public void test_Model_setModelHistory2()
   {
+    M.setMetaId("_001");
     int i = M.setModelHistory(null);
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( false, M.isSetModelHistory() );

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1169,6 +1169,7 @@
   public void test_SBase_setModelHistoryL3()
   {
     SBase sb = new Species(3,1);
+    sb.setMetaId("_s");
     ModelHistory mh = new  ModelHistory();
     ModelCreator mc = new  ModelCreator();
     Date date = new  Date(2005,12,30,12,15,45,1,2,0);
@@ -1193,6 +1194,7 @@
 
   public void test_SBase_setModelHistory_Model()
   {
+    S.setMetaId("_001");
     ModelHistory history = new  ModelHistory();
     ModelCreator mc = new  ModelCreator();
     Date date = new  Date(2005,12,30,12,15,45,1,2,0);

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestL3Species.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestL3Species.py	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestL3Species.py	2012-04-20 12:14:41 UTC (rev 15622)
@@ -53,6 +53,7 @@
     pass  
 
   def test_L3_Species_ModelHistory(self):
+    (self.S).setMetaId("_3")
     history = libsbml.ModelHistory()
     i = (self.S).setModelHistory(history)
     self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT )

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestModel.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestModel.py	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestModel.py	2012-04-20 12:14:41 UTC (rev 15622)
@@ -897,6 +897,7 @@
     pass  
 
   def test_Model_setgetModelHistory(self):
+    self.M.setMetaId("_001")
     history = libsbml.ModelHistory()
     mc = libsbml.ModelCreator()
     date = libsbml.Date(2005,12,30,12,15,45,1,2,0)

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestModel_newSetters.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestModel_newSetters.py	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestModel_newSetters.py	2012-04-20 12:14:41 UTC (rev 15622)
@@ -954,6 +954,7 @@
     pass  
 
   def test_Model_setModelHistory1(self):
+    self.M.setMetaId("_001")
     mh = libsbml.ModelHistory()
     i = self.M.setModelHistory(mh)
     self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT )
@@ -965,6 +966,7 @@
     pass  
 
   def test_Model_setModelHistory2(self):
+    self.M.setMetaId("_001")
     i = self.M.setModelHistory(None)
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( False, self.M.isSetModelHistory() )

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1027,6 +1027,7 @@
 
   def test_SBase_setModelHistoryL3(self):
     sb = libsbml.Species(3,1)
+    sb.setMetaId("_s")
     mh = libsbml.ModelHistory()
     mc = libsbml.ModelCreator()
     date = libsbml.Date(2005,12,30,12,15,45,1,2,0)
@@ -1050,6 +1051,7 @@
     pass  
 
   def test_SBase_setModelHistory_Model(self):
+    self.S.setMetaId("_001")
     history = libsbml.ModelHistory()
     mc = libsbml.ModelCreator()
     date = libsbml.Date(2005,12,30,12,15,45,1,2,0)

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestL3Species.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestL3Species.rb	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestL3Species.rb	2012-04-20 12:14:41 UTC (rev 15622)
@@ -47,6 +47,7 @@
   end
 
   def test_L3_Species_ModelHistory
+    @@s.setMetaId("_3")
     history = LibSBML::ModelHistory.new()
     i = @@s.setModelHistory(history)
     assert( i == LibSBML::LIBSBML_INVALID_OBJECT )

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestModel.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestModel.rb	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestModel.rb	2012-04-20 12:14:41 UTC (rev 15622)
@@ -890,6 +890,7 @@
   end
 
   def test_Model_setgetModelHistory
+    @@m.setMetaId("_001")
     history = LibSBML::ModelHistory.new()
     mc = LibSBML::ModelCreator.new()
     date = LibSBML::Date.new(2005,12,30,12,15,45,1,2,0)

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestModel_newSetters.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestModel_newSetters.rb	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestModel_newSetters.rb	2012-04-20 12:14:41 UTC (rev 15622)
@@ -947,6 +947,7 @@
   end
 
   def test_Model_setModelHistory1
+    @@m.setMetaId("_001")
     mh = LibSBML::ModelHistory.new()
     i = @@m.setModelHistory(mh)
     assert( i == LibSBML::LIBSBML_INVALID_OBJECT )
@@ -958,6 +959,7 @@
   end
 
   def test_Model_setModelHistory2
+    @@m.setMetaId("_001")
     i = @@m.setModelHistory(nil)
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal false, @@m.isSetModelHistory()

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb	2012-04-20 12:14:41 UTC (rev 15622)
@@ -1017,6 +1017,7 @@
 
   def test_SBase_setModelHistoryL3
     sb = LibSBML::Species.new(3,1)
+    sb.setMetaId("_s")
     mh = LibSBML::ModelHistory.new()
     mc = LibSBML::ModelCreator.new()
     date = LibSBML::Date.new(2005,12,30,12,15,45,1,2,0)
@@ -1040,6 +1041,7 @@
   end
 
   def test_SBase_setModelHistory_Model
+    @@s.setMetaId("_001")
     history = LibSBML::ModelHistory.new()
     mc = LibSBML::ModelCreator.new()
     date = LibSBML::Date.new(2005,12,30,12,15,45,1,2,0)

Modified: trunk/libsbml/src/sbml/test/TestL3Species.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestL3Species.c	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/sbml/test/TestL3Species.c	2012-04-20 12:14:41 UTC (rev 15622)
@@ -433,7 +433,7 @@
 START_TEST (test_L3_Species_ModelHistory)
 {
   ModelHistory_t * history = ModelHistory_create();
-  S->setMetaId("_3");
+  SBase_setMetaId((SBase_t *)(S), "_3");
   int i = SBase_setModelHistory((SBase_t *)(S), history);
 
   fail_unless( i == LIBSBML_INVALID_OBJECT );

Modified: trunk/libsbml/src/sbml/test/TestModel.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestModel.c	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/sbml/test/TestModel.c	2012-04-20 12:14:41 UTC (rev 15622)
@@ -188,7 +188,7 @@
 
 START_TEST(test_Model_setgetModelHistory)
 {
-  M->setMetaId("_001");
+  SBase_setMetaId((SBase_t *) (M), "_001");
   ModelHistory_t * history = ModelHistory_create();
   ModelCreator_t * mc = ModelCreator_create();
   Date_t * date = 

Modified: trunk/libsbml/src/sbml/test/TestModel_newSetters.c
===================================================================
--- trunk/libsbml/src/sbml/test/TestModel_newSetters.c	2012-04-20 11:07:34 UTC (rev 15621)
+++ trunk/libsbml/src/sbml/test/TestModel_newSetters.c	2012-04-20 12:14:41 UTC (rev 15622)
@@ -178,7 +178,7 @@
 
 START_TEST (test_Model_setModelHistory1)
 {
-  M->setMetaId("_001");
+  SBase_setMetaId((SBase_t *) (M), "_001");
   ModelHistory_t *mh = ModelHistory_create();
   int i = Model_setModelHistory(M, mh);
 
@@ -197,7 +197,7 @@
 
 START_TEST (test_Model_setModelHistory2)
 {
-  M->setMetaId("_001");
+  SBase_setMetaId((SBase_t *) (M), "_001");
   int i = Model_setModelHistory(M, NULL);
 
   fail_unless( i == LIBSBML_OPERATION_SUCCESS );

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Revision: 15702
          http://sbml.svn.sourceforge.net/sbml/?rev=15702&view=rev
Author:   fbergmann
Date:     2012-04-26 14:43:52 +0000 (Thu, 26 Apr 2012)
Log Message:
-----------
- expose L3 Parser to language bindings

Modified Paths:
--------------
    trunk/libsbml/src/bindings/swig/libsbml.h
    trunk/libsbml/src/bindings/swig/libsbml.i
    trunk/libsbml/src/sbml/math/L3Parser.h
    trunk/libsbml/src/sbml/math/L3ParserSettings.h

Modified: trunk/libsbml/src/bindings/swig/libsbml.h
===================================================================
--- trunk/libsbml/src/bindings/swig/libsbml.h	2012-04-26 07:49:45 UTC (rev 15701)
+++ trunk/libsbml/src/bindings/swig/libsbml.h	2012-04-26 14:43:52 UTC (rev 15702)
@@ -92,6 +92,8 @@
 #include <sbml/math/MathML.h>
 #include <sbml/math/FormulaFormatter.h>
 #include <sbml/math/FormulaParser.h>
+#include <sbml/math/L3Parser.h>
+#include <sbml/math/L3ParserSettings.h>
 
 #include <sbml/xml/XMLAttributes.h>
 #include <sbml/xml/XMLNamespaces.h>

Modified: trunk/libsbml/src/bindings/swig/libsbml.i
===================================================================
--- trunk/libsbml/src/bindings/swig/libsbml.i	2012-04-26 07:49:45 UTC (rev 15701)
+++ trunk/libsbml/src/bindings/swig/libsbml.i	2012-04-26 14:43:52 UTC (rev 15702)
@@ -576,6 +576,8 @@
 %include sbml/math/ASTNode.h
 %include sbml/math/FormulaParser.h
 %include sbml/math/FormulaFormatter.h
+%include sbml/math/L3Parser.h
+%include sbml/math/L3ParserSettings.h
 
 %include sbml/xml/XMLAttributes.h
 %include sbml/xml/XMLConstructorException.h

Modified: trunk/libsbml/src/sbml/math/L3Parser.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.h	2012-04-26 07:49:45 UTC (rev 15701)
+++ trunk/libsbml/src/sbml/math/L3Parser.h	2012-04-26 14:43:52 UTC (rev 15702)
@@ -63,6 +63,8 @@
 class LIBSBML_EXTERN L3Parser
 {
 public:
+
+#ifndef SWIG
   std::stringstream input;
   ASTNode* outputNode;
   std::string error;
@@ -78,7 +80,8 @@
   bool parseunits;
   bool avocsymbol;
 
-
+#endif
+  
   L3Parser();
   ~L3Parser();
 
@@ -323,6 +326,7 @@
   static char* getLastParseL3Error();
 };
 
+#ifndef SWIG
 /** @cond doxygen-libsbml-internal */
 
 /**
@@ -332,8 +336,8 @@
 extern L3Parser* l3p;
 /** @endcond */
 
+#endif
 
-
 LIBSBML_CPP_NAMESPACE_END
 
 #endif  /* __cplusplus */

Modified: trunk/libsbml/src/sbml/math/L3ParserSettings.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-04-26 07:49:45 UTC (rev 15701)
+++ trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-04-26 14:43:52 UTC (rev 15702)
@@ -74,7 +74,7 @@
   */
 typedef enum {L3P_PARSE_LOG_AS_LOG10=0,
       L3P_PARSE_LOG_AS_LN=1,
-      L3P_PARSE_LOG_AS_ERROR=2
+      L3P_PARSE_LOG_AS_ERROR=2
      } l3p_log_type ;
 
 #define L3P_COLLAPSE_UNARY_MINUS true
@@ -232,6 +232,8 @@
 
 #endif  /* __cplusplus */
 
+#ifndef SWIG
+
 LIBSBML_CPP_NAMESPACE_BEGIN
 BEGIN_C_DECLS
 
@@ -323,4 +325,7 @@
 
 END_C_DECLS
 LIBSBML_CPP_NAMESPACE_END
+
+#endif
+
 #endif /* L3ParserSettings_h */

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Revision: 15804
          http://sbml.svn.sourceforge.net/sbml/?rev=15804&view=rev
Author:   mhucka
Date:     2012-05-04 18:20:07 +0000 (Fri, 04 May 2012)
Log Message:
-----------
Removed the use of @docnote alias in doxygen which I couldn't get to work,
and went straight to HTML instead. 

Modified Paths:
--------------
    trunk/libsbml/src/bindings/swig/OStream.h
    trunk/libsbml/src/sbml/ListOf.h
    trunk/libsbml/src/sbml/SBMLDocument.h
    trunk/libsbml/src/sbml/SBMLError.h
    trunk/libsbml/src/sbml/SBMLErrorLog.h
    trunk/libsbml/src/sbml/SBMLNamespaces.cpp
    trunk/libsbml/src/sbml/SBMLNamespaces.h
    trunk/libsbml/src/sbml/SBMLReader.h
    trunk/libsbml/src/sbml/SBase.h
    trunk/libsbml/src/sbml/SyntaxChecker.h
    trunk/libsbml/src/sbml/annotation/CVTerm.h
    trunk/libsbml/src/sbml/annotation/Date.h
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/units/UnitFormulaFormatter.h
    trunk/libsbml/src/sbml/xml/ExpatAttributes.h
    trunk/libsbml/src/sbml/xml/ExpatParser.h
    trunk/libsbml/src/sbml/xml/LibXMLParser.h
    trunk/libsbml/src/sbml/xml/XMLAttributes.h
    trunk/libsbml/src/sbml/xml/XMLError.h
    trunk/libsbml/src/sbml/xml/XMLErrorLog.h
    trunk/libsbml/src/sbml/xml/XMLInputStream.h
    trunk/libsbml/src/sbml/xml/XMLNamespaces.h
    trunk/libsbml/src/sbml/xml/XMLNode.h
    trunk/libsbml/src/sbml/xml/XMLOutputStream.h
    trunk/libsbml/src/sbml/xml/XMLParser.h
    trunk/libsbml/src/sbml/xml/XMLToken.cpp
    trunk/libsbml/src/sbml/xml/XMLToken.h
    trunk/libsbml/src/sbml/xml/XMLTriple.h
    trunk/libsbml/src/sbml/xml/XercesParser.h

Modified: trunk/libsbml/src/bindings/swig/OStream.h
===================================================================
--- trunk/libsbml/src/bindings/swig/OStream.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/bindings/swig/OStream.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -142,7 +142,7 @@
      * @param is_append whether to open the file for appending (default:
      * <code>false</code>, meaning overwrite the content instead)
      * 
-     * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+     * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif
      */
     OFStream (const std::string& filename, bool is_append = false); 
 
@@ -164,7 +164,7 @@
      * @param is_append whether to open the file for appending (default:
      * <code>false</code>, meaning overwrite the content instead)
      * 
-     * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+     * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif
      */
     void open (const std::string& filename, bool is_append = false);
   

Modified: trunk/libsbml/src/sbml/ListOf.h
===================================================================
--- trunk/libsbml/src/sbml/ListOf.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/ListOf.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -112,7 +112,7 @@
    * @param version the Version within the SBML Level; if not assigned,
    * defaults to the value of SBML_DEFAULT_VERSION.
    * 
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   ListOf (unsigned int level   = SBML_DEFAULT_LEVEL, 
           unsigned int version = SBML_DEFAULT_VERSION);
@@ -330,7 +330,7 @@
    * @param doDelete if @c true (default), all items are deleted and cleared.
    * Otherwise, all items are just cleared and not deleted.
    * 
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */ 
   void clear (bool doDelete = true);
 

Modified: trunk/libsbml/src/sbml/SBMLDocument.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SBMLDocument.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -381,7 +381,7 @@
    * of SBML object, are either invalid or mismatched with respect to the
    * parent SBMLDocument object.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    *
    * @see SBMLDocument::setLevelAndVersion(@if java long lev, long ver, boolean strict@...)
    * @see getDefaultLevel()
@@ -633,7 +633,7 @@
    * find out whether it is Level&nbsp;1.  (If the conversion to
    * Level&nbsp;1 failed, the Level of this model will be left unchanged.)
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    * 
    * @see checkL1Compatibility()
    * @see checkL2v1Compatibility()
@@ -683,7 +683,7 @@
    *
    * @param sid the identifier of the new Model to create.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    *
    * @see getModel()
    * @see SBMLDocument::setModel(@if java Model m@...)
@@ -1102,7 +1102,7 @@
    * @param stream the ostream or ostringstream object indicating where
    * the output should be printed.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    *
    * @see getNumErrors()
    * @see getErrorLog()

Modified: trunk/libsbml/src/sbml/SBMLError.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLError.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SBMLError.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -1112,7 +1112,7 @@
    * @param category an integer indicating the category to which the error
    * belongs.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   SBMLError
   (

Modified: trunk/libsbml/src/sbml/SBMLErrorLog.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLErrorLog.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SBMLErrorLog.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -170,7 +170,7 @@
    * @param category an integer indicating the category to which the error
    * belongs.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   void logError
   (

Modified: trunk/libsbml/src/sbml/SBMLNamespaces.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLNamespaces.cpp	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SBMLNamespaces.cpp	2012-05-04 18:20:07 UTC (rev 15804)
@@ -774,18 +774,8 @@
  * @param version the SBML version
  *
  * @return SBMLNamespaces_t structure created
- * 
- * @docnote The native C++ implementation of this method defines a
- * default argument value.  In the documentation generated for different
- * libSBML language bindings, you may or may not see corresponding
- * arguments in the method declarations.  For example, in Java, a default
- * argument is handled by declaring two separate methods, with one of
- * them having the argument and the other one lacking the argument.
- * However, the libSBML documentation will be @em identical for both
- * methods.  Consequently, if you are reading this and do not see an
- * argument even though one is described, please look for descriptions of
- * other variants of this method near where this one appears in the
- * documentation.
+ *
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
  */
 
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/SBMLNamespaces.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLNamespaces.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SBMLNamespaces.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -123,7 +123,7 @@
    * @param level the SBML level
    * @param version the SBML version
    * 
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   SBMLNamespaces(unsigned int level = SBML_DEFAULT_LEVEL, 
                  unsigned int version = SBML_DEFAULT_VERSION);

Modified: trunk/libsbml/src/sbml/SBMLReader.h
===================================================================
--- trunk/libsbml/src/sbml/SBMLReader.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SBMLReader.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -446,7 +446,7 @@
   /**
    * Used by readSBML() and readSBMLFromString().
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   SBMLDocument* readInternal (const char* content, bool isFile = true);
 

Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SBase.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -820,7 +820,7 @@
    * to the given @if clike #SBMLTypeCode_t value@... SBML object type
    * code@..., or @c NULL if no ancestor exists.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   SBase* getAncestorOfType(int type, const std::string pkgName = "core");
 
@@ -864,7 +864,7 @@
    * to the given @if clike #SBMLTypeCode_t value@... SBML object type
    * code@..., or @c NULL if no ancestor exists.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   const SBase* getAncestorOfType(int type, const std::string pkgName = "core") const;
 
@@ -2178,7 +2178,7 @@
    * addition, the caller should make sure to free the original object if
    * it is no longer being used, or else a memory leak will result.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   int addCVTerm(CVTerm * term, bool newBag = false);
 
@@ -3005,7 +3005,7 @@
    *
    * This is essentially a short form of getErrorLog()->logError(...)
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   void logError (  unsigned int       id
                  , const unsigned int level   = 2
@@ -3122,7 +3122,7 @@
    * If the syntax of the unit attribute of this object is incorrect, 
    * an error is logged
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   void checkUnitSyntax(unsigned int flag = 0);
 #endif

Modified: trunk/libsbml/src/sbml/SyntaxChecker.h
===================================================================
--- trunk/libsbml/src/sbml/SyntaxChecker.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/SyntaxChecker.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -263,7 +263,7 @@
    * SyntaxChecker_hasExpectedXHTMLSyntax(). They are functionally
    * identical. @endif@~
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   static bool hasExpectedXHTMLSyntax(const XMLNode * xhtml, 
                                      SBMLNamespaces * sbmlns = NULL); 

Modified: trunk/libsbml/src/sbml/annotation/CVTerm.h
===================================================================
--- trunk/libsbml/src/sbml/annotation/CVTerm.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/annotation/CVTerm.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -259,7 +259,7 @@
    *
    * @param type a @if clike #QualifierType_t value@... qualifier type@...@~
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   CVTerm(QualifierType_t type = UNKNOWN_QUALIFIER);
 

Modified: trunk/libsbml/src/sbml/annotation/Date.h
===================================================================
--- trunk/libsbml/src/sbml/annotation/Date.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/annotation/Date.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -189,7 +189,7 @@
    * this would require a value of @c 1 for the sign field, @c 5 for the
    * hour offset and @c 0 for the minutes offset.
    * 
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   Date(unsigned int year = 2000, unsigned int month = 1, 
     unsigned int day = 1, unsigned int hour = 0, 

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -399,7 +399,7 @@
    * @if clike @link #ASTNodeType_t ASTNodeType_t@... type@...@~
    * code indicating the type of node to create.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   LIBSBML_EXTERN
   ASTNode (ASTNodeType_t type = AST_UNKNOWN);

Modified: trunk/libsbml/src/sbml/units/UnitFormulaFormatter.h
===================================================================
--- trunk/libsbml/src/sbml/units/UnitFormulaFormatter.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/units/UnitFormulaFormatter.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -104,7 +104,7 @@
    * @param reactNo integer indicating which Reaction within the Model
    * contains the KineticLaw under consideration (default = -1).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   UnitDefinition * getUnitDefinition(const ASTNode * node, 
     bool inKL = false, int reactNo = -1);

Modified: trunk/libsbml/src/sbml/xml/ExpatAttributes.h
===================================================================
--- trunk/libsbml/src/sbml/xml/ExpatAttributes.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/ExpatAttributes.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -48,7 +48,7 @@
    * The Expat attribute names are assumed to be in namespace triplet form
    * separated by sepchar.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   ExpatAttributes (const XML_Char** attrs,
 		   const XML_Char* elementName,

Modified: trunk/libsbml/src/sbml/xml/ExpatParser.h
===================================================================
--- trunk/libsbml/src/sbml/xml/ExpatParser.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/ExpatParser.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -140,7 +140,7 @@
   /**
    * Log or otherwise report the given error.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   void reportError (  const XMLErrorCode_t code
 		    , const std::string&   extraMsg     = ""

Modified: trunk/libsbml/src/sbml/xml/LibXMLParser.h
===================================================================
--- trunk/libsbml/src/sbml/xml/LibXMLParser.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/LibXMLParser.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -141,7 +141,7 @@
   /**
    * Log or otherwise report the given error.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
 
  void reportError (  const XMLErrorCode_t code

Modified: trunk/libsbml/src/sbml/xml/XMLAttributes.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLAttributes.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLAttributes.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -143,7 +143,7 @@
    * @note if local name with the same namespace URI already exists in this 
    * attribute set, its value and prefix will be replaced.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   int add (  const std::string& name
 	    , const std::string& value
@@ -522,7 +522,7 @@
    * be used to read a value for an attribute name with a prefix and
    * namespace.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const std::string&  name
                  , bool&               value
@@ -554,7 +554,7 @@
    *
    * @returns @c true if the attribute was read into value, @c false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const XMLTriple& triple
                  , bool&        value
@@ -592,7 +592,7 @@
    * should be used to read a value for an attribute name with a prefix and
    * namespace.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const std::string&  name
                  , double&             value
@@ -624,7 +624,7 @@
    *
    * @returns @c true if the attribute was read into value, @c false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const XMLTriple&  triple
                  , double&           value
@@ -661,7 +661,7 @@
    * be used to read a value for an attribute name with a prefix and
    * namespace.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const std::string&  name
                  , long&               value
@@ -693,7 +693,7 @@
    *
    * @returns @c true if the attribute was read into value, @c false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const XMLTriple& triple
                  , long&            value
@@ -730,7 +730,7 @@
    * be used to read a value for an attribute name with a prefix and
    * namespace.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const std::string&  name
                  , int&                value
@@ -762,7 +762,7 @@
    *
    * @returns @c true if the attribute was read into value, @c false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const XMLTriple& triple
                  , int&             value
@@ -799,7 +799,7 @@
    * ...) const should be used to read a value for an attribute name with a
    * prefix and namespace.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const std::string&  name
                  , unsigned int&       value
@@ -831,7 +831,7 @@
    *
    * @returns @c true if the attribute was read into value, @c false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const XMLTriple& triple
                  , unsigned int&    value
@@ -862,7 +862,7 @@
    * should be used to read a value for an attribute name with a prefix and
    * namespace.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const std::string&  name
                  , std::string&        value
@@ -888,7 +888,7 @@
    *
    * @returns @c true if the attribute was read into value, @c false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool readInto (  const XMLTriple& triple
                  , std::string&     value

Modified: trunk/libsbml/src/sbml/xml/XMLError.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLError.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLError.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -627,7 +627,7 @@
    * @param category an integer indicating the category to which the error
    * belongs.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLError
   (

Modified: trunk/libsbml/src/sbml/xml/XMLErrorLog.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLErrorLog.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLErrorLog.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -200,7 +200,7 @@
    * @param stream the ostream or ostringstream object indicating where
    * the output should be printed.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   void printErrors (std::ostream& stream = std::cerr) const;
 

Modified: trunk/libsbml/src/sbml/xml/XMLInputStream.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLInputStream.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLInputStream.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -72,7 +72,7 @@
    *
    * @p errorLog the XMLErrorLog object to use.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLInputStream (  const char*        content
                   , bool               isFile   = true

Modified: trunk/libsbml/src/sbml/xml/XMLNamespaces.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLNamespaces.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLNamespaces.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -148,7 +148,7 @@
    * @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   int add (const std::string& uri, const std::string& prefix = "");
 
@@ -321,7 +321,7 @@
    * prefix, or an empty string if no such prefix-and-URI pair exists
    * in this XMLNamespaces object
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    * 
    * @see getURI()
    */

Modified: trunk/libsbml/src/sbml/xml/XMLNode.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLNode.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLNode.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -185,7 +185,7 @@
    * @param line an unsigned int, the line number (default = 0).
    * @param column an unsigned int, the column number (default = 0).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLNode (  const XMLTriple&     triple
            , const XMLAttributes& attributes
@@ -202,7 +202,7 @@
    * @param line an unsigned int, the line number (default = 0).
    * @param column an unsigned int, the column number (default = 0).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
   */
   XMLNode (  const XMLTriple&      triple
            , const XMLAttributes&  attributes
@@ -217,7 +217,7 @@
    * @param line an unsigned int, the line number (default = 0).
    * @param column an unsigned int, the column number (default = 0).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLNode (  const XMLTriple&    triple
            , const unsigned int  line   = 0
@@ -231,7 +231,7 @@
    * @param line an unsigned int, the line number (default = 0).
    * @param column an unsigned int, the column number (default = 0).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLNode (  const std::string&  chars
            , const unsigned int  line   = 0
@@ -495,7 +495,7 @@
    * @return a XMLNode which is converted from string @p xmlstr.  If the
    * conversion failed, this method returns @c NULL.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   static XMLNode* convertStringToXMLNode(const std::string& xmlstr,
                                          const XMLNamespaces* xmlns = NULL);

Modified: trunk/libsbml/src/sbml/xml/XMLOutputStream.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLOutputStream.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLOutputStream.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -58,7 +58,7 @@
   /**
    * Creates a new XMLOutputStream that wraps stream.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLOutputStream (  std::ostream&       stream
                    , const std::string&  encoding     = "UTF-8"
@@ -318,7 +318,7 @@
   /**
    * Outputs indentation whitespace.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   void writeIndent (bool isEnd = false);
 
@@ -408,7 +408,7 @@
   /**
    * Creates a new XMLOutputStream that wraps stream.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLOutputStringStream (  std::ostringstream& stream
                          , const std::string&  encoding     = "UTF-8"
@@ -431,7 +431,7 @@
   /**
    * Creates a new XMLOutputStream that wraps stream.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLOutputFileStream (  std::ofstream&      stream
                        , const std::string&  encoding     = "UTF-8"

Modified: trunk/libsbml/src/sbml/xml/XMLParser.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLParser.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLParser.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -64,7 +64,7 @@
    * If the XML compatibility layer has been linked against only a single
    * XML library, the library parameter is ignored.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   static XMLParser* create (  XMLHandler&       handler
                             , const std::string library = "" );
@@ -85,7 +85,7 @@
    *
    * @return true if the parse was successful, false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   virtual bool parse (const char* content, bool isFile = true) = 0;
 
@@ -106,7 +106,7 @@
    * @return true if the first step of the progressive parse was
    * successful, false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   virtual bool parseFirst (const char* content, bool isFile = true) = 0;
 

Modified: trunk/libsbml/src/sbml/xml/XMLToken.cpp
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLToken.cpp	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLToken.cpp	2012-05-04 18:20:07 UTC (rev 15804)
@@ -342,7 +342,7 @@
  * @note if local name with the same namespace URI already exists in the
  * attribute set, its value and prefix will be replaced.
  *
- * @docnote The native C++ implementation of this method defines a
+ * The native C++ implementation of this method defines a
  * default argument value.  In the documentation generated for different
  * libSBML language bindings, you may or may not see corresponding
  * arguments in the method declarations.  For example, in Java, a default
@@ -487,7 +487,7 @@
  * @return the index of an attribute with the given local name and namespace URI, 
  * or -1 if not present.
  *
- * @docnote The native C++ implementation of this method defines a
+ * The native C++ implementation of this method defines a
  * default argument value.  In the documentation generated for different
  * libSBML language bindings, you may or may not see corresponding
  * arguments in the method declarations.  For example, in Java, a default
@@ -645,7 +645,7 @@
  * returned.  
  * Use hasAttr(name, uri) to test for attribute existence.
  *
- * @docnote The native C++ implementation of this method defines a
+ * The native C++ implementation of this method defines a
  * default argument value.  In the documentation generated for different
  * libSBML language bindings, you may or may not see corresponding
  * arguments in the method declarations.  For example, in Java, a default
@@ -711,17 +711,7 @@
  * @return @c true if an attribute with the given local name and namespace 
  * URI exists in the attribute set in this XMLToken, @c false otherwise.
  *
- * @docnote The native C++ implementation of this method defines a
- * default argument value.  In the documentation generated for different
- * libSBML language bindings, you may or may not see corresponding
- * arguments in the method declarations.  For example, in Java, a default
- * argument is handled by declaring two separate methods, with one of
- * them having the argument and the other one lacking the argument.
- * However, the libSBML documentation will be @em identical for both
- * methods.  Consequently, if you are reading this and do not see an
- * argument even though one is described, please look for descriptions of
- * other variants of this method near where this one appears in the
- * documentation.
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
  */
 bool 
 XMLToken::hasAttr (const std::string name, const std::string uri) const

Modified: trunk/libsbml/src/sbml/xml/XMLToken.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLToken.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLToken.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -77,7 +77,7 @@
    * @param line an unsigned int, the line number (default = 0).
    * @param column an unsigned int, the column number (default = 0).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLToken (  const XMLTriple&      triple
             , const XMLAttributes&  attributes
@@ -94,7 +94,7 @@
    * @param line an unsigned int, the line number (default = 0).
    * @param column an unsigned int, the column number (default = 0).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLToken (  const XMLTriple&      triple
             , const XMLAttributes&  attributes
@@ -109,7 +109,7 @@
    * @param line an unsigned int, the line number (default = 0).
    * @param column an unsigned int, the column number (default = 0).
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLToken (  const XMLTriple&    triple
             , const unsigned int  line   = 0
@@ -126,7 +126,7 @@
    * @throws @if python ValueError @else XMLConstructorException @endif@~
    * Thrown if the argument @p orig is @c NULL.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLToken (  const std::string&  chars
             , const unsigned int  line   = 0
@@ -216,7 +216,7 @@
    * @note if local name with the same namespace URI already exists in the
    * attribute set, its value and prefix will be replaced.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   int addAttr (  const std::string& name
 	        , const std::string& value
@@ -317,7 +317,7 @@
    * @return the index of an attribute with the given local name and namespace URI, 
    * or <code>-1</code> if not present.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   int getAttrIndex (const std::string& name, const std::string& uri="") const;
 
@@ -438,7 +438,7 @@
    * Use XMLToken::hasAttr(@if java String name, String uri@...)
    * to test for attribute existence.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   std::string getAttrValue (const std::string name, const std::string uri="") const;
 
@@ -483,7 +483,7 @@
    * @return @c true if an attribute with the given local name and namespace 
    * URI exists in the attribute set in this XMLToken, @c false otherwise.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   bool hasAttr (const std::string name, const std::string uri="") const;
 
@@ -556,7 +556,7 @@
    * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
    * @li @link OperationReturnValues_t#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION @endlink
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   int addNamespace (const std::string& uri, const std::string& prefix = "");
 
@@ -693,7 +693,7 @@
    *
    * @note If @p prefix does not exist, an empty string will be returned.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   std::string getNamespaceURI (const std::string& prefix = "") const;
 

Modified: trunk/libsbml/src/sbml/xml/XMLTriple.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLTriple.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XMLTriple.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -113,7 +113,7 @@
    * @throws @if python ValueError @else XMLConstructorException @endif@~
    * Thrown if the argument @p orig is @c NULL.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   XMLTriple (const std::string& triplet, const char sepchar = ' ');
 

Modified: trunk/libsbml/src/sbml/xml/XercesParser.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XercesParser.h	2012-05-04 17:56:41 UTC (rev 15803)
+++ trunk/libsbml/src/sbml/xml/XercesParser.h	2012-05-04 18:20:07 UTC (rev 15804)
@@ -152,7 +152,7 @@
   /**
    * Log or otherwise report the given error.
    *
-   * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif@~
+   * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
    */
   void reportError (  const XMLErrorCode_t code
 		    , const std::string&   extraMsg     = ""

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 16040
          http://sbml.svn.sourceforge.net/sbml/?rev=16040&view=rev
Author:   sarahkeating
Date:     2012-07-23 10:38:24 +0000 (Mon, 23 Jul 2012)
Log Message:
-----------
added a new function getSBOTermAsURL which returns the identifiers.org resolvableURL for the SBO term on the object

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
    trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
    trunk/libsbml/src/sbml/SBase.cpp
    trunk/libsbml/src/sbml/SBase.h
    trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs	2012-07-23 09:34:29 UTC (rev 16039)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs	2012-07-23 10:38:24 UTC (rev 16040)
@@ -1445,50 +1445,63 @@
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertEquals( true, S.isSetSBOTerm() );
       assertTrue( S.getSBOTerm() == 5 );
-      assertTrue( (  "SBO:0000005" != S.getSBOTermID() ) == false );
+      assertTrue( (  "SBO:0000005" != S.getSBOTermID() ) == false );
+      assertTrue(("http://identifiers.org/biomodels.sbo/SBO:0000005" != S.getSBOTermAsURL()) == false);
       i = S.unsetSBOTerm();
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
-      assertEquals( false, S.isSetSBOTerm() );
+      assertEquals( false, S.isSetSBOTerm() );
+      assertTrue(S.getSBOTermID() == "");
+      assertTrue(S.getSBOTermAsURL() == "");
       i = S.setSBOTerm(0);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertEquals( true, S.isSetSBOTerm() );
       assertTrue( S.getSBOTerm() == 0 );
-      assertTrue( (  "SBO:0000000" != S.getSBOTermID() ) == false );
+      assertTrue( (  "SBO:0000000" != S.getSBOTermID() ) == false );
+      assertTrue(("http://identifiers.org/biomodels.sbo/SBO:0000000" != S.getSBOTermAsURL()) == false);
       i = S.setSBOTerm(9999999);
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertEquals( true, S.isSetSBOTerm() );
       assertTrue( S.getSBOTerm() == 9999999 );
-      assertTrue( (  "SBO:9999999" != S.getSBOTermID() ) == false );
-      i = S.setSBOTerm( "SBO:0000005");
+      assertTrue( (  "SBO:9999999" != S.getSBOTermID() ) == false );
+      assertTrue(("http://identifiers.org/biomodels.sbo/SBO:9999999" != S.getSBOTermAsURL()) == false);
+      i = S.setSBOTerm("SBO:0000005");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertEquals( true, S.isSetSBOTerm() );
       assertTrue( S.getSBOTerm() == 5 );
-      assertTrue( (  "SBO:0000005" != S.getSBOTermID() ) == false );
+      assertTrue( (  "SBO:0000005" != S.getSBOTermID() ) == false );
+      assertTrue(("http://identifiers.org/biomodels.sbo/SBO:0000005" != S.getSBOTermAsURL()) == false);
       i = S.unsetSBOTerm();
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
-      assertEquals( false, S.isSetSBOTerm() );
-      i = S.setSBOTerm( "SBO:0000000");
+      assertEquals( false, S.isSetSBOTerm() );
+      assertTrue(S.getSBOTermID() == "");
+      assertTrue(S.getSBOTermAsURL() == "");
+      i = S.setSBOTerm("SBO:0000000");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertEquals( true, S.isSetSBOTerm() );
       assertTrue( S.getSBOTerm() == 0 );
-      assertTrue( (  "SBO:0000000" != S.getSBOTermID() ) == false );
-      i = S.setSBOTerm( "SBO:9999999");
+      assertTrue( (  "SBO:0000000" != S.getSBOTermID() ) == false );
+      assertTrue(("http://identifiers.org/biomodels.sbo/SBO:0000000" != S.getSBOTermAsURL()) == false);
+      i = S.setSBOTerm("SBO:9999999");
       assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
       assertEquals( true, S.isSetSBOTerm() );
       assertTrue( S.getSBOTerm() == 9999999 );
-      assertTrue( (  "SBO:9999999" != S.getSBOTermID() ) == false );
+      assertTrue( (  "SBO:9999999" != S.getSBOTermID() ) == false );
+      assertTrue(("http://identifiers.org/biomodels.sbo/SBO:9999999" != S.getSBOTermAsURL()) == false);
       i = S.setSBOTerm(SBML_INT_MAX);
       assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
       assertEquals( false, S.isSetSBOTerm() );
-      assertTrue( S.getSBOTermID() == "" );
+      assertTrue( S.getSBOTermID() == "" );
+      assertTrue( S.getSBOTermAsURL() == "");
       i = S.setSBOTerm(-1);
       assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
       assertEquals( false, S.isSetSBOTerm() );
-      assertTrue( S.getSBOTermID() == "" );
+      assertTrue( S.getSBOTermID() == "" );
+      assertTrue(S.getSBOTermAsURL() == "");
       i = S.setSBOTerm(10000000);
       assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
       assertEquals( false, S.isSetSBOTerm() );
-      assertTrue( S.getSBOTermID() == "" );
+      assertTrue( S.getSBOTermID() == "" );
+      assertTrue(S.getSBOTermAsURL() == "");
     }
 
     public void test_SBase_unsetCVTerms()

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java	2012-07-23 09:34:29 UTC (rev 16039)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java	2012-07-23 10:38:24 UTC (rev 16040)
@@ -1436,49 +1436,62 @@
     assertEquals( true, S.isSetSBOTerm() );
     assertTrue( S.getSBOTerm() == 5 );
     assertTrue( !S.getSBOTermID().equals( "SBO:0000005") == false );
+    assertTrue( !S.getSBOTermAsURL().equals( "http://identifiers.org/biomodels.sbo/SBO:0000005") == false );
     i = S.unsetSBOTerm();
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( false, S.isSetSBOTerm() );
+    assertTrue( S.getSBOTermID().equals("") == true );
+    assertTrue( S.getSBOTermAsURL().equals("") == true );
     i = S.setSBOTerm(0);
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( true, S.isSetSBOTerm() );
     assertTrue( S.getSBOTerm() == 0 );
     assertTrue( !S.getSBOTermID().equals( "SBO:0000000") == false );
+    assertTrue( !S.getSBOTermAsURL().equals( "http://identifiers.org/biomodels.sbo/SBO:0000000") == false );
     i = S.setSBOTerm(9999999);
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( true, S.isSetSBOTerm() );
     assertTrue( S.getSBOTerm() == 9999999 );
     assertTrue( !S.getSBOTermID().equals( "SBO:9999999") == false );
+    assertTrue( !S.getSBOTermAsURL().equals( "http://identifiers.org/biomodels.sbo/SBO:9999999") == false );
     i = S.setSBOTerm( "SBO:0000005");
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( true, S.isSetSBOTerm() );
     assertTrue( S.getSBOTerm() == 5 );
     assertTrue( !S.getSBOTermID().equals( "SBO:0000005") == false );
+    assertTrue( !S.getSBOTermAsURL().equals( "http://identifiers.org/biomodels.sbo/SBO:0000005") == false );
     i = S.unsetSBOTerm();
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( false, S.isSetSBOTerm() );
+    assertTrue( S.getSBOTermID().equals("") == true );
+    assertTrue( S.getSBOTermAsURL().equals("") == true );
     i = S.setSBOTerm( "SBO:0000000");
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( true, S.isSetSBOTerm() );
     assertTrue( S.getSBOTerm() == 0 );
     assertTrue( !S.getSBOTermID().equals( "SBO:0000000") == false );
+    assertTrue( !S.getSBOTermAsURL().equals( "http://identifiers.org/biomodels.sbo/SBO:0000000") == false );
     i = S.setSBOTerm( "SBO:9999999");
     assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
     assertEquals( true, S.isSetSBOTerm() );
     assertTrue( S.getSBOTerm() == 9999999 );
     assertTrue( !S.getSBOTermID().equals( "SBO:9999999") == false );
+    assertTrue( !S.getSBOTermAsURL().equals( "http://identifiers.org/biomodels.sbo/SBO:9999999") == false );
     i = S.setSBOTerm(SBML_INT_MAX);
     assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
     assertEquals( false, S.isSetSBOTerm() );
     assertTrue( S.getSBOTermID().equals("") == true );
+    assertTrue( S.getSBOTermAsURL().equals("") == true );
     i = S.setSBOTerm(-1);
     assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
     assertEquals( false, S.isSetSBOTerm() );
     assertTrue( S.getSBOTermID().equals("") == true );
+    assertTrue( S.getSBOTermAsURL().equals("") == true );
     i = S.setSBOTerm(10000000);
     assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE );
     assertEquals( false, S.isSetSBOTerm() );
     assertTrue( S.getSBOTermID().equals("") == true );
+    assertTrue( S.getSBOTermAsURL().equals("") == true );
   }
 
   public void test_SBase_unsetCVTerms()

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py	2012-07-23 09:34:29 UTC (rev 16039)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestSBase_newSetters.py	2012-07-23 10:38:24 UTC (rev 16040)
@@ -1277,49 +1277,62 @@
     self.assertEqual( True, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTerm() == 5 )
     self.assert_( (  "SBO:0000005" != self.S.getSBOTermID() ) == False )
+    self.assert_( (  "http://identifiers.org/biomodels.sbo/SBO:0000005" != self.S.getSBOTermAsURL() ) == False )
     i = self.S.unsetSBOTerm()
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( False, self.S.isSetSBOTerm() )
+    self.assert_( self.S.getSBOTermID() == "" )
+    self.assert_( self.S.getSBOTermAsURL() == "" )
     i = self.S.setSBOTerm(0)
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( True, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTerm() == 0 )
     self.assert_( (  "SBO:0000000" != self.S.getSBOTermID() ) == False )
+    self.assert_( (  "http://identifiers.org/biomodels.sbo/SBO:0000000" != self.S.getSBOTermAsURL() ) == False )
     i = self.S.setSBOTerm(9999999)
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( True, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTerm() == 9999999 )
     self.assert_( (  "SBO:9999999" != self.S.getSBOTermID() ) == False )
+    self.assert_( (  "http://identifiers.org/biomodels.sbo/SBO:9999999" != self.S.getSBOTermAsURL() ) == False )
     i = self.S.setSBOTerm( "SBO:0000005")
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( True, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTerm() == 5 )
     self.assert_( (  "SBO:0000005" != self.S.getSBOTermID() ) == False )
+    self.assert_( (  "http://identifiers.org/biomodels.sbo/SBO:0000005" != self.S.getSBOTermAsURL() ) == False )
     i = self.S.unsetSBOTerm()
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( False, self.S.isSetSBOTerm() )
+    self.assert_( self.S.getSBOTermID() == "" )
+    self.assert_( self.S.getSBOTermAsURL() == "" )
     i = self.S.setSBOTerm( "SBO:0000000")
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( True, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTerm() == 0 )
     self.assert_( (  "SBO:0000000" != self.S.getSBOTermID() ) == False )
+    self.assert_( (  "http://identifiers.org/biomodels.sbo/SBO:0000000" != self.S.getSBOTermAsURL() ) == False )
     i = self.S.setSBOTerm( "SBO:9999999")
     self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
     self.assertEqual( True, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTerm() == 9999999 )
     self.assert_( (  "SBO:9999999" != self.S.getSBOTermID() ) == False )
+    self.assert_( (  "http://identifiers.org/biomodels.sbo/SBO:9999999" != self.S.getSBOTermAsURL() ) == False )
     i = self.S.setSBOTerm(SBML_INT_MAX)
     self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE )
     self.assertEqual( False, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTermID() == "" )
+    self.assert_( self.S.getSBOTermAsURL() == "" )
     i = self.S.setSBOTerm(-1)
     self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE )
     self.assertEqual( False, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTermID() == "" )
+    self.assert_( self.S.getSBOTermAsURL() == "" )
     i = self.S.setSBOTerm(10000000)
     self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE )
     self.assertEqual( False, self.S.isSetSBOTerm() )
     self.assert_( self.S.getSBOTermID() == "" )
+    self.assert_( self.S.getSBOTermAsURL() == "" )
     pass  
 
   def test_SBase_unsetCVTerms(self):

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb	2012-07-23 09:34:29 UTC (rev 16039)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb	2012-07-23 10:38:24 UTC (rev 16040)
@@ -1267,49 +1267,62 @@
     assert_equal true, @@s.isSetSBOTerm()
     assert( @@s.getSBOTerm() == 5 )
     assert( (  "SBO:0000005" != @@s.getSBOTermID() ) == false )
+    assert( (  "http://identifiers.org/biomodels.sbo/SBO:0000005" != @@s.getSBOTermAsURL() ) == false )
     i = @@s.unsetSBOTerm()
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal false, @@s.isSetSBOTerm()
+    assert( @@s.getSBOTermID() == "" )
+    assert( @@s.getSBOTermAsURL() == "" )
     i = @@s.setSBOTerm(0)
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal true, @@s.isSetSBOTerm()
     assert( @@s.getSBOTerm() == 0 )
     assert( (  "SBO:0000000" != @@s.getSBOTermID() ) == false )
+    assert( (  "http://identifiers.org/biomodels.sbo/SBO:0000000" != @@s.getSBOTermAsURL() ) == false )
     i = @@s.setSBOTerm(9999999)
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal true, @@s.isSetSBOTerm()
     assert( @@s.getSBOTerm() == 9999999 )
     assert( (  "SBO:9999999" != @@s.getSBOTermID() ) == false )
+    assert( (  "http://identifiers.org/biomodels.sbo/SBO:9999999" != @@s.getSBOTermAsURL() ) == false )
     i = @@s.setSBOTerm( "SBO:0000005")
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal true, @@s.isSetSBOTerm()
     assert( @@s.getSBOTerm() == 5 )
     assert( (  "SBO:0000005" != @@s.getSBOTermID() ) == false )
+    assert( (  "http://identifiers.org/biomodels.sbo/SBO:0000005" != @@s.getSBOTermAsURL() ) == false )
     i = @@s.unsetSBOTerm()
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal false, @@s.isSetSBOTerm()
+    assert( @@s.getSBOTermID() == "" )
+    assert( @@s.getSBOTermAsURL() == "" )
     i = @@s.setSBOTerm( "SBO:0000000")
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal true, @@s.isSetSBOTerm()
     assert( @@s.getSBOTerm() == 0 )
     assert( (  "SBO:0000000" != @@s.getSBOTermID() ) == false )
+    assert( (  "http://identifiers.org/biomodels.sbo/SBO:0000000" != @@s.getSBOTermAsURL() ) == false )
     i = @@s.setSBOTerm( "SBO:9999999")
     assert( i == LibSBML::LIBSBML_OPERATION_SUCCESS )
     assert_equal true, @@s.isSetSBOTerm()
     assert( @@s.getSBOTerm() == 9999999 )
     assert( (  "SBO:9999999" != @@s.getSBOTermID() ) == false )
+    assert( (  "http://identifiers.org/biomodels.sbo/SBO:9999999" != @@s.getSBOTermAsURL() ) == false )
     i = @@s.setSBOTerm(@@SBML_INT_MAX)
     assert( i == LibSBML::LIBSBML_INVALID_ATTRIBUTE_VALUE )
     assert_equal false, @@s.isSetSBOTerm()
     assert( @@s.getSBOTermID() == "" )
+    assert( @@s.getSBOTermAsURL() == "" )
     i = @@s.setSBOTerm(-1)
     assert( i == LibSBML::LIBSBML_INVALID_ATTRIBUTE_VALUE )
     assert_equal false, @@s.isSetSBOTerm()
     assert( @@s.getSBOTermID() == "" )
+    assert( @@s.getSBOTermAsURL() == "" )
     i = @@s.setSBOTerm(10000000)
     assert( i == LibSBML::LIBSBML_INVALID_ATTRIBUTE_VALUE )
     assert_equal false, @@s.isSetSBOTerm()
     assert( @@s.getSBOTermID() == "" )
+    assert( @@s.getSBOTermAsURL() == "" )
   end
   
   def test_SBase_unsetCVTerms

Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp	2012-07-23 09:34:29 UTC (rev 16039)
+++ trunk/libsbml/src/sbml/SBase.cpp	2012-07-23 10:38:24 UTC (rev 16040)
@@ -900,6 +900,27 @@
 
 
 /*
+ * @return the sboTerm as a identoifoers.org url.  If not set,
+ * return an empty string.
+ */
+std::string
+SBase::getSBOTermAsURL () const
+{
+  std::string result = "";
+
+  if ( SBO::checkTerm(mSBOTerm) )
+  {
+    ostringstream stream;
+    stream << "http://identifiers.org/biomodels.sbo/SBO:";
+    stream << setw(7) << setfill('0') << mSBOTerm;
+    result = stream.str();
+  }
+
+  return result;
+}
+
+
+/*
  * @return the line number of this SBML object.
  */
 unsigned int
@@ -6197,6 +6218,22 @@
 
 
 /**
+ * Returns the identifiers.org URL  representation of the "sboTerm" attribute of
+ * this object.
+ *
+ * @return the value of the "sboTerm" attribute as a string of the form
+ * http://identifiers.org/biomodels.sbo/SBO:NNNNNNN, or @c NULL if the value is not set.
+ */
+LIBSBML_EXTERN
+char*
+SBase_getSBOTermAsURL (const SBase_t *sb)
+{
+  return (sb != NULL && sb->isSetSBOTerm())? 
+    safe_strdup(sb->getSBOTermAsURL().c_str()) : NULL;
+}
+
+
+/**
  * Returns the SBML Level of the overall SBML document.
  *
  * @param sb the SBase_t structure to query

Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h	2012-07-23 09:34:29 UTC (rev 16039)
+++ trunk/libsbml/src/sbml/SBase.h	2012-07-23 10:38:24 UTC (rev 16040)
@@ -932,6 +932,28 @@
 
 
   /**
+   * Returns the identifiers.org URL representation of the "sboTerm" attribute of
+   * this object.
+   *
+   * This method returns the entire SBO
+   * identifier as a text string in the form 
+   * "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN".
+   *
+   * SBO terms are a type of optional annotation, and each different class
+   * of SBML object derived from SBase imposes its own requirements about
+   * the values permitted for "sboTerm".  Please consult the SBML
+   * Level&nbsp;2 Version&nbsp;4 specification for more information about
+   * the use of SBO and the "sboTerm" attribute.
+   *
+   * @return the value of the "sboTerm" attribute as an identifiers.org URL
+   * (its value will be of the form 
+   * "http://identifiers.org/biomodels.sbo/SBO:NNNNNNN"), or an empty string if
+   * the value is not set.
+   */
+  std::string getSBOTermAsURL () const;
+
+
+  /**
    * Returns the line number on which this object first appears in the XML
    * representation of the SBML document.
    * 
@@ -3507,6 +3529,11 @@
 
 
 LIBSBML_EXTERN
+char*
+SBase_getSBOTermAsURL (const SBase_t *sb);
+
+
+LIBSBML_EXTERN
 unsigned int
 SBase_getLine (const SBase_t *sb);
 

Modified: trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp	2012-07-23 09:34:29 UTC (rev 16039)
+++ trunk/libsbml/src/sbml/test/TestSBase_newSetters.cpp	2012-07-23 10:38:24 UTC (rev 16040)
@@ -1978,11 +1978,16 @@
   fail_unless( SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTerm(S) == 5 );
   fail_unless( strcmp(SBase_getSBOTermID(S), "SBO:0000005") == 0);
+  fail_unless( strcmp(SBase_getSBOTermAsURL(S), 
+               "http://identifiers.org/biomodels.sbo/SBO:0000005") == 0);
 
   i = SBase_unsetSBOTerm(S);
 
   fail_unless( i == LIBSBML_OPERATION_SUCCESS );
   fail_unless( !SBase_isSetSBOTerm(S) );
+  fail_unless( SBase_getSBOTerm(S) == -1 );
+  fail_unless( SBase_getSBOTermID(S) == NULL);
+  fail_unless( SBase_getSBOTermAsURL(S) == NULL);
 
   i = SBase_setSBOTerm(S, 0);
 
@@ -1990,6 +1995,8 @@
   fail_unless( SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTerm(S) == 0 );
   fail_unless( strcmp(SBase_getSBOTermID(S), "SBO:0000000") == 0);
+  fail_unless( strcmp(SBase_getSBOTermAsURL(S), 
+               "http://identifiers.org/biomodels.sbo/SBO:0000000") == 0);
 
   i = SBase_setSBOTerm(S, 9999999);
 
@@ -1997,6 +2004,8 @@
   fail_unless( SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTerm(S) == 9999999 );
   fail_unless( strcmp(SBase_getSBOTermID(S), "SBO:9999999") == 0);
+  fail_unless( strcmp(SBase_getSBOTermAsURL(S), 
+               "http://identifiers.org/biomodels.sbo/SBO:9999999") == 0);
 
   /* set an SBOTerm by ID */
 
@@ -2006,11 +2015,15 @@
   fail_unless( SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTerm(S) == 5 );
   fail_unless( strcmp(SBase_getSBOTermID(S), "SBO:0000005") == 0);
+  fail_unless( strcmp(SBase_getSBOTermAsURL(S), 
+               "http://identifiers.org/biomodels.sbo/SBO:0000005") == 0);
 
   i = SBase_unsetSBOTerm(S);
 
   fail_unless( i == LIBSBML_OPERATION_SUCCESS );
   fail_unless( !SBase_isSetSBOTerm(S) );
+  fail_unless( SBase_getSBOTermID(S) == NULL);
+  fail_unless( SBase_getSBOTermAsURL(S) == NULL);
 
   i = SBase_setSBOTermID(S, "SBO:0000000");
 
@@ -2018,6 +2031,8 @@
   fail_unless( SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTerm(S) == 0 );
   fail_unless( strcmp(SBase_getSBOTermID(S), "SBO:0000000") == 0);
+  fail_unless( strcmp(SBase_getSBOTermAsURL(S), 
+               "http://identifiers.org/biomodels.sbo/SBO:0000000") == 0);
 
   i = SBase_setSBOTermID(S, "SBO:9999999");
 
@@ -2025,6 +2040,8 @@
   fail_unless( SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTerm(S) == 9999999 );
   fail_unless( strcmp(SBase_getSBOTermID(S), "SBO:9999999") == 0);
+  fail_unless( strcmp(SBase_getSBOTermAsURL(S), 
+               "http://identifiers.org/biomodels.sbo/SBO:9999999") == 0);
 
   /* check invalid attribute value */
 
@@ -2033,18 +2050,21 @@
   fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
   fail_unless( !SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTermID(S) == NULL);
+  fail_unless( SBase_getSBOTermAsURL(S) == NULL);
 
   i = SBase_setSBOTerm(S, -1);
 
   fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
   fail_unless( !SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTermID(S) == NULL);
+  fail_unless( SBase_getSBOTermAsURL(S) == NULL);
 
   i = SBase_setSBOTerm(S, 10000000);
 
   fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
   fail_unless( !SBase_isSetSBOTerm(S) );
   fail_unless( SBase_getSBOTermID(S) == NULL);
+  fail_unless( SBase_getSBOTermAsURL(S) == NULL);
 
 }
 END_TEST

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 16467
          http://sbml.svn.sourceforge.net/sbml/?rev=16467&view=rev
Author:   sarahkeating
Date:     2012-11-25 11:17:24 +0000 (Sun, 25 Nov 2012)
Log Message:
-----------
added the ability to set notes from a string without it being enclosed in xhtml markup

This is done by having an optional boolean flag on the setNotes(string, bool) function. Th edefault is false which means existing code is unaffected. If true the code will take the text string and wrap it in the <p> xhtml tag.

Modified Paths:
--------------
    trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase.cs
    trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase.java
    trunk/libsbml/src/bindings/python/test/sbml/TestSBase.py
    trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase.rb
    trunk/libsbml/src/sbml/SBase.cpp
    trunk/libsbml/src/sbml/SBase.h
    trunk/libsbml/src/sbml/test/TestSBase.cpp

Modified: trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase.cs	2012-11-23 15:59:26 UTC (rev 16466)
+++ trunk/libsbml/src/bindings/csharp/test/sbml/TestSBase.cs	2012-11-25 11:17:24 UTC (rev 16467)
@@ -1267,9 +1267,60 @@
 			assertTrue (t1.getNumChildren () == 1);
 			t2 = t1.getChild (0);
 			assertTrue (("This is a test note" == t2.getCharacters ()));
-		}
-
-		public void test_SBase_unsetAnnotationWithCVTerms ()
+		}
+
+    public void test_SBase_setNotesString_l3()
+    {
+      SBase c = new Model(3, 1);
+      string notes = "This is a test note";
+      string taggednotes = "<notes>\n" + "  <p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note</p>\n" + "</notes>";
+      c.setNotes(notes);
+      assertTrue(c.isSetNotes() == false);
+    }
+
+    public void test_SBase_setNotesString_l3_addMarkup()
+    {
+      SBase c = new Model(3, 1);
+      string notes = "This is a test note";
+      string taggednotes = "<notes>\n" + "  <p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note</p>\n" + "</notes>";
+      c.setNotes(notes, true);
+      assertTrue(c.isSetNotes() == true);
+      if ((taggednotes != c.getNotesString()))
+        ;
+      {
+      }
+      XMLNode t1 = c.getNotes();
+      assertTrue(t1.getNumChildren() == 1);
+      XMLNode t2 = t1.getChild(0);
+      assertTrue(t2.getNumChildren() == 1);
+      XMLNode t3 = t2.getChild(0);
+      assertTrue(("This is a test note" == t3.getCharacters()));
+      c.setNotes(c.getNotesString(), true);
+      t1 = c.getNotes();
+      assertTrue(t1.getNumChildren() == 1);
+      string chars = c.getNotesString();
+      assertTrue((taggednotes == chars));
+      c.setNotes("", true);
+      assertTrue(c.isSetNotes() == false);
+      if (c.getNotesString() != null)
+        ;
+      {
+      }
+      c.setNotes(taggednotes, true);
+      assertTrue(c.isSetNotes() == true);
+      if ((taggednotes != c.getNotesString()))
+        ;
+      {
+      }
+      t1 = c.getNotes();
+      assertTrue(t1.getNumChildren() == 1);
+      t2 = t1.getChild(0);
+      assertTrue(t2.getNumChildren() == 1);
+      t3 = t2.getChild(0);
+      assertTrue(("This is a test note" == t3.getCharacters()));
+    }
+
+    public void test_SBase_unsetAnnotationWithCVTerms()
 		{
 			CVTerm cv;
 			string annt = "<annotation>\n" + "  <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" + "</annotation>";

Modified: trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase.java
===================================================================
--- trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase.java	2012-11-23 15:59:26 UTC (rev 16466)
+++ trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase.java	2012-11-25 11:17:24 UTC (rev 16467)
@@ -1383,6 +1383,53 @@
     assertTrue(t2.getCharacters().equals( "This is a test note"));
   }
 
+  public void test_SBase_setNotesString_l3()
+  {
+    SBase c = new Model(3,1);
+    String notes =  "This is a test note";
+    String taggednotes = "<notes>\n" + "  <p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note</p>\n" + "</notes>";
+    c.setNotes(notes);
+    assertTrue( c.isSetNotes() == false );
+  }
+
+  public void test_SBase_setNotesString_l3_addMarkup()
+  {
+    SBase c = new Model(3,1);
+    String notes =  "This is a test note";
+    String taggednotes = "<notes>\n" + "  <p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note</p>\n" + "</notes>";
+    c.setNotes(notes, true);
+    assertTrue( c.isSetNotes() == true );
+    if (!c.getNotesString().equals(taggednotes));
+    {
+    }
+    XMLNode t1 = c.getNotes();
+    assertTrue( t1.getNumChildren() == 1 );
+    XMLNode t2 = t1.getChild(0);
+    assertTrue( t2.getNumChildren() == 1 );
+    XMLNode t3 = t2.getChild(0);
+    assertTrue(t3.getCharacters().equals( "This is a test note"));
+    c.setNotes(c.getNotesString());
+    t1 = c.getNotes();
+    assertTrue( t1.getNumChildren() == 1 );
+    String chars = c.getNotesString();
+    assertTrue(chars.equals(taggednotes));
+    c.setNotes("", true);
+    assertTrue( c.isSetNotes() == false );
+    if (c.getNotesString() != null);
+    {
+    }
+    c.setNotes(taggednotes, true);
+    assertTrue( c.isSetNotes() == true );
+    if (!c.getNotesString().equals(taggednotes));
+    {
+    }
+    t1 = c.getNotes();
+    assertTrue( t1.getNumChildren() == 1 );
+    t2 = t1.getChild(0);
+    assertTrue( t2.getNumChildren() == 1 );
+    t3 = t2.getChild(0);
+    assertTrue(t3.getCharacters().equals( "This is a test note"));
+  }
   public void test_SBase_unsetAnnotationWithCVTerms()
   {
     CVTerm cv;

Modified: trunk/libsbml/src/bindings/python/test/sbml/TestSBase.py
===================================================================
--- trunk/libsbml/src/bindings/python/test/sbml/TestSBase.py	2012-11-23 15:59:26 UTC (rev 16466)
+++ trunk/libsbml/src/bindings/python/test/sbml/TestSBase.py	2012-11-25 11:17:24 UTC (rev 16467)
@@ -1025,13 +1025,13 @@
 
   def test_SBase_appendNotesString8(self):
     notes = wrapString("<body xmlns=\"http://www.w3.org/1999/xhtml\">\n" + "  <p>This is a test note </p>\n" + "</body>")
-    taggednewnotes = wrapString("<notes>\n" + 
+    taggednewnotes =  ("<notes>\n" + 
     "  <body xmlns=\"http://www.w3.org/1999/xhtml\">\n" + 
     "    <p>This is a test note </p>\n" + 
     "    <p xmlns=\"http://www.w3.org/1999/xhtml\">This is more test notes </p>\n" + 
     "  </body>\n" + 
     "</notes>")
-    taggednewnotes2 = wrapString("<notes>\n" + 
+    taggednewnotes2 =  ("<notes>\n" + 
     "  <body xmlns=\"http://www.w3.org/1999/xhtml\">\n" + 
     "    <p>This is a test note </p>\n" + 
     "    <p xmlns=\"http://www.w3.org/1999/xhtml\">This is more test notes 1</p>\n" + 
@@ -1242,6 +1242,51 @@
     self.assert_((  "This is a test note" == t2.getCharacters() ))
     pass  
 
+  def test_SBase_setNotesString_l3(self):
+    c = libsbml.Model(3,1)
+    notes =  "This is a test note";
+    c.setNotes(notes)
+    self.assert_( c.isSetNotes() == False )
+    pass  
+
+  def test_SBase_setNotesString_l3_addMarkup(self):
+    c = libsbml.Model(3,1)
+    notes =  "This is a test note";
+    taggednotes = wrapString("<notes>\n" + "  <p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note</p>\n" + 
+    "</notes>")
+    c.setNotes(notes, True)
+    self.assert_( c.isSetNotes() == True )
+    if (( taggednotes != c.getNotesString() )):
+      pass    
+    t1 = c.getNotes()
+    self.assert_( t1.getNumChildren() == 1 )
+    t2 = t1.getChild(0)
+    self.assert_( t2.getNumChildren() == 1 )
+    t3 = t2.getChild(0)
+    self.assert_((  "This is a test note" == t3.getCharacters() ))
+    c.setNotes(c.getNotesString(), True)
+    t1 = c.getNotes()
+    self.assert_( t1.getNumChildren() == 1 )
+    chars = c.getNotesString()
+    print chars
+    print taggednotes
+    self.assert_(( taggednotes == chars ))
+    c.setNotes("", True)
+    self.assert_( c.isSetNotes() == False )
+    if (c.getNotesString() != None):
+      pass    
+    c.setNotes(taggednotes, True)
+    self.assert_( c.isSetNotes() == True )
+    if (( taggednotes != c.getNotesString() )):
+      pass    
+    t1 = c.getNotes()
+    self.assert_( t1.getNumChildren() == 1 )
+    t2 = t1.getChild(0)
+    self.assert_( t2.getNumChildren() == 1 )
+    t3 = t2.getChild(0)
+    self.assert_((  "This is a test note" == t3.getCharacters() ))
+    pass  
+
   def test_SBase_unsetAnnotationWithCVTerms(self):
     annt = wrapString("<annotation>\n" + 
     "  <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" + 

Modified: trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase.rb
===================================================================
--- trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase.rb	2012-11-23 15:59:26 UTC (rev 16466)
+++ trunk/libsbml/src/bindings/ruby/test/sbml/TestSBase.rb	2012-11-25 11:17:24 UTC (rev 16467)
@@ -1232,6 +1232,51 @@
     assert ((  "This is a test note" == t2.getCharacters() ))
   end
 
+  def test_SBase_setNotesString_l3
+    c = LibSBML::Model.new(3,1)
+    notes =  "This is a test note";
+    c.setNotes(notes)
+    assert( c.isSetNotes() == false )
+  end
+
+  def test_SBase_setNotesString_l3_addMarkup
+    c = LibSBML::Model.new(3,1)
+    notes =  "This is a test note";
+    taggednotes = "<notes>\n" + 
+    "  <p xmlns=\"http://www.w3.org/1999/xhtml\">" + 
+    "This is a test note</p>\n" + 
+    "</notes>"
+    c.setNotes(notes, true)
+    assert( c.isSetNotes() == true )
+    if (( taggednotes != c.getNotesString() ))
+    end
+    t1 = c.getNotes()
+    assert( t1.getNumChildren() == 1 )
+    t2 = t1.getChild(0)
+    assert( t2.getNumChildren() == 1 )
+    t3 = t2.getChild(0)
+    assert ((  "This is a test note" == t3.getCharacters() ))
+    c.setNotes(c.getNotesString(), true)
+    t1 = c.getNotes()
+    assert( t1.getNumChildren() == 1 )
+    chars = c.getNotesString()
+    assert (( taggednotes == chars ))
+    c.setNotes("", true)
+    assert( c.isSetNotes() == false )
+    if (c.getNotesString() != nil)
+    end
+    c.setNotes(taggednotes, true)
+    assert( c.isSetNotes() == true )
+    if (( taggednotes != c.getNotesString() ))
+    end
+    t1 = c.getNotes()
+    assert( t1.getNumChildren() == 1 )
+    t2 = t1.getChild(0)
+    assert( t2.getNumChildren() == 1 )
+    t3 = t2.getChild(0)
+    assert ((  "This is a test note" == t3.getCharacters() ))
+  end
+
   def test_SBase_unsetAnnotationWithCVTerms
     annt = "<annotation>\n" + 
     "  <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" + 

Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp	2012-11-23 15:59:26 UTC (rev 16466)
+++ trunk/libsbml/src/sbml/SBase.cpp	2012-11-25 11:17:24 UTC (rev 16467)
@@ -1622,7 +1622,7 @@
  * Sets the notes (by std::string) of this SBML object to a copy of notes.
  */
 int
-SBase::setNotes(const std::string& notes)
+SBase::setNotes(const std::string& notes, bool addXHTMLMarkup)
 {
   int success = LIBSBML_OPERATION_FAILED;
   if (&(notes) == NULL)
@@ -1650,7 +1650,46 @@
 
     if(notes_xmln != NULL)
     {
-      success = setNotes(notes_xmln);
+      if (addXHTMLMarkup == true)
+      {
+        // user has specified that they want the markup added
+        if (getLevel() > 2 
+          || (getLevel() == 2 && getVersion() > 1))
+        {
+          // just say the user passed a string that did not represent xhtml
+          // the xmlnode will not get set as it is invalid
+          if (notes_xmln->getNumChildren() == 0 
+            && notes_xmln->isStart() == false
+            && notes_xmln->isEnd() == false 
+            && notes_xmln->isText() == true)
+          {
+            //create a parent node of xhtml type p
+            XMLAttributes blank_att = XMLAttributes();
+            XMLTriple triple = XMLTriple("p", "http://www.w3.org/1999/xhtml", "");
+            XMLNamespaces xmlns = XMLNamespaces();
+            xmlns.add("http://www.w3.org/1999/xhtml", "");
+            XMLNode *xmlnode = new XMLNode(XMLToken(triple, blank_att, xmlns));
+
+            // create a text node from the text given
+            xmlnode->addChild(*notes_xmln);
+            success = setNotes(xmlnode);
+            delete xmlnode;
+          }
+          else
+          {
+            success = setNotes(notes_xmln);
+          }
+          
+        }
+        else
+        {
+          success = setNotes(notes_xmln);
+        }
+      }
+      else
+      {
+        success = setNotes(notes_xmln);
+      }
       delete notes_xmln;
     }
   }
@@ -6865,6 +6904,40 @@
 
 
 /**
+ * Sets the notes for the given SBML object.
+ *
+ * @param sb the given SBML object.
+ * @param notes the string (const char*) respresenting the notes.
+ *
+ * @return integer value indicating success/failure of the
+ * function.  @if clike The value is drawn from the
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
+ * returned by this function are:
+ * @li LIBSBML_OPERATION_SUCCESS
+ * @li LIBSBML_INVALID_OBJECT
+ * @li LIBSBML_OPERATION_FAILED
+ */
+LIBSBML_EXTERN
+int
+SBase_setNotesStringAddMarkup (SBase_t *sb, char *notes)
+{
+  if (sb != NULL)
+  {
+    if(notes == NULL)
+    {
+      return sb->unsetNotes();
+    }
+    else
+    {
+      return sb->setNotes(notes, true);
+    }
+  }
+  else
+    return LIBSBML_INVALID_OBJECT;
+}
+
+
+/**
  * Appends the notes for the given SBML object.
  *
  * @param sb the given SBML object.

Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h	2012-11-23 15:59:26 UTC (rev 16466)
+++ trunk/libsbml/src/sbml/SBase.h	2012-11-25 11:17:24 UTC (rev 16467)
@@ -1910,7 +1910,7 @@
    * @see unsetNotes()
    * @see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@...)
    */
-  int setNotes(const std::string& notes);
+  int setNotes(const std::string& notes, bool addXHTMLMarkup = false);
 
 
   /**
@@ -3810,6 +3810,11 @@
 
 LIBSBML_EXTERN
 int
+SBase_setNotesStringAddMarkup (SBase_t *sb, char *notes);
+
+
+LIBSBML_EXTERN
+int
 SBase_appendNotes (SBase_t *sb, XMLNode_t *notes);
 
 

Modified: trunk/libsbml/src/sbml/test/TestSBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestSBase.cpp	2012-11-23 15:59:26 UTC (rev 16466)
+++ trunk/libsbml/src/sbml/test/TestSBase.cpp	2012-11-25 11:17:24 UTC (rev 16467)
@@ -398,7 +398,7 @@
 
 START_TEST (test_SBase_setNotesString)
 {
-  SBase_t *c = new(std::nothrow) Model(1, 2);
+  SBase_t *c = new(std::nothrow) Model(1,2);
   char * notes = "This is a test note";
   char * taggednotes = "<notes>This is a test note</notes>";
 
@@ -450,6 +450,66 @@
 END_TEST
 
 
+START_TEST (test_SBase_setNotesString_l3)
+{
+  SBase_t *c = new(std::nothrow) Model(3, 1);
+  char * notes = "This is a test note";
+  char * taggednotes = "<notes>\n  <p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note</p>\n</notes>";
+
+  // this should not set the notes since they are invalid xhtml
+  SBase_setNotesString(c, notes);
+
+  fail_unless(SBase_isSetNotes(c) == 0);
+
+}
+END_TEST
+
+
+START_TEST (test_SBase_setNotesString_l3_addMarkup)
+{
+  SBase_t *c = new(std::nothrow) Model(3, 1);
+  char * notes = "This is a test note";
+  char * taggednotes = "<notes>\n  <p xmlns=\"http://www.w3.org/1999/xhtml\">This is a test note</p>\n</notes>";
+
+  SBase_setNotesStringAddMarkup(c, notes);
+
+  fail_unless(SBase_isSetNotes(c) == 1);
+
+  if (strcmp(SBase_getNotesString(c), taggednotes))
+  {
+    fail("SBase_setNotesString(...) did not make a copy of node.");
+  }
+  XMLNode_t *t1 = SBase_getNotes(c);
+  fail_unless(XMLNode_getNumChildren(t1) == 1);
+
+  const XMLNode_t *t2 = XMLNode_getChild(t1,0);
+  fail_unless(XMLNode_getNumChildren(t2) == 1);
+
+  const XMLNode_t *t3 = XMLNode_getChild(t2,0);
+  fail_unless(!strcmp(XMLNode_getCharacters(t3), "This is a test note"));
+
+
+  SBase_setNotesStringAddMarkup(c, taggednotes);
+
+  fail_unless(SBase_isSetNotes(c) == 1);
+
+  if (strcmp(SBase_getNotesString(c), taggednotes))
+  {
+    fail("SBase_setNotesString(...) did not make a copy of node.");
+  }
+  t1 = SBase_getNotes(c);
+  fail_unless(XMLNode_getNumChildren(t1) == 1);
+
+  t2 = XMLNode_getChild(t1,0);
+  fail_unless(XMLNode_getNumChildren(t2) == 1);
+
+  t3 = XMLNode_getChild(t2,0);
+  fail_unless(!strcmp(XMLNode_getCharacters(t3), "This is a test note"));
+
+}
+END_TEST
+
+
 START_TEST (test_SBase_setAnnotationString)
 {
   char * annotation = "This is a test note";
@@ -2402,6 +2462,8 @@
   tcase_add_test(tcase, test_SBase_setAnnotation );
   tcase_add_test(tcase, test_SBase_setNotes);
   tcase_add_test(tcase, test_SBase_setNotesString);
+  tcase_add_test(tcase, test_SBase_setNotesString_l3);
+  tcase_add_test(tcase, test_SBase_setNotesString_l3_addMarkup);
   tcase_add_test(tcase, test_SBase_setAnnotationString);
   tcase_add_test(tcase, test_SBase_unsetAnnotationWithCVTerms );
   tcase_add_test(tcase, test_SBase_unsetAnnotationWithModelHistory );

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 16981
          http://sbml.svn.sourceforge.net/sbml/?rev=16981&view=rev
Author:   luciansmith
Date:     2013-01-29 08:17:51 +0000 (Tue, 29 Jan 2013)
Log Message:
-----------
A few .cpp and .h files that didn't have svn:eol-style set before, now have it set.  Some odd omissions in there, but anyway.

Modified Paths:
--------------
    trunk/libsbml/src/bindings/r/local.cpp
    trunk/libsbml/src/sbml/AlgebraicRule.cpp
    trunk/libsbml/src/sbml/AlgebraicRule.h
    trunk/libsbml/src/sbml/AssignmentRule.cpp
    trunk/libsbml/src/sbml/AssignmentRule.h
    trunk/libsbml/src/sbml/ExpectedAttributes.cpp
    trunk/libsbml/src/sbml/ModifierSpeciesReference.cpp
    trunk/libsbml/src/sbml/ModifierSpeciesReference.h
    trunk/libsbml/src/sbml/RateRule.cpp
    trunk/libsbml/src/sbml/RateRule.h
    trunk/libsbml/src/sbml/SBMLConstructorException.cpp
    trunk/libsbml/src/sbml/SimpleSpeciesReference.cpp
    trunk/libsbml/src/sbml/SimpleSpeciesReference.h
    trunk/libsbml/src/sbml/annotation/Date.h
    trunk/libsbml/src/sbml/annotation/ModelCreator.h
    trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.h
    trunk/libsbml/src/sbml/annotation/test/TestRDFAnnotationMetaid.cpp
    trunk/libsbml/src/sbml/annotation/test/TestSyncAnnotation.cpp
    trunk/libsbml/src/sbml/conversion/SBMLRuleConverter.cpp
    trunk/libsbml/src/sbml/conversion/SBMLRuleConverter.h
    trunk/libsbml/src/sbml/conversion/SBMLUnitsConverter.cpp
    trunk/libsbml/src/sbml/conversion/SBMLUnitsConverter.h
    trunk/libsbml/src/sbml/conversion/test/TestSBMLRuleConverter.cpp
    trunk/libsbml/src/sbml/conversion/test/TestUnitsConverter.cpp
    trunk/libsbml/src/sbml/conversion/test/TestUnitsConverter2.cpp
    trunk/libsbml/src/sbml/conversion/test/TestUnitsConverterL2.cpp
    trunk/libsbml/src/sbml/extension/ISBMLExtensionNamespaces.cpp
    trunk/libsbml/src/sbml/extension/SBMLDocumentPluginNotRequired.cpp
    trunk/libsbml/src/sbml/extension/SBMLDocumentPluginNotRequired.h
    trunk/libsbml/src/sbml/math/L3ParserSettings.cpp
    trunk/libsbml/src/sbml/math/L3ParserSettings.h
    trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
    trunk/libsbml/src/sbml/math/test/TestWriteMathMLFromAST.cpp
    trunk/libsbml/src/sbml/test/TestRemoveFromParent.cpp
    trunk/libsbml/src/sbml/test/TestRenameIDs.cpp
    trunk/libsbml/src/sbml/test/TestSBMLValidators.cpp
    trunk/libsbml/src/sbml/validator/SBMLExternalValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLExternalValidator.h
    trunk/libsbml/src/sbml/validator/SBMLInternalValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLInternalValidator.h
    trunk/libsbml/src/sbml/validator/SBMLValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLValidator.h
    trunk/libsbml/src/sbml/xml/XMLConstructorException.cpp
    trunk/libsbml/src/sbml/xml/XMLConstructorException.h

Property Changed:
----------------
    trunk/libsbml/src/bindings/r/local-downcast-extension-layout.cpp
    trunk/libsbml/src/bindings/r/local-downcast-namespaces-layout.cpp
    trunk/libsbml/src/bindings/r/local-downcast-packages-layout.cpp
    trunk/libsbml/src/bindings/r/local-downcast-plugins-layout.cpp
    trunk/libsbml/src/bindings/r/local.cpp
    trunk/libsbml/src/sbml/AlgebraicRule.cpp
    trunk/libsbml/src/sbml/AlgebraicRule.h
    trunk/libsbml/src/sbml/AssignmentRule.cpp
    trunk/libsbml/src/sbml/AssignmentRule.h
    trunk/libsbml/src/sbml/ExpectedAttributes.cpp
    trunk/libsbml/src/sbml/ModifierSpeciesReference.cpp
    trunk/libsbml/src/sbml/ModifierSpeciesReference.h
    trunk/libsbml/src/sbml/RateRule.cpp
    trunk/libsbml/src/sbml/RateRule.h
    trunk/libsbml/src/sbml/SBMLConstructorException.cpp
    trunk/libsbml/src/sbml/SimpleSpeciesReference.cpp
    trunk/libsbml/src/sbml/SimpleSpeciesReference.h
    trunk/libsbml/src/sbml/annotation/Date.cpp
    trunk/libsbml/src/sbml/annotation/Date.h
    trunk/libsbml/src/sbml/annotation/ModelCreator.cpp
    trunk/libsbml/src/sbml/annotation/ModelCreator.h
    trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.cpp
    trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.h
    trunk/libsbml/src/sbml/annotation/test/TestRDFAnnotationMetaid.cpp
    trunk/libsbml/src/sbml/annotation/test/TestSyncAnnotation.cpp
    trunk/libsbml/src/sbml/conversion/SBMLRuleConverter.cpp
    trunk/libsbml/src/sbml/conversion/SBMLRuleConverter.h
    trunk/libsbml/src/sbml/conversion/SBMLUnitsConverter.cpp
    trunk/libsbml/src/sbml/conversion/SBMLUnitsConverter.h
    trunk/libsbml/src/sbml/conversion/test/TestSBMLRuleConverter.cpp
    trunk/libsbml/src/sbml/conversion/test/TestUnitsConverter.cpp
    trunk/libsbml/src/sbml/conversion/test/TestUnitsConverter2.cpp
    trunk/libsbml/src/sbml/conversion/test/TestUnitsConverterL2.cpp
    trunk/libsbml/src/sbml/extension/ISBMLExtensionNamespaces.cpp
    trunk/libsbml/src/sbml/extension/SBMLDocumentPluginNotRequired.cpp
    trunk/libsbml/src/sbml/extension/SBMLDocumentPluginNotRequired.h
    trunk/libsbml/src/sbml/math/L3ParserSettings.cpp
    trunk/libsbml/src/sbml/math/L3ParserSettings.h
    trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
    trunk/libsbml/src/sbml/math/test/TestWriteMathMLFromAST.cpp
    trunk/libsbml/src/sbml/packages/layout/sbml/GeneralGlyph.cpp
    trunk/libsbml/src/sbml/packages/layout/sbml/GeneralGlyph.h
    trunk/libsbml/src/sbml/packages/layout/sbml/ReferenceGlyph.cpp
    trunk/libsbml/src/sbml/packages/layout/sbml/ReferenceGlyph.h
    trunk/libsbml/src/sbml/packages/layout/sbml/test/TestGeneralGlyph.cpp
    trunk/libsbml/src/sbml/packages/layout/sbml/test/TestReferenceGlyph.cpp
    trunk/libsbml/src/sbml/packages/layout-register.h
    trunk/libsbml/src/sbml/test/TestRemoveFromParent.cpp
    trunk/libsbml/src/sbml/test/TestRenameIDs.cpp
    trunk/libsbml/src/sbml/test/TestSBMLValidators.cpp
    trunk/libsbml/src/sbml/validator/SBMLExternalValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLExternalValidator.h
    trunk/libsbml/src/sbml/validator/SBMLInternalValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLInternalValidator.h
    trunk/libsbml/src/sbml/validator/SBMLValidator.cpp
    trunk/libsbml/src/sbml/validator/SBMLValidator.h
    trunk/libsbml/src/sbml/xml/XMLConstructorException.cpp
    trunk/libsbml/src/sbml/xml/XMLConstructorException.h


Property changes on: trunk/libsbml/src/bindings/r/local-downcast-extension-layout.cpp
___________________________________________________________________
Added: svn:eol-style
   + native


Property changes on: trunk/libsbml/src/bindings/r/local-downcast-namespaces-layout.cpp
___________________________________________________________________
Added: svn:eol-style
   + native


Property changes on: trunk/libsbml/src/bindings/r/local-downcast-packages-layout.cpp
___________________________________________________________________
Added: svn:eol-style
   + native


Property changes on: trunk/libsbml/src/bindings/r/local-downcast-plugins-layout.cpp
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/bindings/r/local.cpp
===================================================================
--- trunk/libsbml/src/bindings/r/local.cpp	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/bindings/r/local.cpp	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,268 +1,268 @@
-/**
- * @file    local.cpp
- * @brief   Python-specific SWIG support code for wrapping libSBML API
- * @author  Ben Bornstein
- * @author  Ben Kovitz
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ---------------------------------------------------------------------- -->*/
-
-#include "sbml/SBase.h"
-#include <sstream>
-#include <R.h>
-using namespace std;
-/**
- * @return the most specific Swig type for the given SBMLExtension object.
- */
-struct swig_type_info*
-GetDowncastSwigType (SBMLExtension* se)
-{
-  if (se == 0) return SWIGTYPE_p_SBMLExtension;
-		
-  const std::string pkgName = se->getName();
-
-#include "local-downcast-extension.cpp"
-
-  return SWIGTYPE_p_SBMLExtension;
-}
-
-/**
- * @return the most specific Swig type for the given SBMLNamespaces object.
- */
-struct swig_type_info*
-GetDowncastSwigType (SBMLNamespaces* se)
-{
-	if (se == 0) return SWIGTYPE_p_SBMLNamespaces;
-	
-	const std::string pkgName = se->getPackageName();
-	
-#include "local-downcast-namespaces.cpp"
-	
-	return SWIGTYPE_p_SBMLNamespaces;
-}
-
-
-/**
- * @return the most specific Swig type for the given SBasePlugin object.
- */
-struct swig_type_info*
-GetDowncastSwigType (SBasePlugin* sbp)
-{
-  if (sbp == 0) return SWIGTYPE_p_SBasePlugin;
-
-  const std::string pkgName = sbp->getPackageName();
-  SBase* sb = sbp->getParentSBMLObject();
-  if (!sb) return SWIGTYPE_p_SBasePlugin;
-
-#include "local-downcast-plugins.cpp"
-	
-  return SWIGTYPE_p_SBasePlugin;
-}
-
-struct swig_type_info*
-GetDowncastSwigTypeForPackage (SBase* sb, const std::string &pkgName);
-
-/**
- * @return the most specific Swig type for the given SBase object.
- */
-struct swig_type_info*
-GetDowncastSwigType (SBase* sb)
-{
-  if (sb == 0) return SWIGTYPE_p_SBase;  
-  const std::string pkgName = sb->getPackageName();
-  return GetDowncastSwigTypeForPackage(sb, pkgName);
-}
-/**
- * @return the most specific Swig type for the given SBase object.
- */
-struct swig_type_info*
-GetDowncastSwigTypeForPackage (SBase* sb, const std::string &pkgName)
-{
-  if (sb == 0) return SWIGTYPE_p_SBase;
-  
-  std::string name;
-
-  if (pkgName == "core")
-  {
-    switch (sb->getTypeCode())
-    {
-      case SBML_COMPARTMENT:
-        return SWIGTYPE_p_Compartment;
-  
-      case SBML_COMPARTMENT_TYPE:
-        return SWIGTYPE_p_CompartmentType;
-  
-      case SBML_CONSTRAINT:
-        return SWIGTYPE_p_Constraint;
-
-      case SBML_DOCUMENT:
-        return SWIGTYPE_p_SBMLDocument;
-  
-      case SBML_EVENT:
-        return SWIGTYPE_p_Event;
-  
-      case SBML_EVENT_ASSIGNMENT:
-        return SWIGTYPE_p_EventAssignment;
-  
-      case SBML_FUNCTION_DEFINITION:
-        return SWIGTYPE_p_FunctionDefinition;
-  
-      case SBML_INITIAL_ASSIGNMENT:
-        return SWIGTYPE_p_InitialAssignment;
-  
-      case SBML_KINETIC_LAW:
-        return SWIGTYPE_p_KineticLaw;
-  
-      case SBML_LIST_OF:
-        name = sb->getElementName();
-        if(name == "listOf"){
-          return SWIGTYPE_p_ListOf;
-        }
-        else if(name == "listOfCompartments"){
-          return SWIGTYPE_p_ListOfCompartments;
-        }
-        else if(name == "listOfCompartmentTypes"){
-          return SWIGTYPE_p_ListOfCompartmentTypes;
-        }
-        else if(name == "listOfConstraints"){
-          return SWIGTYPE_p_ListOfConstraints;
-        }
-        else if(name == "listOfEvents"){
-          return SWIGTYPE_p_ListOfEvents;
-        }
-        else if(name == "listOfEventAssignments"){
-          return SWIGTYPE_p_ListOfEventAssignments;
-        }
-        else if(name == "listOfFunctionDefinitions"){
-          return SWIGTYPE_p_ListOfFunctionDefinitions;
-        }
-        else if(name == "listOfInitialAssignments"){
-          return SWIGTYPE_p_ListOfInitialAssignments;
-        }
-        else if(name == "listOfParameters"){
-          return SWIGTYPE_p_ListOfParameters;
-        }
-        else if(name == "listOfLocalParameters"){
-          return SWIGTYPE_p_ListOfLocalParameters;
-        }
-        else if(name == "listOfReactions"){
-          return SWIGTYPE_p_ListOfReactions;
-        }
-        else if(name == "listOfRules"){
-          return SWIGTYPE_p_ListOfRules;
-        }
-        else if(name == "listOfSpecies"){
-          return SWIGTYPE_p_ListOfSpecies;
-        }
-        else if(name == "listOfUnknowns"){
-          return SWIGTYPE_p_ListOfSpeciesReferences;
-        }
-        else if(name == "listOfReactants"){
-          return SWIGTYPE_p_ListOfSpeciesReferences;
-        }
-        else if(name == "listOfProducts"){
-          return SWIGTYPE_p_ListOfSpeciesReferences;
-        }
-        else if(name == "listOfModifiers"){
-          return SWIGTYPE_p_ListOfSpeciesReferences;
-        }
-        else if(name == "listOfSpeciesTypes"){
-          return SWIGTYPE_p_ListOfSpeciesTypes;
-        }
-        else if(name == "listOfUnits"){
-          return SWIGTYPE_p_ListOfUnits;
-        }
-        else if(name == "listOfUnitDefinitions"){
-          return SWIGTYPE_p_ListOfUnitDefinitions;
-        }
-      return SWIGTYPE_p_ListOf;
-
-      case SBML_MODEL:
-        return SWIGTYPE_p_Model;
-
-      case SBML_PARAMETER:
-        return SWIGTYPE_p_Parameter;
-  
-      case SBML_LOCAL_PARAMETER:
-        return SWIGTYPE_p_LocalParameter;
-
-      case SBML_REACTION:
-        return SWIGTYPE_p_Reaction;
-
-      case SBML_SPECIES:
-        return SWIGTYPE_p_Species;
-
-      case SBML_SPECIES_REFERENCE:
-        return SWIGTYPE_p_SpeciesReference;
-
-      case SBML_MODIFIER_SPECIES_REFERENCE:
-        return SWIGTYPE_p_ModifierSpeciesReference;
-
-      case SBML_SPECIES_TYPE:
-        return SWIGTYPE_p_SpeciesType;
-
-      case SBML_UNIT_DEFINITION:
-        return SWIGTYPE_p_UnitDefinition;
-
-      case SBML_UNIT:
-        return SWIGTYPE_p_Unit;
-
-      case SBML_ALGEBRAIC_RULE:
-        return SWIGTYPE_p_AlgebraicRule;
-
-      case SBML_ASSIGNMENT_RULE:
-        return SWIGTYPE_p_AssignmentRule;
-
-      case SBML_RATE_RULE:
-        return SWIGTYPE_p_RateRule;
-
-      case SBML_DELAY:
-        return SWIGTYPE_p_Delay;
-
-      case SBML_TRIGGER:
-        return SWIGTYPE_p_Trigger;
-
-      case SBML_STOICHIOMETRY_MATH:
-       return SWIGTYPE_p_StoichiometryMath;
-      
-    case SBML_PRIORITY:
-      return SWIGTYPE_p_Priority;
-
-      default:
-        return SWIGTYPE_p_SBase;
-    }
-  }
-
-#include "local-downcast.cpp"		  
-	
-  return SWIGTYPE_p_SBase;
-}
-
-int fixNegativeIndex(int i, ListOf *l){
-  if (i < 0){
-    return i + l->size();
-  } else {
-    return i;
-  }
-}
-  
-
+/**
+ * @file    local.cpp
+ * @brief   Python-specific SWIG support code for wrapping libSBML API
+ * @author  Ben Bornstein
+ * @author  Ben Kovitz
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#include "sbml/SBase.h"
+#include <sstream>
+#include <R.h>
+using namespace std;
+/**
+ * @return the most specific Swig type for the given SBMLExtension object.
+ */
+struct swig_type_info*
+GetDowncastSwigType (SBMLExtension* se)
+{
+  if (se == 0) return SWIGTYPE_p_SBMLExtension;
+		
+  const std::string pkgName = se->getName();
+
+#include "local-downcast-extension.cpp"
+
+  return SWIGTYPE_p_SBMLExtension;
+}
+
+/**
+ * @return the most specific Swig type for the given SBMLNamespaces object.
+ */
+struct swig_type_info*
+GetDowncastSwigType (SBMLNamespaces* se)
+{
+	if (se == 0) return SWIGTYPE_p_SBMLNamespaces;
+	
+	const std::string pkgName = se->getPackageName();
+	
+#include "local-downcast-namespaces.cpp"
+	
+	return SWIGTYPE_p_SBMLNamespaces;
+}
+
+
+/**
+ * @return the most specific Swig type for the given SBasePlugin object.
+ */
+struct swig_type_info*
+GetDowncastSwigType (SBasePlugin* sbp)
+{
+  if (sbp == 0) return SWIGTYPE_p_SBasePlugin;
+
+  const std::string pkgName = sbp->getPackageName();
+  SBase* sb = sbp->getParentSBMLObject();
+  if (!sb) return SWIGTYPE_p_SBasePlugin;
+
+#include "local-downcast-plugins.cpp"
+	
+  return SWIGTYPE_p_SBasePlugin;
+}
+
+struct swig_type_info*
+GetDowncastSwigTypeForPackage (SBase* sb, const std::string &pkgName);
+
+/**
+ * @return the most specific Swig type for the given SBase object.
+ */
+struct swig_type_info*
+GetDowncastSwigType (SBase* sb)
+{
+  if (sb == 0) return SWIGTYPE_p_SBase;  
+  const std::string pkgName = sb->getPackageName();
+  return GetDowncastSwigTypeForPackage(sb, pkgName);
+}
+/**
+ * @return the most specific Swig type for the given SBase object.
+ */
+struct swig_type_info*
+GetDowncastSwigTypeForPackage (SBase* sb, const std::string &pkgName)
+{
+  if (sb == 0) return SWIGTYPE_p_SBase;
+  
+  std::string name;
+
+  if (pkgName == "core")
+  {
+    switch (sb->getTypeCode())
+    {
+      case SBML_COMPARTMENT:
+        return SWIGTYPE_p_Compartment;
+  
+      case SBML_COMPARTMENT_TYPE:
+        return SWIGTYPE_p_CompartmentType;
+  
+      case SBML_CONSTRAINT:
+        return SWIGTYPE_p_Constraint;
+
+      case SBML_DOCUMENT:
+        return SWIGTYPE_p_SBMLDocument;
+  
+      case SBML_EVENT:
+        return SWIGTYPE_p_Event;
+  
+      case SBML_EVENT_ASSIGNMENT:
+        return SWIGTYPE_p_EventAssignment;
+  
+      case SBML_FUNCTION_DEFINITION:
+        return SWIGTYPE_p_FunctionDefinition;
+  
+      case SBML_INITIAL_ASSIGNMENT:
+        return SWIGTYPE_p_InitialAssignment;
+  
+      case SBML_KINETIC_LAW:
+        return SWIGTYPE_p_KineticLaw;
+  
+      case SBML_LIST_OF:
+        name = sb->getElementName();
+        if(name == "listOf"){
+          return SWIGTYPE_p_ListOf;
+        }
+        else if(name == "listOfCompartments"){
+          return SWIGTYPE_p_ListOfCompartments;
+        }
+        else if(name == "listOfCompartmentTypes"){
+          return SWIGTYPE_p_ListOfCompartmentTypes;
+        }
+        else if(name == "listOfConstraints"){
+          return SWIGTYPE_p_ListOfConstraints;
+        }
+        else if(name == "listOfEvents"){
+          return SWIGTYPE_p_ListOfEvents;
+        }
+        else if(name == "listOfEventAssignments"){
+          return SWIGTYPE_p_ListOfEventAssignments;
+        }
+        else if(name == "listOfFunctionDefinitions"){
+          return SWIGTYPE_p_ListOfFunctionDefinitions;
+        }
+        else if(name == "listOfInitialAssignments"){
+          return SWIGTYPE_p_ListOfInitialAssignments;
+        }
+        else if(name == "listOfParameters"){
+          return SWIGTYPE_p_ListOfParameters;
+        }
+        else if(name == "listOfLocalParameters"){
+          return SWIGTYPE_p_ListOfLocalParameters;
+        }
+        else if(name == "listOfReactions"){
+          return SWIGTYPE_p_ListOfReactions;
+        }
+        else if(name == "listOfRules"){
+          return SWIGTYPE_p_ListOfRules;
+        }
+        else if(name == "listOfSpecies"){
+          return SWIGTYPE_p_ListOfSpecies;
+        }
+        else if(name == "listOfUnknowns"){
+          return SWIGTYPE_p_ListOfSpeciesReferences;
+        }
+        else if(name == "listOfReactants"){
+          return SWIGTYPE_p_ListOfSpeciesReferences;
+        }
+        else if(name == "listOfProducts"){
+          return SWIGTYPE_p_ListOfSpeciesReferences;
+        }
+        else if(name == "listOfModifiers"){
+          return SWIGTYPE_p_ListOfSpeciesReferences;
+        }
+        else if(name == "listOfSpeciesTypes"){
+          return SWIGTYPE_p_ListOfSpeciesTypes;
+        }
+        else if(name == "listOfUnits"){
+          return SWIGTYPE_p_ListOfUnits;
+        }
+        else if(name == "listOfUnitDefinitions"){
+          return SWIGTYPE_p_ListOfUnitDefinitions;
+        }
+      return SWIGTYPE_p_ListOf;
+
+      case SBML_MODEL:
+        return SWIGTYPE_p_Model;
+
+      case SBML_PARAMETER:
+        return SWIGTYPE_p_Parameter;
+  
+      case SBML_LOCAL_PARAMETER:
+        return SWIGTYPE_p_LocalParameter;
+
+      case SBML_REACTION:
+        return SWIGTYPE_p_Reaction;
+
+      case SBML_SPECIES:
+        return SWIGTYPE_p_Species;
+
+      case SBML_SPECIES_REFERENCE:
+        return SWIGTYPE_p_SpeciesReference;
+
+      case SBML_MODIFIER_SPECIES_REFERENCE:
+        return SWIGTYPE_p_ModifierSpeciesReference;
+
+      case SBML_SPECIES_TYPE:
+        return SWIGTYPE_p_SpeciesType;
+
+      case SBML_UNIT_DEFINITION:
+        return SWIGTYPE_p_UnitDefinition;
+
+      case SBML_UNIT:
+        return SWIGTYPE_p_Unit;
+
+      case SBML_ALGEBRAIC_RULE:
+        return SWIGTYPE_p_AlgebraicRule;
+
+      case SBML_ASSIGNMENT_RULE:
+        return SWIGTYPE_p_AssignmentRule;
+
+      case SBML_RATE_RULE:
+        return SWIGTYPE_p_RateRule;
+
+      case SBML_DELAY:
+        return SWIGTYPE_p_Delay;
+
+      case SBML_TRIGGER:
+        return SWIGTYPE_p_Trigger;
+
+      case SBML_STOICHIOMETRY_MATH:
+       return SWIGTYPE_p_StoichiometryMath;
+      
+    case SBML_PRIORITY:
+      return SWIGTYPE_p_Priority;
+
+      default:
+        return SWIGTYPE_p_SBase;
+    }
+  }
+
+#include "local-downcast.cpp"		  
+	
+  return SWIGTYPE_p_SBase;
+}
+
+int fixNegativeIndex(int i, ListOf *l){
+  if (i < 0){
+    return i + l->size();
+  } else {
+    return i;
+  }
+}
+  
+


Property changes on: trunk/libsbml/src/bindings/r/local.cpp
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/sbml/AlgebraicRule.cpp
===================================================================
--- trunk/libsbml/src/sbml/AlgebraicRule.cpp	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/sbml/AlgebraicRule.cpp	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,143 +1,143 @@
-/**
- * @file    AlgebraicRule.cpp
- * @brief   Implementations of AlgebraicRule.
- * @author  Ben Bornstein
- *
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ---------------------------------------------------------------------- -->*/
-
-#include <sbml/xml/XMLNode.h>
-#include <sbml/xml/XMLAttributes.h>
-#include <sbml/xml/XMLInputStream.h>
-#include <sbml/xml/XMLOutputStream.h>
-#include <sbml/xml/XMLNamespaces.h>
-
-#include <sbml/math/FormulaFormatter.h>
-#include <sbml/math/FormulaParser.h>
-#include <sbml/math/MathML.h>
-#include <sbml/math/ASTNode.h>
-
-#include <sbml/SBO.h>
-#include <sbml/SBMLTypeCodes.h>
-#include <sbml/SBMLVisitor.h>
-#include <sbml/SBMLError.h>
-#include <sbml/SBMLDocument.h>
-#include <sbml/Model.h>
-#include <sbml/AlgebraicRule.h>
-
-/** @cond doxygen-ignored */
-
-using namespace std;
-
-/** @endcond */
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-
-AlgebraicRule::AlgebraicRule (unsigned int level, unsigned int version) :
-  Rule(SBML_ALGEBRAIC_RULE, level, version)
-{
-  if (!hasValidLevelVersionNamespaceCombination())
-    throw SBMLConstructorException();
-
-  mInternalIdOnly = false;
-}
-
-
-AlgebraicRule::AlgebraicRule (SBMLNamespaces * sbmlns) :
-  Rule(SBML_ALGEBRAIC_RULE, sbmlns)
-{
-  if (!hasValidLevelVersionNamespaceCombination())
-  {
-    throw SBMLConstructorException(getElementName(), sbmlns);
-  }
-
-  mInternalIdOnly = false;
-
-  loadPlugins(sbmlns);
-}
-
-
-/*
- * Destroys this AlgebraicRule.
- */
-AlgebraicRule::~AlgebraicRule ()
-{
-}
-
-/*
- * @return a (deep) copy of this Rule.
- */
-AlgebraicRule*
-AlgebraicRule::clone () const
-{
-  return new AlgebraicRule(*this);
-}
-
-
-/*
- * Accepts the given SBMLVisitor.
- *
- * @return the result of calling <code>v.visit()</code>, which indicates
- * whether or not the Visitor would like to visit the Model's next Rule
- * (if available).
- */
-bool
-AlgebraicRule::accept (SBMLVisitor& v) const
-{
-  return v.visit(*this);
-}
-
-bool 
-AlgebraicRule::hasRequiredAttributes() const
-{
-  bool allPresent = Rule::hasRequiredAttributes();
-
-  return allPresent;
-}
-
-
-
-/** @cond doxygen-libsbml-internal */
-
-/*
- * sets the mInternalIdOnly flag
- */
-void 
-AlgebraicRule::setInternalIdOnly()
-{
-  mInternalIdOnly = true;
-}
-
-/*
- * gets the mInternalIdOnly flag
- */
-bool 
-AlgebraicRule::getInternalIdOnly() const
-{
-  return mInternalIdOnly;
-}
-
-/** @endcond */
-
-LIBSBML_CPP_NAMESPACE_END
+/**
+ * @file    AlgebraicRule.cpp
+ * @brief   Implementations of AlgebraicRule.
+ * @author  Ben Bornstein
+ *
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#include <sbml/xml/XMLNode.h>
+#include <sbml/xml/XMLAttributes.h>
+#include <sbml/xml/XMLInputStream.h>
+#include <sbml/xml/XMLOutputStream.h>
+#include <sbml/xml/XMLNamespaces.h>
+
+#include <sbml/math/FormulaFormatter.h>
+#include <sbml/math/FormulaParser.h>
+#include <sbml/math/MathML.h>
+#include <sbml/math/ASTNode.h>
+
+#include <sbml/SBO.h>
+#include <sbml/SBMLTypeCodes.h>
+#include <sbml/SBMLVisitor.h>
+#include <sbml/SBMLError.h>
+#include <sbml/SBMLDocument.h>
+#include <sbml/Model.h>
+#include <sbml/AlgebraicRule.h>
+
+/** @cond doxygen-ignored */
+
+using namespace std;
+
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+
+AlgebraicRule::AlgebraicRule (unsigned int level, unsigned int version) :
+  Rule(SBML_ALGEBRAIC_RULE, level, version)
+{
+  if (!hasValidLevelVersionNamespaceCombination())
+    throw SBMLConstructorException();
+
+  mInternalIdOnly = false;
+}
+
+
+AlgebraicRule::AlgebraicRule (SBMLNamespaces * sbmlns) :
+  Rule(SBML_ALGEBRAIC_RULE, sbmlns)
+{
+  if (!hasValidLevelVersionNamespaceCombination())
+  {
+    throw SBMLConstructorException(getElementName(), sbmlns);
+  }
+
+  mInternalIdOnly = false;
+
+  loadPlugins(sbmlns);
+}
+
+
+/*
+ * Destroys this AlgebraicRule.
+ */
+AlgebraicRule::~AlgebraicRule ()
+{
+}
+
+/*
+ * @return a (deep) copy of this Rule.
+ */
+AlgebraicRule*
+AlgebraicRule::clone () const
+{
+  return new AlgebraicRule(*this);
+}
+
+
+/*
+ * Accepts the given SBMLVisitor.
+ *
+ * @return the result of calling <code>v.visit()</code>, which indicates
+ * whether or not the Visitor would like to visit the Model's next Rule
+ * (if available).
+ */
+bool
+AlgebraicRule::accept (SBMLVisitor& v) const
+{
+  return v.visit(*this);
+}
+
+bool 
+AlgebraicRule::hasRequiredAttributes() const
+{
+  bool allPresent = Rule::hasRequiredAttributes();
+
+  return allPresent;
+}
+
+
+
+/** @cond doxygen-libsbml-internal */
+
+/*
+ * sets the mInternalIdOnly flag
+ */
+void 
+AlgebraicRule::setInternalIdOnly()
+{
+  mInternalIdOnly = true;
+}
+
+/*
+ * gets the mInternalIdOnly flag
+ */
+bool 
+AlgebraicRule::getInternalIdOnly() const
+{
+  return mInternalIdOnly;
+}
+
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_END


Property changes on: trunk/libsbml/src/sbml/AlgebraicRule.cpp
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/sbml/AlgebraicRule.h
===================================================================
--- trunk/libsbml/src/sbml/AlgebraicRule.h	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/sbml/AlgebraicRule.h	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,282 +1,282 @@
-/**
- * @file    AlgebraicRule.h
- * @brief   Definitions of AlgebraicRule.
- * @author  Ben Bornstein
- *
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ------------------------------------------------------------------------ -->
- *
- * @class AlgebraicRule
- * @brief LibSBML implementation of %SBML's %AlgebraicRule construct.
- *
- * The rule type AlgebraicRule is derived from the parent class Rule.  It
- * is used to express equations that are neither assignments of model
- * variables nor rates of change.  AlgebraicRule does not add any
- * attributes to the basic Rule; its role is simply to distinguish this
- * case from the other cases.
- *
- * In the context of a simulation, algebraic rules are in effect at all
- * times, <em>t</em> \f$\geq\f$ <em>0</em>.  For purposes of evaluating
- * expressions that involve the delay "csymbol" (see the SBML
- * specification), algebraic rules are considered to apply also at
- * <em>t</em> \f$\leq\f$ <em>0</em>.  Please consult the relevant SBML
- * specification for additional information about the semantics of
- * assignments, rules, and entity values for simulation time <em>t</em>
- * \f$\leq\f$ <em>0</em>.
- *
- * An SBML model must not be overdetermined.  The ability to define
- * arbitrary algebraic expressions in an SBML model introduces the
- * possibility that a model is mathematically overdetermined by the overall
- * system of equations constructed from its rules, reactions and events.
- * Therefore, if an algebraic rule is introduced in a model, for at least
- * one of the entities referenced in the rule's "math" element the value of
- * that entity must not be completely determined by other constructs in the
- * model.  This means that at least this entity must not have the attribute
- * "constant"=@c true and there must also not be a rate rule or assignment
- * rule for it.  Furthermore, if the entity is a Species object, its value
- * must not be determined by reactions, which means that it must either
- * have the attribute "boundaryCondition"=@c true or else not be involved
- * in any reaction at all.  These restrictions are explained in more detail
- * in the SBML specification documents.
- *
- * In SBML Levels 2 and&nbsp;3, Reaction object identifiers can be
- * referenced in the "math" expression of an algebraic rule, but reaction
- * rates can never be <em>determined</em> by algebraic rules.  This is true
- * even when a reaction does not contain a KineticLaw element.  (In such
- * cases of missing KineticLaw elements, the model is valid but incomplete;
- * the rates of reactions lacking kinetic laws are simply undefined, and
- * not determined by the algebraic rule.)
- * 
- * @section general General summary of SBML rules
- *
- * @htmlinclude rules-general-summary.html
- * 
- * @section additional-restrictions Additional restrictions on SBML rules
- * 
- * @htmlinclude rules-additional-restrictions.html
- * 
- * @section RuleType_t Rule types for SBML Level 1
- *
- * SBML Level 1 uses a different scheme than SBML Level 2 and Level 3 for
- * distinguishing rules; specifically, it uses an attribute whose value is
- * drawn from an enumeration of 3 values.  LibSBML supports this using methods
- * that work @if clike a libSBML enumeration type, RuleType_t, whose values
- * are @else with the enumeration values @endif@~ listed below.
- *
- * @li @link RuleType_t#RULE_TYPE_RATE RULE_TYPE_RATE@...: Indicates
- * the rule is a "rate" rule.
- * @li @link RuleType_t#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@...:
- * Indicates the rule is a "scalar" rule.
- * @li @link RuleType_t#RULE_TYPE_INVALID RULE_TYPE_INVALID@...:
- * Indicates the rule type is unknown or not yet set.
- *
- * <!-- leave this next break as-is to work around some doxygen bug -->
- */ 
-
-
-#ifndef AlgebraicRule_h
-#define AlgebraicRule_h
-
-
-#include <sbml/common/extern.h>
-#include <sbml/common/sbmlfwd.h>
-
-
-
-#ifdef __cplusplus
-
-
-#include <string>
-
-#include <sbml/Rule.h>
-#include <sbml/SBMLVisitor.h>
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-class SBMLNamespaces;
-
-class LIBSBML_EXTERN AlgebraicRule : public Rule
-{
-public:
-
-  /**
-   * Creates a new AlgebraicRule using the given SBML @p level and @p version
-   * values.
-   *
-   * @param level an unsigned int, the SBML Level to assign to this AlgebraicRule
-   *
-   * @param version an unsigned int, the SBML Version to assign to this
-   * AlgebraicRule
-   *
-   * @throws @if python ValueError @else SBMLConstructorException @endif
-   * Thrown if the given @p level and @p version combination, or this kind
-   * of SBML object, are either invalid or mismatched with respect to the
-   * parent SBMLDocument object.
-   * 
-   * @note Upon the addition of an AlgebraicRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif), the SBML Level, SBML Version
-   * and XML namespace of the document @em override the values used
-   * when creating the AlgebraicRule object via this constructor.  This is
-   * necessary to ensure that an SBML document is a consistent structure.
-   * Nevertheless, the ability to supply the values at the time of creation
-   * of a AlgebraicRule is an important aid to producing valid SBML.
-   * Knowledge of the intented SBML Level and Version determine whether it
-   * is valid to assign a particular value to an attribute, or whether it
-   * is valid to add an object to an existing SBMLDocument.
-   */
-  AlgebraicRule (unsigned int level, unsigned int version);
-
-
-  /**
-   * Creates a new AlgebraicRule using the given SBMLNamespaces object
-   * @p sbmlns.
-   *
-   * The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
-   * information.  It is used to communicate the SBML Level, Version, and
-   * (in Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.
-   * A common approach to using this class constructor is to create an
-   * SBMLNamespaces object somewhere in a program, once, then pass it to
-   * object constructors such as this one when needed.
-   *
-   * @param sbmlns an SBMLNamespaces object.
-   *
-   * @throws @if python ValueError @else SBMLConstructorException @endif
-   * Thrown if the given @p level and @p version combination, or this kind
-   * of SBML object, are either invalid or mismatched with respect to the
-   * parent SBMLDocument object.
-   *
-   * @note Upon the addition of a AlgebraicRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML XML namespace of the
-   * document @em overrides the value used when creating the AlgebraicRule
-   * object via this constructor.  This is necessary to ensure that an SBML
-   * document is a consistent structure.  Nevertheless, the ability to
-   * supply the values at the time of creation of a AlgebraicRule is an
-   * important aid to producing valid SBML.  Knowledge of the intented SBML
-   * Level and Version determine whether it is valid to assign a particular
-   * value to an attribute, or whether it is valid to add an object to an
-   * existing SBMLDocument.
-   */
-  AlgebraicRule (SBMLNamespaces* sbmlns);
-
-
-  /**
-   * Destroys this AlgebraicRule.
-   */
-  virtual ~AlgebraicRule ();
-
-
-  /**
-   * Creates and returns a deep copy of this Rule.
-   * 
-   * @return a (deep) copy of this Rule.
-   */
-  virtual AlgebraicRule* clone () const;
-
-
-  /**
-   * Accepts the given SBMLVisitor for this instance of AlgebraicRule.
-   *
-   * @param v the SBMLVisitor instance to be used.
-   *
-   * @return the result of calling <code>v.visit()</code>, which indicates
-   * whether the Visitor would like to visit the next AlgebraicRule object
-   * in the list of rules within which @em the present object is embedded.
-   */
-  virtual bool accept (SBMLVisitor& v) const;
-
-
-  /** @cond doxygen-libsbml-internal */
-
-  /**
-   * sets the mInternalIdOnly flag
-   */
-
-  void setInternalIdOnly();
-  bool getInternalIdOnly() const;
-  
-  /** @endcond */
-
-
-  /**
-   * Predicate returning @c true if
-   * all the required attributes for this AlgebraicRule object
-   * have been set.
-   *
-   * @note In SBML Levels&nbsp;2&ndash;3, there is no required attribute
-   * for an AlgebraicRule object.  For Level&nbsp;1, the only required
-   * attribute is "formula".
-   * 
-   * @return @c true if the required attributes have been set, @c false
-   * otherwise.
-   */
-  virtual bool hasRequiredAttributes() const ;
-
-
-protected:
-  /** @cond doxygen-libsbml-internal */
-
-  bool mInternalIdOnly;
-
-  /* the validator classes need to be friends to access the 
-   * protected constructor that takes no arguments
-   */
-  friend class Validator;
-  friend class ConsistencyValidator;
-  friend class IdentifierConsistencyValidator;
-  friend class InternalConsistencyValidator;
-  friend class L1CompatibilityValidator;
-  friend class L2v1CompatibilityValidator;
-  friend class L2v2CompatibilityValidator;
-  friend class L2v3CompatibilityValidator;
-  friend class L2v4CompatibilityValidator;
-  friend class MathMLConsistencyValidator;
-  friend class ModelingPracticeValidator;
-  friend class OverdeterminedValidator;
-  friend class SBOConsistencyValidator;
-  friend class UnitConsistencyValidator;
-
-  /** @endcond */
-
-};
-
-LIBSBML_CPP_NAMESPACE_END
-
-#endif  /* __cplusplus */
-
-
-#ifndef SWIG
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-BEGIN_C_DECLS
-
-/* ----------------------------------------------------------------------------
- * See the .cpp file for the documentation of the following functions.
- * --------------------------------------------------------------------------*/
-
-
-END_C_DECLS
-LIBSBML_CPP_NAMESPACE_END
-
-#endif  /* !SWIG  */
-#endif  /* AlgebraicRule_h */
-
+/**
+ * @file    AlgebraicRule.h
+ * @brief   Definitions of AlgebraicRule.
+ * @author  Ben Bornstein
+ *
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ------------------------------------------------------------------------ -->
+ *
+ * @class AlgebraicRule
+ * @brief LibSBML implementation of %SBML's %AlgebraicRule construct.
+ *
+ * The rule type AlgebraicRule is derived from the parent class Rule.  It
+ * is used to express equations that are neither assignments of model
+ * variables nor rates of change.  AlgebraicRule does not add any
+ * attributes to the basic Rule; its role is simply to distinguish this
+ * case from the other cases.
+ *
+ * In the context of a simulation, algebraic rules are in effect at all
+ * times, <em>t</em> \f$\geq\f$ <em>0</em>.  For purposes of evaluating
+ * expressions that involve the delay "csymbol" (see the SBML
+ * specification), algebraic rules are considered to apply also at
+ * <em>t</em> \f$\leq\f$ <em>0</em>.  Please consult the relevant SBML
+ * specification for additional information about the semantics of
+ * assignments, rules, and entity values for simulation time <em>t</em>
+ * \f$\leq\f$ <em>0</em>.
+ *
+ * An SBML model must not be overdetermined.  The ability to define
+ * arbitrary algebraic expressions in an SBML model introduces the
+ * possibility that a model is mathematically overdetermined by the overall
+ * system of equations constructed from its rules, reactions and events.
+ * Therefore, if an algebraic rule is introduced in a model, for at least
+ * one of the entities referenced in the rule's "math" element the value of
+ * that entity must not be completely determined by other constructs in the
+ * model.  This means that at least this entity must not have the attribute
+ * "constant"=@c true and there must also not be a rate rule or assignment
+ * rule for it.  Furthermore, if the entity is a Species object, its value
+ * must not be determined by reactions, which means that it must either
+ * have the attribute "boundaryCondition"=@c true or else not be involved
+ * in any reaction at all.  These restrictions are explained in more detail
+ * in the SBML specification documents.
+ *
+ * In SBML Levels 2 and&nbsp;3, Reaction object identifiers can be
+ * referenced in the "math" expression of an algebraic rule, but reaction
+ * rates can never be <em>determined</em> by algebraic rules.  This is true
+ * even when a reaction does not contain a KineticLaw element.  (In such
+ * cases of missing KineticLaw elements, the model is valid but incomplete;
+ * the rates of reactions lacking kinetic laws are simply undefined, and
+ * not determined by the algebraic rule.)
+ * 
+ * @section general General summary of SBML rules
+ *
+ * @htmlinclude rules-general-summary.html
+ * 
+ * @section additional-restrictions Additional restrictions on SBML rules
+ * 
+ * @htmlinclude rules-additional-restrictions.html
+ * 
+ * @section RuleType_t Rule types for SBML Level 1
+ *
+ * SBML Level 1 uses a different scheme than SBML Level 2 and Level 3 for
+ * distinguishing rules; specifically, it uses an attribute whose value is
+ * drawn from an enumeration of 3 values.  LibSBML supports this using methods
+ * that work @if clike a libSBML enumeration type, RuleType_t, whose values
+ * are @else with the enumeration values @endif@~ listed below.
+ *
+ * @li @link RuleType_t#RULE_TYPE_RATE RULE_TYPE_RATE@...: Indicates
+ * the rule is a "rate" rule.
+ * @li @link RuleType_t#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@...:
+ * Indicates the rule is a "scalar" rule.
+ * @li @link RuleType_t#RULE_TYPE_INVALID RULE_TYPE_INVALID@...:
+ * Indicates the rule type is unknown or not yet set.
+ *
+ * <!-- leave this next break as-is to work around some doxygen bug -->
+ */ 
+
+
+#ifndef AlgebraicRule_h
+#define AlgebraicRule_h
+
+
+#include <sbml/common/extern.h>
+#include <sbml/common/sbmlfwd.h>
+
+
+
+#ifdef __cplusplus
+
+
+#include <string>
+
+#include <sbml/Rule.h>
+#include <sbml/SBMLVisitor.h>
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class SBMLNamespaces;
+
+class LIBSBML_EXTERN AlgebraicRule : public Rule
+{
+public:
+
+  /**
+   * Creates a new AlgebraicRule using the given SBML @p level and @p version
+   * values.
+   *
+   * @param level an unsigned int, the SBML Level to assign to this AlgebraicRule
+   *
+   * @param version an unsigned int, the SBML Version to assign to this
+   * AlgebraicRule
+   *
+   * @throws @if python ValueError @else SBMLConstructorException @endif
+   * Thrown if the given @p level and @p version combination, or this kind
+   * of SBML object, are either invalid or mismatched with respect to the
+   * parent SBMLDocument object.
+   * 
+   * @note Upon the addition of an AlgebraicRule object to an SBMLDocument
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif), the SBML Level, SBML Version
+   * and XML namespace of the document @em override the values used
+   * when creating the AlgebraicRule object via this constructor.  This is
+   * necessary to ensure that an SBML document is a consistent structure.
+   * Nevertheless, the ability to supply the values at the time of creation
+   * of a AlgebraicRule is an important aid to producing valid SBML.
+   * Knowledge of the intented SBML Level and Version determine whether it
+   * is valid to assign a particular value to an attribute, or whether it
+   * is valid to add an object to an existing SBMLDocument.
+   */
+  AlgebraicRule (unsigned int level, unsigned int version);
+
+
+  /**
+   * Creates a new AlgebraicRule using the given SBMLNamespaces object
+   * @p sbmlns.
+   *
+   * The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
+   * information.  It is used to communicate the SBML Level, Version, and
+   * (in Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.
+   * A common approach to using this class constructor is to create an
+   * SBMLNamespaces object somewhere in a program, once, then pass it to
+   * object constructors such as this one when needed.
+   *
+   * @param sbmlns an SBMLNamespaces object.
+   *
+   * @throws @if python ValueError @else SBMLConstructorException @endif
+   * Thrown if the given @p level and @p version combination, or this kind
+   * of SBML object, are either invalid or mismatched with respect to the
+   * parent SBMLDocument object.
+   *
+   * @note Upon the addition of a AlgebraicRule object to an SBMLDocument
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML XML namespace of the
+   * document @em overrides the value used when creating the AlgebraicRule
+   * object via this constructor.  This is necessary to ensure that an SBML
+   * document is a consistent structure.  Nevertheless, the ability to
+   * supply the values at the time of creation of a AlgebraicRule is an
+   * important aid to producing valid SBML.  Knowledge of the intented SBML
+   * Level and Version determine whether it is valid to assign a particular
+   * value to an attribute, or whether it is valid to add an object to an
+   * existing SBMLDocument.
+   */
+  AlgebraicRule (SBMLNamespaces* sbmlns);
+
+
+  /**
+   * Destroys this AlgebraicRule.
+   */
+  virtual ~AlgebraicRule ();
+
+
+  /**
+   * Creates and returns a deep copy of this Rule.
+   * 
+   * @return a (deep) copy of this Rule.
+   */
+  virtual AlgebraicRule* clone () const;
+
+
+  /**
+   * Accepts the given SBMLVisitor for this instance of AlgebraicRule.
+   *
+   * @param v the SBMLVisitor instance to be used.
+   *
+   * @return the result of calling <code>v.visit()</code>, which indicates
+   * whether the Visitor would like to visit the next AlgebraicRule object
+   * in the list of rules within which @em the present object is embedded.
+   */
+  virtual bool accept (SBMLVisitor& v) const;
+
+
+  /** @cond doxygen-libsbml-internal */
+
+  /**
+   * sets the mInternalIdOnly flag
+   */
+
+  void setInternalIdOnly();
+  bool getInternalIdOnly() const;
+  
+  /** @endcond */
+
+
+  /**
+   * Predicate returning @c true if
+   * all the required attributes for this AlgebraicRule object
+   * have been set.
+   *
+   * @note In SBML Levels&nbsp;2&ndash;3, there is no required attribute
+   * for an AlgebraicRule object.  For Level&nbsp;1, the only required
+   * attribute is "formula".
+   * 
+   * @return @c true if the required attributes have been set, @c false
+   * otherwise.
+   */
+  virtual bool hasRequiredAttributes() const ;
+
+
+protected:
+  /** @cond doxygen-libsbml-internal */
+
+  bool mInternalIdOnly;
+
+  /* the validator classes need to be friends to access the 
+   * protected constructor that takes no arguments
+   */
+  friend class Validator;
+  friend class ConsistencyValidator;
+  friend class IdentifierConsistencyValidator;
+  friend class InternalConsistencyValidator;
+  friend class L1CompatibilityValidator;
+  friend class L2v1CompatibilityValidator;
+  friend class L2v2CompatibilityValidator;
+  friend class L2v3CompatibilityValidator;
+  friend class L2v4CompatibilityValidator;
+  friend class MathMLConsistencyValidator;
+  friend class ModelingPracticeValidator;
+  friend class OverdeterminedValidator;
+  friend class SBOConsistencyValidator;
+  friend class UnitConsistencyValidator;
+
+  /** @endcond */
+
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif  /* __cplusplus */
+
+
+#ifndef SWIG
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+BEGIN_C_DECLS
+
+/* ----------------------------------------------------------------------------
+ * See the .cpp file for the documentation of the following functions.
+ * --------------------------------------------------------------------------*/
+
+
+END_C_DECLS
+LIBSBML_CPP_NAMESPACE_END
+
+#endif  /* !SWIG  */
+#endif  /* AlgebraicRule_h */
+


Property changes on: trunk/libsbml/src/sbml/AlgebraicRule.h
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/sbml/AssignmentRule.cpp
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.cpp	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/sbml/AssignmentRule.cpp	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,133 +1,133 @@
-/**
- * @file    AssignmentRule.cpp
- * @brief   Implementations of AssignmentRule.
- * @author  Ben Bornstein
- *
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ---------------------------------------------------------------------- -->*/
-
-#include <sbml/xml/XMLNode.h>
-#include <sbml/xml/XMLAttributes.h>
-#include <sbml/xml/XMLInputStream.h>
-#include <sbml/xml/XMLOutputStream.h>
-#include <sbml/xml/XMLNamespaces.h>
-
-#include <sbml/math/FormulaFormatter.h>
-#include <sbml/math/FormulaParser.h>
-#include <sbml/math/MathML.h>
-#include <sbml/math/ASTNode.h>
-
-#include <sbml/SBO.h>
-#include <sbml/SBMLTypeCodes.h>
-#include <sbml/SBMLVisitor.h>
-#include <sbml/SBMLError.h>
-#include <sbml/SBMLDocument.h>
-#include <sbml/Model.h>
-#include <sbml/AssignmentRule.h>
-
-/** @cond doxygen-ignored */
-
-using namespace std;
-
-/** @endcond */
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-
-AssignmentRule::AssignmentRule (unsigned int level, unsigned int version) :
-  Rule(SBML_ASSIGNMENT_RULE, level, version)
-{
-  if (!hasValidLevelVersionNamespaceCombination())
-    throw SBMLConstructorException();
-}
-
-AssignmentRule::AssignmentRule (SBMLNamespaces *sbmlns) :
-  Rule(SBML_ASSIGNMENT_RULE, sbmlns)
-{
-  if (!hasValidLevelVersionNamespaceCombination())
-  {
-    throw SBMLConstructorException(getElementName(), sbmlns);
-  }
-
-  loadPlugins(sbmlns);
-}
-
-
-/*
- * Destroys this AssignmentRule.
- */
-AssignmentRule::~AssignmentRule ()
-{
-}
-
-
-/*
- * @return a (deep) copy of this Rule.
- */
-AssignmentRule*
-AssignmentRule::clone () const
-{
-  return new AssignmentRule(*this);
-}
-
-
-/*
- * Accepts the given SBMLVisitor.
- *
- * @return the result of calling <code>v.visit()</code>, which indicates
- * whether or not the Visitor would like to visit the Model's next Rule
- * (if available).
- */
-bool
-AssignmentRule::accept (SBMLVisitor& v) const
-{
-  return v.visit(*this);
-}
-
-
-bool 
-AssignmentRule::hasRequiredAttributes() const
-{
-  bool allPresent = Rule::hasRequiredAttributes();
-
-  /* required attributes for assignment: variable (comp/species/name in L1) */
-
-  if (!isSetVariable())
-    allPresent = false;
-
-  return allPresent;
-}
-
-
-void
-AssignmentRule::renameSIdRefs(std::string oldid, std::string newid)
-{
-  Rule::renameSIdRefs(oldid, newid);
-  if (isSetVariable()) {
-    if (getVariable()==oldid) {
-      setVariable(newid);
-    }
-  }
-}
-
-LIBSBML_CPP_NAMESPACE_END
+/**
+ * @file    AssignmentRule.cpp
+ * @brief   Implementations of AssignmentRule.
+ * @author  Ben Bornstein
+ *
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#include <sbml/xml/XMLNode.h>
+#include <sbml/xml/XMLAttributes.h>
+#include <sbml/xml/XMLInputStream.h>
+#include <sbml/xml/XMLOutputStream.h>
+#include <sbml/xml/XMLNamespaces.h>
+
+#include <sbml/math/FormulaFormatter.h>
+#include <sbml/math/FormulaParser.h>
+#include <sbml/math/MathML.h>
+#include <sbml/math/ASTNode.h>
+
+#include <sbml/SBO.h>
+#include <sbml/SBMLTypeCodes.h>
+#include <sbml/SBMLVisitor.h>
+#include <sbml/SBMLError.h>
+#include <sbml/SBMLDocument.h>
+#include <sbml/Model.h>
+#include <sbml/AssignmentRule.h>
+
+/** @cond doxygen-ignored */
+
+using namespace std;
+
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+
+AssignmentRule::AssignmentRule (unsigned int level, unsigned int version) :
+  Rule(SBML_ASSIGNMENT_RULE, level, version)
+{
+  if (!hasValidLevelVersionNamespaceCombination())
+    throw SBMLConstructorException();
+}
+
+AssignmentRule::AssignmentRule (SBMLNamespaces *sbmlns) :
+  Rule(SBML_ASSIGNMENT_RULE, sbmlns)
+{
+  if (!hasValidLevelVersionNamespaceCombination())
+  {
+    throw SBMLConstructorException(getElementName(), sbmlns);
+  }
+
+  loadPlugins(sbmlns);
+}
+
+
+/*
+ * Destroys this AssignmentRule.
+ */
+AssignmentRule::~AssignmentRule ()
+{
+}
+
+
+/*
+ * @return a (deep) copy of this Rule.
+ */
+AssignmentRule*
+AssignmentRule::clone () const
+{
+  return new AssignmentRule(*this);
+}
+
+
+/*
+ * Accepts the given SBMLVisitor.
+ *
+ * @return the result of calling <code>v.visit()</code>, which indicates
+ * whether or not the Visitor would like to visit the Model's next Rule
+ * (if available).
+ */
+bool
+AssignmentRule::accept (SBMLVisitor& v) const
+{
+  return v.visit(*this);
+}
+
+
+bool 
+AssignmentRule::hasRequiredAttributes() const
+{
+  bool allPresent = Rule::hasRequiredAttributes();
+
+  /* required attributes for assignment: variable (comp/species/name in L1) */
+
+  if (!isSetVariable())
+    allPresent = false;
+
+  return allPresent;
+}
+
+
+void
+AssignmentRule::renameSIdRefs(std::string oldid, std::string newid)
+{
+  Rule::renameSIdRefs(oldid, newid);
+  if (isSetVariable()) {
+    if (getVariable()==oldid) {
+      setVariable(newid);
+    }
+  }
+}
+
+LIBSBML_CPP_NAMESPACE_END


Property changes on: trunk/libsbml/src/sbml/AssignmentRule.cpp
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/sbml/AssignmentRule.h
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.h	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/sbml/AssignmentRule.h	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,321 +1,321 @@
-/**
- * @file    AssignmentRule.h
- * @brief   Definitions of AssignmentRule.
- * @author  Ben Bornstein
- *
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ------------------------------------------------------------------------ -->
- * 
- * @class AssignmentRule
- * @brief LibSBML implementation of %SBML's %AssignmentRule construct.
- *
- * The rule type AssignmentRule is derived from the parent class Rule.  It
- * is used to express equations that set the values of variables.  The
- * left-hand side (the attribute named "variable") of an assignment rule
- * can refer to the identifier of a Species, SpeciesReference (in SBML
- * Level&nbsp;3), Compartment, or Parameter object in the model (but not a
- * Reaction).  The entity identified must have its "constant" attribute set
- * to @c false.  The effects of an AssignmentRule are in general terms the
- * same, but differ in the precise details depending on the type of
- * variable being set: <ul>
-
- * <li> <em>In the case of a species</em>, an AssignmentRule sets the
- * referenced species' quantity (whether a "concentration" or "amount") to
- * the value determined by the formula in the MathML subelement "math".
- * The unit associated with the value produced by the "math" formula @em
- * should (in SBML Level&nbsp;2 Version&nbsp;4 and in SBML Level&nbsp;3) or @em must (in
- * SBML releases prior to Level&nbsp;2 version&nbsp;4) be equal to the unit
- * associated with the species' quantity.  <em>Restrictions</em>: There
- * must not be both an AssignmentRule "variable" attribute and a
- * SpeciesReference "species" attribute having the same value, unless the
- * referenced Species object has its "boundaryCondition" attribute set to
- * @c true.  In other words, an assignment rule cannot be defined for a
- * species that is created or destroyed in a reaction unless that species
- * is defined as a boundary condition in the model.
- *
- * <li> (For SBML Level&nbsp;3 only) <em>In the case of a species
- * reference</em>, an AssignmentRule sets the stoichiometry of the
- * referenced reactant or product to the value determined by the formula in
- * "math".  The unit associated with the value produced by the "math"
- * formula should be consistent with the unit "dimensionless", because
- * reactant and product stoichiometries in reactions are dimensionless
- * quantities.
-  *
- * <li> <em>In the case of a compartment</em>, an AssignmentRule sets the
- * referenced compartment's size to the value determined by the formula in
- * the "math" subelement of the AssignmentRule object.  The overall units
- * of the formula in "math" @em should (in SBML Level&nbsp;2 Version&nbsp;4
- * and in SBML Level&nbsp;3) or @em must (in SBML releases prior to Level&nbsp;2
- * version&nbsp;4) be the same as the units of the size of the compartment.
- *
- * <li> <em>In the case of a parameter</em>, an AssignmentRule sets the
- * referenced parameter's value to that determined by the formula in the
- * "math" subelement of the AssignmentRule object.  The overall units of
- * the formula in the "math" subelement @em should (in SBML Level&nbsp;2
- * Version&nbsp;4 and in SBML Level&nbsp;3) or @em must (in SBML releases prior to
- * Level&nbsp;2 version&nbsp;4) be the same as the units defined for the
- * parameter.  </ul>
- * 
- * In the context of a simulation, assignment rules are in effect at all
- * times, <em>t</em> \f$\geq\f$ <em>0</em>.  For purposes of evaluating
- * expressions that involve the <em>delay</em> "csymbol" (see the SBML
- * Level&nbsp;2 specification), assignment rules are considered to apply
- * also at <em>t</em> \f$\leq\f$ <em>0</em>.  Please consult the relevant
- * SBML specification for additional information about the semantics of
- * assignments, rules, and entity values for simulation time <em>t</em>
- * \f$\leq\f$ <em>0</em>.
- *
- * A model must not contain more than one AssignmentRule or RateRule
- * object having the same value of "variable"; in other words, in the set
- * of all assignment rules and rate rules in an SBML model, each variable
- * appearing in the left-hand sides can only appear once.  This simply
- * follows from the fact that an indeterminate system would result if a
- * model contained more than one assignment rule for the same variable or
- * both an assignment rule and a rate rule for the same variable.
- *
- * Similarly, a model must also not contain <em>both</em> an AssignmentRule
- * and an InitialAssignment for the same variable, because both kinds of
- * constructs apply prior to and at the start of simulation time, i.e.,
- * <em>t</em> \f$\leq\f$ <em>0</em>.  If a model contained both an initial
- * assignment and an assignment rule for the same variable, an
- * indeterminate system would result.
- *
- * The value calculated by an AssignmentRule object overrides the value
- * assigned to the given symbol by the object defining that symbol.  For
- * example, if a Compartment object's "size" attribute value is set in its
- * definition, and the model also contains an AssignmentRule object having
- * that compartment's "id" as its "variable" value, then the "size"
- * assigned in the Compartment object definition is ignored and the value
- * assigned based on the computation defined in the AssignmentRule.  This
- * does <em>not</em> mean that a definition for a given symbol can be
- * omitted if there is an AssignmentRule object for it.  For example, there
- * must be a Parameter definition for a given parameter if there is an
- * AssignmentRule for that parameter.  It is only a question of which value
- * definition takes precedence.
- * 
- * @section general General summary of SBML rules
- *
- * @htmlinclude rules-general-summary.html
- * 
- * @section additional-restrictions Additional restrictions on SBML rules
- * 
- * @htmlinclude rules-additional-restrictions.html
- * 
- * @section RuleType_t Rule types for SBML Level 1
- *
- * SBML Level 1 uses a different scheme than SBML Level 2 and Level 3 for
- * distinguishing rules; specifically, it uses an attribute whose value is
- * drawn from an enumeration of 3 values.  LibSBML supports this using methods
- * that work @if clike a libSBML enumeration type, RuleType_t, whose values
- * are @else with the enumeration values @endif@~ listed below.
- *
- * @li @link RuleType_t#RULE_TYPE_RATE RULE_TYPE_RATE@...: Indicates
- * the rule is a "rate" rule.
- * @li @link RuleType_t#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@...:
- * Indicates the rule is a "scalar" rule.
- * @li @link RuleType_t#RULE_TYPE_INVALID RULE_TYPE_INVALID@...:
- * Indicates the rule type is unknown or not yet set.
- *
- * <!-- leave this next break as-is to work around some doxygen bug -->
- */ 
-
-
-#ifndef AssignmentRule_h
-#define AssignmentRule_h
-
-
-#include <sbml/common/extern.h>
-#include <sbml/common/sbmlfwd.h>
-
-
-
-#ifdef __cplusplus
-
-
-#include <string>
-
-#include <sbml/Rule.h>
-#include <sbml/SBMLVisitor.h>
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-class SBMLNamespaces;
-
-class LIBSBML_EXTERN AssignmentRule : public Rule
-{
-public:
-
-  /**
-   * Creates a new AssignmentRule using the given SBML @p level and @p version
-   * values.
-   *
-   * @param level an unsigned int, the SBML Level to assign to this AssignmentRule
-   *
-   * @param version an unsigned int, the SBML Version to assign to this
-   * AssignmentRule
-   *
-   * @throws @if python ValueError @else SBMLConstructorException @endif@~
-   * Thrown if the given @p level and @p version combination, or this kind
-   * of SBML object, are either invalid or mismatched with respect to the
-   * parent SBMLDocument object.
-   * 
-   * @note Upon the addition of an AssignmentRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML Level, SBML Version
-   * and XML namespace of the document @em override the values used
-   * when creating the AssignmentRule object via this constructor.  This is
-   * necessary to ensure that an SBML document is a consistent structure.
-   * Nevertheless, the ability to supply the values at the time of creation
-   * of a AssignmentRule is an important aid to producing valid SBML.
-   * Knowledge of the intented SBML Level and Version determine whether it
-   * is valid to assign a particular value to an attribute, or whether it
-   * is valid to add an object to an existing SBMLDocument.
-   */
-  AssignmentRule (unsigned int level, unsigned int version);
-
-
-  /**
-   * Creates a new AssignmentRule using the given SBMLNamespaces object
-   * @p sbmlns.
-   *
-   * The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
-   * information.  It is used to communicate the SBML Level, Version, and
-   * (in Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.
-   * A common approach to using this class constructor is to create an
-   * SBMLNamespaces object somewhere in a program, once, then pass it to
-   * object constructors such as this one when needed.
-   *
-   * @param sbmlns an SBMLNamespaces object.
-   *
-   * @throws @if python ValueError @else SBMLConstructorException @endif@~
-   * Thrown if the given @p level and @p version combination, or this kind
-   * of SBML object, are either invalid or mismatched with respect to the
-   * parent SBMLDocument object.
-   *
-   * @note Upon the addition of a AssignmentRule object to an SBMLDocument
-   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML XML namespace of
-   * the document @em overrides the value used when creating the
-   * AssignmentRule object via this constructor.  This is necessary to
-   * ensure that an SBML document is a consistent structure.  Nevertheless,
-   * the ability to supply the values at the time of creation of a
-   * AssignmentRule is an important aid to producing valid SBML.  Knowledge
-   * of the intented SBML Level and Version determine whether it is valid
-   * to assign a particular value to an attribute, or whether it is valid
-   * to add an object to an existing SBMLDocument.
-   */
-  AssignmentRule (SBMLNamespaces* sbmlns);
-
-
-  /**
-   * Destroys this AssignmentRule.
-   */
-  virtual ~AssignmentRule ();
-
-
-  /**
-   * Creates and returns a deep copy of this Rule.
-   * 
-   * @return a (deep) copy of this Rule.
-   */
-  virtual AssignmentRule* clone () const;
-
-
-  /**
-   * Accepts the given SBMLVisitor for this instance of AssignmentRule.
-   *
-   * @param v the SBMLVisitor instance to be used.
-   *
-   * @return the result of calling <code>v.visit()</code>, which indicates
-   * whether the Visitor would like to visit the next AssignmentRule object
-   * in the list of rules within which @em the present object is embedded.
-   */
-  virtual bool accept (SBMLVisitor& v) const;
-
-
-  /**
-   * Predicate returning @c true if
-   * all the required attributes for this AssignmentRule object
-   * have been set.
-   *
-   * @note In SBML Levels&nbsp;2&ndash;3, the only required attribute for
-   * an AssignmentRule object is "variable".  For Level&nbsp;1, where the
-   * equivalent attribute is known by different names ("compartment",
-   * "species", or "name", depending on the type of object), there is an
-   * additional required attribute called "formula".
-   * 
-   * @return @c true if the required attributes have been set, @c false
-   * otherwise.
-   */
-  virtual bool hasRequiredAttributes() const ;
-
-
-  /**
-   * Renames all the SIdRef attributes on this element, including any found in MathML
-   */
-  virtual void renameSIdRefs(std::string oldid, std::string newid);
-
-
-protected:
-  /** @cond doxygen-libsbml-internal */
-
-  /* the validator classes need to be friends to access the 
-   * protected constructor that takes no arguments
-   */
-  friend class Validator;
-  friend class ConsistencyValidator;
-  friend class IdentifierConsistencyValidator;
-  friend class InternalConsistencyValidator;
-  friend class L1CompatibilityValidator;
-  friend class L2v1CompatibilityValidator;
-  friend class L2v2CompatibilityValidator;
-  friend class L2v3CompatibilityValidator;
-  friend class L2v4CompatibilityValidator;
-  friend class MathMLConsistencyValidator;
-  friend class ModelingPracticeValidator;
-  friend class OverdeterminedValidator;
-  friend class SBOConsistencyValidator;
-  friend class UnitConsistencyValidator;
-
-  /** @endcond */
-};
-
-LIBSBML_CPP_NAMESPACE_END
-
-#endif  /* __cplusplus */
-
-
-#ifndef SWIG
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-BEGIN_C_DECLS
-
-/* ----------------------------------------------------------------------------
- * See the .cpp file for the documentation of the following functions.
- * --------------------------------------------------------------------------*/
-
-
-END_C_DECLS
-LIBSBML_CPP_NAMESPACE_END
-
-#endif  /* !SWIG  */
-#endif  /* AssignmentRule_h */
-
+/**
+ * @file    AssignmentRule.h
+ * @brief   Definitions of AssignmentRule.
+ * @author  Ben Bornstein
+ *
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ------------------------------------------------------------------------ -->
+ * 
+ * @class AssignmentRule
+ * @brief LibSBML implementation of %SBML's %AssignmentRule construct.
+ *
+ * The rule type AssignmentRule is derived from the parent class Rule.  It
+ * is used to express equations that set the values of variables.  The
+ * left-hand side (the attribute named "variable") of an assignment rule
+ * can refer to the identifier of a Species, SpeciesReference (in SBML
+ * Level&nbsp;3), Compartment, or Parameter object in the model (but not a
+ * Reaction).  The entity identified must have its "constant" attribute set
+ * to @c false.  The effects of an AssignmentRule are in general terms the
+ * same, but differ in the precise details depending on the type of
+ * variable being set: <ul>
+
+ * <li> <em>In the case of a species</em>, an AssignmentRule sets the
+ * referenced species' quantity (whether a "concentration" or "amount") to
+ * the value determined by the formula in the MathML subelement "math".
+ * The unit associated with the value produced by the "math" formula @em
+ * should (in SBML Level&nbsp;2 Version&nbsp;4 and in SBML Level&nbsp;3) or @em must (in
+ * SBML releases prior to Level&nbsp;2 version&nbsp;4) be equal to the unit
+ * associated with the species' quantity.  <em>Restrictions</em>: There
+ * must not be both an AssignmentRule "variable" attribute and a
+ * SpeciesReference "species" attribute having the same value, unless the
+ * referenced Species object has its "boundaryCondition" attribute set to
+ * @c true.  In other words, an assignment rule cannot be defined for a
+ * species that is created or destroyed in a reaction unless that species
+ * is defined as a boundary condition in the model.
+ *
+ * <li> (For SBML Level&nbsp;3 only) <em>In the case of a species
+ * reference</em>, an AssignmentRule sets the stoichiometry of the
+ * referenced reactant or product to the value determined by the formula in
+ * "math".  The unit associated with the value produced by the "math"
+ * formula should be consistent with the unit "dimensionless", because
+ * reactant and product stoichiometries in reactions are dimensionless
+ * quantities.
+  *
+ * <li> <em>In the case of a compartment</em>, an AssignmentRule sets the
+ * referenced compartment's size to the value determined by the formula in
+ * the "math" subelement of the AssignmentRule object.  The overall units
+ * of the formula in "math" @em should (in SBML Level&nbsp;2 Version&nbsp;4
+ * and in SBML Level&nbsp;3) or @em must (in SBML releases prior to Level&nbsp;2
+ * version&nbsp;4) be the same as the units of the size of the compartment.
+ *
+ * <li> <em>In the case of a parameter</em>, an AssignmentRule sets the
+ * referenced parameter's value to that determined by the formula in the
+ * "math" subelement of the AssignmentRule object.  The overall units of
+ * the formula in the "math" subelement @em should (in SBML Level&nbsp;2
+ * Version&nbsp;4 and in SBML Level&nbsp;3) or @em must (in SBML releases prior to
+ * Level&nbsp;2 version&nbsp;4) be the same as the units defined for the
+ * parameter.  </ul>
+ * 
+ * In the context of a simulation, assignment rules are in effect at all
+ * times, <em>t</em> \f$\geq\f$ <em>0</em>.  For purposes of evaluating
+ * expressions that involve the <em>delay</em> "csymbol" (see the SBML
+ * Level&nbsp;2 specification), assignment rules are considered to apply
+ * also at <em>t</em> \f$\leq\f$ <em>0</em>.  Please consult the relevant
+ * SBML specification for additional information about the semantics of
+ * assignments, rules, and entity values for simulation time <em>t</em>
+ * \f$\leq\f$ <em>0</em>.
+ *
+ * A model must not contain more than one AssignmentRule or RateRule
+ * object having the same value of "variable"; in other words, in the set
+ * of all assignment rules and rate rules in an SBML model, each variable
+ * appearing in the left-hand sides can only appear once.  This simply
+ * follows from the fact that an indeterminate system would result if a
+ * model contained more than one assignment rule for the same variable or
+ * both an assignment rule and a rate rule for the same variable.
+ *
+ * Similarly, a model must also not contain <em>both</em> an AssignmentRule
+ * and an InitialAssignment for the same variable, because both kinds of
+ * constructs apply prior to and at the start of simulation time, i.e.,
+ * <em>t</em> \f$\leq\f$ <em>0</em>.  If a model contained both an initial
+ * assignment and an assignment rule for the same variable, an
+ * indeterminate system would result.
+ *
+ * The value calculated by an AssignmentRule object overrides the value
+ * assigned to the given symbol by the object defining that symbol.  For
+ * example, if a Compartment object's "size" attribute value is set in its
+ * definition, and the model also contains an AssignmentRule object having
+ * that compartment's "id" as its "variable" value, then the "size"
+ * assigned in the Compartment object definition is ignored and the value
+ * assigned based on the computation defined in the AssignmentRule.  This
+ * does <em>not</em> mean that a definition for a given symbol can be
+ * omitted if there is an AssignmentRule object for it.  For example, there
+ * must be a Parameter definition for a given parameter if there is an
+ * AssignmentRule for that parameter.  It is only a question of which value
+ * definition takes precedence.
+ * 
+ * @section general General summary of SBML rules
+ *
+ * @htmlinclude rules-general-summary.html
+ * 
+ * @section additional-restrictions Additional restrictions on SBML rules
+ * 
+ * @htmlinclude rules-additional-restrictions.html
+ * 
+ * @section RuleType_t Rule types for SBML Level 1
+ *
+ * SBML Level 1 uses a different scheme than SBML Level 2 and Level 3 for
+ * distinguishing rules; specifically, it uses an attribute whose value is
+ * drawn from an enumeration of 3 values.  LibSBML supports this using methods
+ * that work @if clike a libSBML enumeration type, RuleType_t, whose values
+ * are @else with the enumeration values @endif@~ listed below.
+ *
+ * @li @link RuleType_t#RULE_TYPE_RATE RULE_TYPE_RATE@...: Indicates
+ * the rule is a "rate" rule.
+ * @li @link RuleType_t#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@...:
+ * Indicates the rule is a "scalar" rule.
+ * @li @link RuleType_t#RULE_TYPE_INVALID RULE_TYPE_INVALID@...:
+ * Indicates the rule type is unknown or not yet set.
+ *
+ * <!-- leave this next break as-is to work around some doxygen bug -->
+ */ 
+
+
+#ifndef AssignmentRule_h
+#define AssignmentRule_h
+
+
+#include <sbml/common/extern.h>
+#include <sbml/common/sbmlfwd.h>
+
+
+
+#ifdef __cplusplus
+
+
+#include <string>
+
+#include <sbml/Rule.h>
+#include <sbml/SBMLVisitor.h>
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class SBMLNamespaces;
+
+class LIBSBML_EXTERN AssignmentRule : public Rule
+{
+public:
+
+  /**
+   * Creates a new AssignmentRule using the given SBML @p level and @p version
+   * values.
+   *
+   * @param level an unsigned int, the SBML Level to assign to this AssignmentRule
+   *
+   * @param version an unsigned int, the SBML Version to assign to this
+   * AssignmentRule
+   *
+   * @throws @if python ValueError @else SBMLConstructorException @endif@~
+   * Thrown if the given @p level and @p version combination, or this kind
+   * of SBML object, are either invalid or mismatched with respect to the
+   * parent SBMLDocument object.
+   * 
+   * @note Upon the addition of an AssignmentRule object to an SBMLDocument
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML Level, SBML Version
+   * and XML namespace of the document @em override the values used
+   * when creating the AssignmentRule object via this constructor.  This is
+   * necessary to ensure that an SBML document is a consistent structure.
+   * Nevertheless, the ability to supply the values at the time of creation
+   * of a AssignmentRule is an important aid to producing valid SBML.
+   * Knowledge of the intented SBML Level and Version determine whether it
+   * is valid to assign a particular value to an attribute, or whether it
+   * is valid to add an object to an existing SBMLDocument.
+   */
+  AssignmentRule (unsigned int level, unsigned int version);
+
+
+  /**
+   * Creates a new AssignmentRule using the given SBMLNamespaces object
+   * @p sbmlns.
+   *
+   * The SBMLNamespaces object encapsulates SBML Level/Version/namespaces
+   * information.  It is used to communicate the SBML Level, Version, and
+   * (in Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.
+   * A common approach to using this class constructor is to create an
+   * SBMLNamespaces object somewhere in a program, once, then pass it to
+   * object constructors such as this one when needed.
+   *
+   * @param sbmlns an SBMLNamespaces object.
+   *
+   * @throws @if python ValueError @else SBMLConstructorException @endif@~
+   * Thrown if the given @p level and @p version combination, or this kind
+   * of SBML object, are either invalid or mismatched with respect to the
+   * parent SBMLDocument object.
+   *
+   * @note Upon the addition of a AssignmentRule object to an SBMLDocument
+   * (e.g., using&nbsp; @if java Model::addRule(Rule r)@else Model::addRule()@endif, the SBML XML namespace of
+   * the document @em overrides the value used when creating the
+   * AssignmentRule object via this constructor.  This is necessary to
+   * ensure that an SBML document is a consistent structure.  Nevertheless,
+   * the ability to supply the values at the time of creation of a
+   * AssignmentRule is an important aid to producing valid SBML.  Knowledge
+   * of the intented SBML Level and Version determine whether it is valid
+   * to assign a particular value to an attribute, or whether it is valid
+   * to add an object to an existing SBMLDocument.
+   */
+  AssignmentRule (SBMLNamespaces* sbmlns);
+
+
+  /**
+   * Destroys this AssignmentRule.
+   */
+  virtual ~AssignmentRule ();
+
+
+  /**
+   * Creates and returns a deep copy of this Rule.
+   * 
+   * @return a (deep) copy of this Rule.
+   */
+  virtual AssignmentRule* clone () const;
+
+
+  /**
+   * Accepts the given SBMLVisitor for this instance of AssignmentRule.
+   *
+   * @param v the SBMLVisitor instance to be used.
+   *
+   * @return the result of calling <code>v.visit()</code>, which indicates
+   * whether the Visitor would like to visit the next AssignmentRule object
+   * in the list of rules within which @em the present object is embedded.
+   */
+  virtual bool accept (SBMLVisitor& v) const;
+
+
+  /**
+   * Predicate returning @c true if
+   * all the required attributes for this AssignmentRule object
+   * have been set.
+   *
+   * @note In SBML Levels&nbsp;2&ndash;3, the only required attribute for
+   * an AssignmentRule object is "variable".  For Level&nbsp;1, where the
+   * equivalent attribute is known by different names ("compartment",
+   * "species", or "name", depending on the type of object), there is an
+   * additional required attribute called "formula".
+   * 
+   * @return @c true if the required attributes have been set, @c false
+   * otherwise.
+   */
+  virtual bool hasRequiredAttributes() const ;
+
+
+  /**
+   * Renames all the SIdRef attributes on this element, including any found in MathML
+   */
+  virtual void renameSIdRefs(std::string oldid, std::string newid);
+
+
+protected:
+  /** @cond doxygen-libsbml-internal */
+
+  /* the validator classes need to be friends to access the 
+   * protected constructor that takes no arguments
+   */
+  friend class Validator;
+  friend class ConsistencyValidator;
+  friend class IdentifierConsistencyValidator;
+  friend class InternalConsistencyValidator;
+  friend class L1CompatibilityValidator;
+  friend class L2v1CompatibilityValidator;
+  friend class L2v2CompatibilityValidator;
+  friend class L2v3CompatibilityValidator;
+  friend class L2v4CompatibilityValidator;
+  friend class MathMLConsistencyValidator;
+  friend class ModelingPracticeValidator;
+  friend class OverdeterminedValidator;
+  friend class SBOConsistencyValidator;
+  friend class UnitConsistencyValidator;
+
+  /** @endcond */
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif  /* __cplusplus */
+
+
+#ifndef SWIG
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+BEGIN_C_DECLS
+
+/* ----------------------------------------------------------------------------
+ * See the .cpp file for the documentation of the following functions.
+ * --------------------------------------------------------------------------*/
+
+
+END_C_DECLS
+LIBSBML_CPP_NAMESPACE_END
+
+#endif  /* !SWIG  */
+#endif  /* AssignmentRule_h */
+


Property changes on: trunk/libsbml/src/sbml/AssignmentRule.h
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/sbml/ExpectedAttributes.cpp
===================================================================
--- trunk/libsbml/src/sbml/ExpectedAttributes.cpp	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/sbml/ExpectedAttributes.cpp	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,85 +1,85 @@
-/**
- * @file    ExpectedAttributes.cpp
- * @brief   Implementation of ExpectedAttributes, the class allowing the specification
- *          of attributes to expect.
- * @author  Ben Bornstein
- * 
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ------------------------------------------------------------------------ -->
- */
-
-
-#include <sbml/common/sbmlfwd.h>
-#include <sbml/common/common.h>
-#include <sbml/common/operationReturnValues.h>
-#include <sbml/ExpectedAttributes.h>
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-/** @cond doxygen-c-only */
-
-
-LIBSBML_EXTERN 
-ExpectedAttributes_t *
-ExpectedAttributes_create()
-{
-  return new ExpectedAttributes();
-}
-
-LIBSBML_EXTERN 
-ExpectedAttributes_t *
-ExpectedAttributes_clone(ExpectedAttributes_t *attr)
-{
-  if (attr == NULL) return NULL;
-  return new ExpectedAttributes(*attr);
-}
-
-LIBSBML_EXTERN 
-int
-ExpectedAttributes_add(ExpectedAttributes_t *attr, const char* attribute)
-{
-  if (attr == NULL || attribute == NULL) return LIBSBML_INVALID_OBJECT;
-  attr->add(std::string(attribute));
-  return LIBSBML_OPERATION_SUCCESS;
-}
-
-LIBSBML_EXTERN 
-char*
-ExpectedAttributes_get(ExpectedAttributes_t *attr, unsigned int index)
-{
-  if (attr == NULL) return NULL;
-  return safe_strdup(attr->get(index).c_str());
-}
-
-LIBSBML_EXTERN 
-int
-ExpectedAttributes_hasAttribute(ExpectedAttributes_t *attr, const char* attribute)
-{
-  if (attr == NULL) return (int)false;
-  return attr->hasAttribute(std::string(attribute));
-}
-
-
-/** @endcond */
-
-LIBSBML_CPP_NAMESPACE_END
-
+/**
+ * @file    ExpectedAttributes.cpp
+ * @brief   Implementation of ExpectedAttributes, the class allowing the specification
+ *          of attributes to expect.
+ * @author  Ben Bornstein
+ * 
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ------------------------------------------------------------------------ -->
+ */
+
+
+#include <sbml/common/sbmlfwd.h>
+#include <sbml/common/common.h>
+#include <sbml/common/operationReturnValues.h>
+#include <sbml/ExpectedAttributes.h>
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+/** @cond doxygen-c-only */
+
+
+LIBSBML_EXTERN 
+ExpectedAttributes_t *
+ExpectedAttributes_create()
+{
+  return new ExpectedAttributes();
+}
+
+LIBSBML_EXTERN 
+ExpectedAttributes_t *
+ExpectedAttributes_clone(ExpectedAttributes_t *attr)
+{
+  if (attr == NULL) return NULL;
+  return new ExpectedAttributes(*attr);
+}
+
+LIBSBML_EXTERN 
+int
+ExpectedAttributes_add(ExpectedAttributes_t *attr, const char* attribute)
+{
+  if (attr == NULL || attribute == NULL) return LIBSBML_INVALID_OBJECT;
+  attr->add(std::string(attribute));
+  return LIBSBML_OPERATION_SUCCESS;
+}
+
+LIBSBML_EXTERN 
+char*
+ExpectedAttributes_get(ExpectedAttributes_t *attr, unsigned int index)
+{
+  if (attr == NULL) return NULL;
+  return safe_strdup(attr->get(index).c_str());
+}
+
+LIBSBML_EXTERN 
+int
+ExpectedAttributes_hasAttribute(ExpectedAttributes_t *attr, const char* attribute)
+{
+  if (attr == NULL) return (int)false;
+  return attr->hasAttribute(std::string(attribute));
+}
+
+
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_END
+


Property changes on: trunk/libsbml/src/sbml/ExpectedAttributes.cpp
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/sbml/ModifierSpeciesReference.cpp
===================================================================
--- trunk/libsbml/src/sbml/ModifierSpeciesReference.cpp	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/sbml/ModifierSpeciesReference.cpp	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,142 +1,142 @@
-/**
- * @file    ModifierSpeciesReference.cpp
- * @brief   Implementation of ModifierSpeciesReference. 
- * @author  Ben Bornstein
- *
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ---------------------------------------------------------------------- -->*/
-
-
-#include <sbml/xml/XMLNode.h>
-#include <sbml/xml/XMLAttributes.h>
-#include <sbml/xml/XMLInputStream.h>
-#include <sbml/xml/XMLOutputStream.h>
-
-#include <sbml/math/FormulaParser.h>
-#include <sbml/math/MathML.h>
-#include <sbml/math/ASTNode.h>
-
-#include <sbml/SBO.h>
-#include <sbml/SBMLVisitor.h>
-#include <sbml/SBMLError.h>
-#include <sbml/SBMLDocument.h>
-#include <sbml/Model.h>
-#include <sbml/ModifierSpeciesReference.h>
-#include <sbml/extension/SBasePlugin.h>
-
-/** @cond doxygen-ignored */
-
-using namespace std;
-
-/** @endcond */
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-
-ModifierSpeciesReference::ModifierSpeciesReference (unsigned int level, 
-                          unsigned int version) :
-  SimpleSpeciesReference(level, version)
-{
-  if (!hasValidLevelVersionNamespaceCombination())
-    throw SBMLConstructorException();
-}
-
-
-ModifierSpeciesReference::ModifierSpeciesReference (SBMLNamespaces *sbmlns) :
-  SimpleSpeciesReference(sbmlns)
-{
-  if (!hasValidLevelVersionNamespaceCombination())
-    throw SBMLConstructorException();
-
-  loadPlugins(sbmlns);
-}
-
-
-/*
- * Destroys this ModifierSpeciesReference.
- */
-ModifierSpeciesReference::~ModifierSpeciesReference ()
-{
-}
-
-
-/*
- * Accepts the given SBMLVisitor.
- *
- * @return the result of calling <code>v.visit()</code>, which indicates
- * whether or not the Visitor would like to visit the Reaction's next
- * ModifierSpeciesReference (if available).
- */
-bool
-ModifierSpeciesReference::accept (SBMLVisitor& v) const
-{
-  return v.visit(*this);
-}
-
-
-/*
- * @return a (deep) copy of this ModifierSpeciesReference.
- */
-ModifierSpeciesReference*
-ModifierSpeciesReference::clone () const
-{
-  return new ModifierSpeciesReference(*this);
-}
-
-
-/*
- * @return the typecode (int) of SBML objects contained in this ListOf or
- * (default).
- *
- * @see getElementName()
- */
-int
-ModifierSpeciesReference::getTypeCode () const
-{
-  return SBML_MODIFIER_SPECIES_REFERENCE;
-}
-
-
-/*
- * @return the name of this element ie "modifierSpeciesReference".
- 
- */
-const string&
-ModifierSpeciesReference::getElementName () const
-{
-  static const string name = "modifierSpeciesReference";
-  return name;
-}
-
-
-bool 
-ModifierSpeciesReference::hasRequiredAttributes() const
-{
-  bool allPresent = SimpleSpeciesReference::hasRequiredAttributes();
-
-  return allPresent;
-}
-
-
-LIBSBML_CPP_NAMESPACE_END
-
+/**
+ * @file    ModifierSpeciesReference.cpp
+ * @brief   Implementation of ModifierSpeciesReference. 
+ * @author  Ben Bornstein
+ *
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+
+#include <sbml/xml/XMLNode.h>
+#include <sbml/xml/XMLAttributes.h>
+#include <sbml/xml/XMLInputStream.h>
+#include <sbml/xml/XMLOutputStream.h>
+
+#include <sbml/math/FormulaParser.h>
+#include <sbml/math/MathML.h>
+#include <sbml/math/ASTNode.h>
+
+#include <sbml/SBO.h>
+#include <sbml/SBMLVisitor.h>
+#include <sbml/SBMLError.h>
+#include <sbml/SBMLDocument.h>
+#include <sbml/Model.h>
+#include <sbml/ModifierSpeciesReference.h>
+#include <sbml/extension/SBasePlugin.h>
+
+/** @cond doxygen-ignored */
+
+using namespace std;
+
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+
+ModifierSpeciesReference::ModifierSpeciesReference (unsigned int level, 
+                          unsigned int version) :
+  SimpleSpeciesReference(level, version)
+{
+  if (!hasValidLevelVersionNamespaceCombination())
+    throw SBMLConstructorException();
+}
+
+
+ModifierSpeciesReference::ModifierSpeciesReference (SBMLNamespaces *sbmlns) :
+  SimpleSpeciesReference(sbmlns)
+{
+  if (!hasValidLevelVersionNamespaceCombination())
+    throw SBMLConstructorException();
+
+  loadPlugins(sbmlns);
+}
+
+
+/*
+ * Destroys this ModifierSpeciesReference.
+ */
+ModifierSpeciesReference::~ModifierSpeciesReference ()
+{
+}
+
+
+/*
+ * Accepts the given SBMLVisitor.
+ *
+ * @return the result of calling <code>v.visit()</code>, which indicates
+ * whether or not the Visitor would like to visit the Reaction's next
+ * ModifierSpeciesReference (if available).
+ */
+bool
+ModifierSpeciesReference::accept (SBMLVisitor& v) const
+{
+  return v.visit(*this);
+}
+
+
+/*
+ * @return a (deep) copy of this ModifierSpeciesReference.
+ */
+ModifierSpeciesReference*
+ModifierSpeciesReference::clone () const
+{
+  return new ModifierSpeciesReference(*this);
+}
+
+
+/*
+ * @return the typecode (int) of SBML objects contained in this ListOf or
+ * (default).
+ *
+ * @see getElementName()
+ */
+int
+ModifierSpeciesReference::getTypeCode () const
+{
+  return SBML_MODIFIER_SPECIES_REFERENCE;
+}
+
+
+/*
+ * @return the name of this element ie "modifierSpeciesReference".
+ 
+ */
+const string&
+ModifierSpeciesReference::getElementName () const
+{
+  static const string name = "modifierSpeciesReference";
+  return name;
+}
+
+
+bool 
+ModifierSpeciesReference::hasRequiredAttributes() const
+{
+  bool allPresent = SimpleSpeciesReference::hasRequiredAttributes();
+
+  return allPresent;
+}
+
+
+LIBSBML_CPP_NAMESPACE_END
+


Property changes on: trunk/libsbml/src/sbml/ModifierSpeciesReference.cpp
___________________________________________________________________
Added: svn:eol-style
   + native

Modified: trunk/libsbml/src/sbml/ModifierSpeciesReference.h
===================================================================
--- trunk/libsbml/src/sbml/ModifierSpeciesReference.h	2013-01-29 08:01:44 UTC (rev 16980)
+++ trunk/libsbml/src/sbml/ModifierSpeciesReference.h	2013-01-29 08:17:51 UTC (rev 16981)
@@ -1,249 +1,249 @@
-/**
- * @file    ModifierSpeciesReference.h
- * @brief   Definitions of ModifierSpeciesReference. 
- * @author  Ben Bornstein
- *
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML.  Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2009-2013 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *  
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- *     Pasadena, CA, USA 
- *  
- * Copyright (C) 2002-2005 jointly by the following organizations: 
- *     1. California Institute of Technology, Pasadena, CA, USA
- *     2. Japan Science and Technology Agency, Japan
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation.  A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as http://sbml.org/software/libsbml/license.html
- * ------------------------------------------------------------------------ -->
- *
- * @class ModifierSpeciesReference
- * @brief LibSBML implementation of %SBML's %ModifierSpeciesReference construct.
- *
- * Sometimes a species appears in the kinetic rate formula of a reaction
- * but is itself neither created nor destroyed in that reaction (for
- * example, because it acts as a catalyst or inhibitor).  In SBML, all such
- * species are simply called @em modifiers without regard to the detailed
- * role of those species in the model.  The Reaction structure provides a
- * way to express which species act as modifiers in a given reaction.  This
- * is the purpose of the list of modifiers available in Reaction.  The list
- * contains instances of ModifierSpeciesReference structures.
- *
- * The ModifierSpeciesReference structure inherits the mandatory attribute
- * "species" and optional attributes "id" and "name" from the parent class
- * SimpleSpeciesReference.  See the description of SimpleSpeciesReference
- * for more information about these.
- *
- * The value of the "species" attribute must be the identifier of a species
- * defined in the enclosing Model; this species is designated as a modifier
- * for the current reaction.  A reaction may have any number of modifiers.
- * It is permissible for a modifier species to appear simultaneously in the
- * list of reactants and products of the same reaction where it is
- * designated as a modifier, as well as to appear in the list of reactants,
- * products and modifiers of other reactions in the model.
- *
- * 
- */
-
-
-#ifndef ModifierSpeciesReference_h
-#define ModifierSpeciesReference_h
-
-
-#include <sbml/common/extern.h>
-#include <sbml/common/sbmlfwd.h>
-
-
-#ifdef __cplusplus
-
-
-#include <string>
-
-#include <sbml/SimpleSpeciesReference.h>
-#include <sbml/SBMLVisitor.h>
-#include <sbml/ListOf.h>
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-class SBMLNamespaces;
-
-class LIBSBML_EXTERN ModifierSpeciesReference : public SimpleSpeciesReference
-{
-public:
-
-  /**
-   * Creates a new ModifierSpeciesReference using the given SBML @p level and @p version
-   * values.
-   *
-   * @param level an unsigned int, the SBML Level to assign to this ModifierSpeciesReference
-   *
-   * @param version an unsigned int, the SBML Version to assign to this
-   * ModifierSpeciesReference
-   * 
-   * @note Upon the addition of a ModifierSpeciesReference object to an
-   * SBMLDocument (e.g., using Reaction::addModifier(@if java ModifierSpeciesReference msr@...)), the
-   * SBML Level, SBML Version and XML namespace of the document @em
-   * override the values used when creating the ModifierSpeciesReference
-   * object via this constructor.  This is necessary to ensure that an SBML
-   * document is a consistent structure.  Nevertheless, the ability to
-   * supply the values at the time of creation of a
-   * ModifierSpeciesReference is an important aid to producing valid SBML.
-   * Knowledge of the intented SBML Level and Version determine whether it
-   * is valid to assign a particular value to an attribute, or whether it
-   * is valid to add an object to an existing SBMLDocument.
-   */
-  ModifierSpeciesReference (unsigned int level, unsigned int version);
-
-
-  /**
-   * Creates a new ModifierSpeciesReference using the given SBMLNamespaces object
-   * @p sbmlns.
-   *
-   * @param sbmlns an SBMLNamespaces object.
-   *
-   * @note Upon the addition of a ModifierSpeciesReference object to an
-   * SBMLDocument (e.g., using Reaction::addModifier(@if java ModifierSpeciesReference msr@...)), the
-   * SBML XML namespace of the document @em overrides the value used when
-   * creating the ModifierSpeciesReference object via this constructor.
-   * This is necessary to ensure that an SBML document is a consistent
-   * structure.  Nevertheless, the ability to supply the values at the time
-   * of creation of a ModifierSpeciesReference is an important aid to
-   * producing valid SBML.  Knowledge of the intented SBML Level and
-   * Version determine whether it is valid to assign a particular value to
-   * an attribute, or whether it is valid to add an object to an existing
-   * SBMLDocument.
-   */
-  ModifierSpeciesReference (SBMLNamespaces* sbmlns);
-
-
-  /**
-   * Destroys this ModifierSpeciesReference.
-   */
-  virtual ~ModifierSpeciesReference();
-
-
-  /**
-   * Accepts the given SBMLVisitor.
-   *
-   * @param v the SBMLVisitor instance to be used.
-   *
-   * @return the result of calling <code>v.visit()</code>.
-   */
-  virtual bool accept (SBMLVisitor& v) const;
-
-
-  /**
-   * Creates and returns a deep copy of this ModifierSpeciesReference
-   * instance.
-   *
-   * @return a (deep) copy of this ModifierSpeciesReference.
-   */
-  virtual ModifierSpeciesReference* clone () const;
-
-
-  /**
-   * Returns the libSBML type code for this %SBML object.
-   * 
-   * @if clike LibSBML attaches an identifying code to every kind of SBML
-   * object.  These are known as <em>SBML type codes</em>.  The set of
-   * possible type codes is defined in the enumeration #SBMLTypeCode_t.
-   * The names of the type codes all begin with the characters @c
-   * SBML_. @endif@... java LibSBML attaches an identifying code to every
-   * kind of SBML object.  These are known as <em>SBML type codes</em>.  In
-   * other languages, the set of type codes is stored in an enumeration; in
-   * the Java language interface for libSBML, the type codes are defined as

@@ Diff output truncated at 100000 characters. @@
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