/// 
///  @file    TestWriteSBML.cs
///  @brief   Write SBML unit tests
///  @author  Frank Bergmann (Csharp conversion)
///  @author  Akiya Jouraku (Csharp conversion)
///  @author  Ben Bornstein 
/// 
///  $Id: TestWriteSBML.cs 8825 2009-01-12 23:22:45Z ajouraku $
///  $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/csharp/test/sbml/TestWriteSBML.cs $
/// 
///  This test file was converted from src/sbml/test/TestWriteSBML.cpp
///  with the help of conversion sciprt (ctest_converter.pl).
/// 
/// <!---------------------------------------------------------------------------
///  This file is part of libSBML.  Please visit http://sbml.org for more
///  information about SBML, and the latest version of libSBML.
/// 
///  Copyright 2005-2009 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.IO;

  public class TestWriteSBML {
    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.Equals(b))
      {
        return;
      }
  
      throw new AssertionError();
    }

    static void assertNotEquals(object a, object b)
    {
      if ( (a == null) && (b == null) )
      {
        throw new AssertionError();
      }
      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();
    }

    private SBMLDocument D;
    private string S;
    private OStringStream OSS;
    private XMLOutputStream XOS;

    public string LV_L1v1()
    {
      return "level=\"1\" version=\"1\">\n";
    }

    public string LV_L1v2()
    {
      return "level=\"1\" version=\"2\">\n";
    }

    public string LV_L2v1()
    {
      return "level=\"2\" version=\"1\">\n";
    }

    public string LV_L2v2()
    {
      return "level=\"2\" version=\"2\">\n";
    }

    public string LV_L2v3()
    {
      return "level=\"2\" version=\"3\">\n";
    }

    public string NS_L1()
    {
      return "xmlns=\"http://www.sbml.org/sbml/level1\" ";
    }

    public string NS_L2v1()
    {
      return "xmlns=\"http://www.sbml.org/sbml/level2\" ";
    }

    public string NS_L2v2()
    {
      return "xmlns=\"http://www.sbml.org/sbml/level2/version2\" ";
    }

    public string NS_L2v3()
    {
      return "xmlns=\"http://www.sbml.org/sbml/level2/version3\" ";
    }

    public string SBML_END()
    {
      return "</sbml>\n";
    }

    public string SBML_START()
    {
      return "<sbml ";
    }

    public string XML_START()
    {
      return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
    }

    public string wrapSBML_L1v1(string s)
    {
      string r = XML_START();
      r += SBML_START();
      r += NS_L1();
      r += LV_L1v1();
      r += s;
      r += SBML_END();
      return r;
    }

    public string wrapSBML_L1v2(string s)
    {
      string r = XML_START();
      r += SBML_START();
      r += NS_L1();
      r += LV_L1v2();
      r += s;
      r += SBML_END();
      return r;
    }

    public string wrapSBML_L2v1(string s)
    {
      string r = XML_START();
      r += SBML_START();
      r += NS_L2v1();
      r += LV_L2v1();
      r += s;
      r += SBML_END();
      return r;
    }

    public string wrapSBML_L2v2(string s)
    {
      string r = XML_START();
      r += SBML_START();
      r += NS_L2v2();
      r += LV_L2v2();
      r += s;
      r += SBML_END();
      return r;
    }

    public string wrapSBML_L2v3(string s)
    {
      string r = XML_START();
      r += SBML_START();
      r += NS_L2v3();
      r += LV_L2v3();
      r += s;
      r += SBML_END();
      return r;
    }

    public string wrapXML(string s)
    {
      string r = XML_START();
      r += s;
      return r;
    }


  public double util_NaN()
  {
    double z = 0.0;
    return 0.0/z;
  }

  public double util_PosInf()
  {
    double z = 0.0;
    return 1.0/z;
  }

  public double util_NegInf()
  {
    double z = 0.0;
    return -1.0/z;
  }

  public bool equals(string s)
  {
    return s == OSS.str();
  }

  public bool equals(string s1, string s2)
  {
    return (s1 ==s2);
  }

    public void setUp()
    {
      D = new SBMLDocument();
      S = null;
      OSS = new OStringStream();
      XOS = new XMLOutputStream(OSS);
    }

    public void tearDown()
    {
      S = null;
    }

    public void test_WriteSBML_AlgebraicRule()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<algebraicRule formula=\"x + 1\"/>");
      AlgebraicRule r = new AlgebraicRule( "x + 1" );
      r.setSBMLDocument(D);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_AlgebraicRule_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<algebraicRule>\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <plus/>\n" + 
    "      <ci> x </ci>\n" + 
    "      <cn type=\"integer\"> 1 </cn>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</algebraicRule>");
      AlgebraicRule r = new AlgebraicRule( "x + 1" );
      r.setSBMLDocument(D);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_AlgebraicRule_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<algebraicRule sboTerm=\"SBO:0000004\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <plus/>\n" + 
    "      <ci> x </ci>\n" + 
    "      <cn type=\"integer\"> 1 </cn>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</algebraicRule>");
      AlgebraicRule r = new AlgebraicRule( "x + 1" );
      r.setSBOTerm(4);
      r.setSBMLDocument(D);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Compartment()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<compartment name=\"A\" volume=\"2.1\" outside=\"B\"/>"  
    );
      Compartment c = new Compartment( "A" );
      c.setSize(2.1);
      c.setOutside("B");
      c.setSBMLDocument(D);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_CompartmentType()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<compartmentType id=\"ct\"/>");
      CompartmentType ct = new CompartmentType();
      ct.setId("ct");
      ct.setSBOTerm(4);
      ct.setSBMLDocument(D);
      ct.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_CompartmentType_withSBO()
    {
      D.setLevelAndVersion(2,3);
      string expected = wrapXML("<compartmentType id=\"ct\" sboTerm=\"SBO:0000004\"/>");
      CompartmentType ct = new CompartmentType();
      ct.setId("ct");
      ct.setSBOTerm(4);
      ct.setSBMLDocument(D);
      ct.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_CompartmentVolumeRule()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<compartmentVolumeRule " + "formula=\"v + c\" type=\"rate\" compartment=\"c\"/>");
      D.createModel();
      D.getModel().createCompartment().setId("c");
      Rule r = D.getModel().createRateRule();
      r.setVariable("c");
      r.setFormula("v + c");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_CompartmentVolumeRule_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<assignmentRule variable=\"c\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <plus/>\n" + 
    "      <ci> v </ci>\n" + 
    "      <ci> c </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</assignmentRule>");
      D.createModel();
      D.getModel().createCompartment().setId("c");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("c");
      r.setFormula("v + c");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_CompartmentVolumeRule_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<assignmentRule variable=\"c\" sboTerm=\"SBO:0000005\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <plus/>\n" + 
    "      <ci> v </ci>\n" + 
    "      <ci> c </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</assignmentRule>");
      D.createModel();
      D.getModel().createCompartment().setId("c");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("c");
      r.setFormula("v + c");
      r.setSBOTerm(5);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_CompartmentVolumeRule_defaults()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<compartmentVolumeRule formula=\"v + c\" compartment=\"c\"/>"  
    );
      D.createModel();
      D.getModel().createCompartment().setId("c");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("c");
      r.setFormula("v + c");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Compartment_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<compartment id=\"M\" spatialDimensions=\"2\" size=\"2.5\"/>"  
    );
      Compartment c = new Compartment( "M" );
      c.setSize(2.5);
      c.setSpatialDimensions(2);
      c.setSBMLDocument(D);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Compartment_L2v1_constant()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<compartment id=\"cell\" size=\"1.2\" constant=\"false\"/>"  
    );
      Compartment c = new Compartment( "cell" );
      c.setSize(1.2);
      c.setConstant(false);
      c.setSBMLDocument(D);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Compartment_L2v1_unsetSize()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<compartment id=\"A\"/>");
      Compartment c = new Compartment();
      c.setId("A");
      c.unsetSize();
      c.setSBMLDocument(D);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Compartment_L2v2_compartmentType()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<compartment id=\"cell\" compartmentType=\"ct\"/>"  
    );
      Compartment c = new Compartment( "cell" );
      c.setCompartmentType("ct");
      c.setSBMLDocument(D);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Compartment_L2v3_SBO()
    {
      D.setLevelAndVersion(2,3);
      string expected = wrapXML("<compartment id=\"cell\" sboTerm=\"SBO:0000005\"/>"  
    );
      Compartment c = new Compartment( "cell" );
      c.setSBOTerm(5);
      c.setSBMLDocument(D);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Compartment_unsetVolume()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<compartment name=\"A\"/>");
      Compartment c = new Compartment();
      c.setId("A");
      c.unsetVolume();
      c.setSBMLDocument(D);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Constraint()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<constraint sboTerm=\"SBO:0000064\"/>");
      Constraint ct = new Constraint();
      ct.setSBOTerm(64);
      ct.setSBMLDocument(D);
      ct.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Constraint_full()
    {
      string expected = wrapXML("<constraint sboTerm=\"SBO:0000064\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <leq/>\n" + 
    "      <ci> P1 </ci>\n" + 
    "      <ci> t </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "  <message>\n" + 
    "    <p xmlns=\"http://www.w3.org/1999/xhtml\"> Species P1 is out of range </p>\n" + 
    "  </message>\n" + 
    "</constraint>");
      Constraint c = new Constraint();
      ASTNode node = libsbml.parseFormula("leq(P1,t)");
      c.setMath(node);
      c.setSBOTerm(64);
      XMLNode text = XMLNode.convertStringToXMLNode(" Species P1 is out of range ");
      XMLTriple triple = new XMLTriple("p", "http://www.w3.org/1999/xhtml", "");
      XMLAttributes att = new XMLAttributes();
      att.add("xmlns", "http://www.w3.org/1999/xhtml");
      XMLNode p = new XMLNode(triple,att);
      p.addChild(text);
      XMLTriple triple1 = new XMLTriple("message", "", "");
      XMLAttributes att1 = new XMLAttributes();
      XMLNode message = new XMLNode(triple1,att1);
      message.addChild(p);
      c.setMessage(message);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Constraint_math()
    {
      string expected = wrapXML("<constraint>\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <leq/>\n" + 
    "      <ci> P1 </ci>\n" + 
    "      <ci> t </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</constraint>");
      Constraint c = new Constraint();
      ASTNode node = libsbml.parseFormula("leq(P1,t)");
      c.setMath(node);
      c.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event()
    {
      string expected = wrapXML("<event id=\"e\"/>");
      Event e = new Event();
      e.setId("e");
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_WithSBO()
    {
      string expected = wrapXML("<event id=\"e\" sboTerm=\"SBO:0000076\"/>");
      Event e = new Event();
      e.setId("e");
      e.setSBOTerm(76);
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_WithUseValuesFromTriggerTime()
    {
      string expected = wrapXML("<event id=\"e\" useValuesFromTriggerTime=\"false\"/>");
      D.setLevelAndVersion(2,4);
      Event e = new Event();
      e.setId("e");
      e.setUseValuesFromTriggerTime(false);
      e.setSBMLDocument(D);
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_both()
    {
      string expected = wrapXML("<event id=\"e\">\n" + 
    "  <trigger>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <apply>\n" + 
    "        <leq/>\n" + 
    "        <ci> P1 </ci>\n" + 
    "        <ci> t </ci>\n" + 
    "      </apply>\n" + 
    "    </math>\n" + 
    "  </trigger>\n" + 
    "  <delay>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <cn type=\"integer\"> 5 </cn>\n" + 
    "    </math>\n" + 
    "  </delay>\n" + 
    "</event>");
      Event e = new Event( "e" );
      ASTNode node1 = libsbml.parseFormula("leq(P1,t)");
      Trigger t = new Trigger( node1 );
      ASTNode node = libsbml.parseFormula("5");
      Delay d = new Delay( node );
      e.setDelay(d);
      e.setTrigger(t);
      e.setTimeUnits("second");
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_delay()
    {
      string expected = wrapXML("<event id=\"e\">\n" + 
    "  <delay>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <cn type=\"integer\"> 5 </cn>\n" + 
    "    </math>\n" + 
    "  </delay>\n" + 
    "</event>");
      Event e = new Event( "e" );
      ASTNode node = libsbml.parseFormula("5");
      Delay d = new Delay( node );
      e.setDelay(d);
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_delayWithSBO()
    {
      string expected = wrapXML("<event id=\"e\">\n" + 
    "  <delay sboTerm=\"SBO:0000064\">\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <cn type=\"integer\"> 5 </cn>\n" + 
    "    </math>\n" + 
    "  </delay>\n" + 
    "</event>");
      Event e = new Event( "e" );
      ASTNode node = libsbml.parseFormula("5");
      Delay d = new Delay( node );
      d.setSBOTerm(64);
      e.setDelay(d);
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_full()
    {
      string expected = wrapXML("<event id=\"e\">\n" + 
    "  <trigger>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <apply>\n" + 
    "        <leq/>\n" + 
    "        <ci> P1 </ci>\n" + 
    "        <ci> t </ci>\n" + 
    "      </apply>\n" + 
    "    </math>\n" + 
    "  </trigger>\n" + 
    "  <listOfEventAssignments>\n" + 
    "    <eventAssignment variable=\"k2\" sboTerm=\"SBO:0000064\">\n" + 
    "      <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "        <cn type=\"integer\"> 0 </cn>\n" + 
    "      </math>\n" + 
    "    </eventAssignment>\n" + 
    "  </listOfEventAssignments>\n" + 
    "</event>");
      Event e = new Event( "e" );
      ASTNode node = libsbml.parseFormula("leq(P1,t)");
      Trigger t = new Trigger( node );
      ASTNode math = libsbml.parseFormula("0");
      EventAssignment ea = new EventAssignment( "k2",math );
      ea.setSBOTerm(64);
      e.setTrigger(t);
      e.addEventAssignment(ea);
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_trigger()
    {
      string expected = wrapXML("<event id=\"e\">\n" + 
    "  <trigger>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <apply>\n" + 
    "        <leq/>\n" + 
    "        <ci> P1 </ci>\n" + 
    "        <ci> t </ci>\n" + 
    "      </apply>\n" + 
    "    </math>\n" + 
    "  </trigger>\n" + 
    "</event>");
      Event e = new Event( "e" );
      ASTNode node = libsbml.parseFormula("leq(P1,t)");
      Trigger t = new Trigger( node );
      e.setTrigger(t);
      e.setTimeUnits("second");
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Event_trigger_withSBO()
    {
      string expected = wrapXML("<event id=\"e\">\n" + 
    "  <trigger sboTerm=\"SBO:0000064\">\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <apply>\n" + 
    "        <leq/>\n" + 
    "        <ci> P1 </ci>\n" + 
    "        <ci> t </ci>\n" + 
    "      </apply>\n" + 
    "    </math>\n" + 
    "  </trigger>\n" + 
    "</event>");
      Event e = new Event( "e" );
      ASTNode node = libsbml.parseFormula("leq(P1,t)");
      Trigger t = new Trigger( node );
      t.setSBOTerm(64);
      e.setTrigger(t);
      e.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_FunctionDefinition()
    {
      string expected = wrapXML("<functionDefinition id=\"pow3\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <lambda>\n" + 
    "      <bvar>\n" + 
    "        <ci> x </ci>\n" + 
    "      </bvar>\n" + 
    "      <apply>\n" + 
    "        <power/>\n" + 
    "        <ci> x </ci>\n" + 
    "        <cn type=\"integer\"> 3 </cn>\n" + 
    "      </apply>\n" + 
    "    </lambda>\n" + 
    "  </math>\n" + 
    "</functionDefinition>");
      FunctionDefinition fd = new FunctionDefinition( "pow3", "lambda(x, x^3)" );
      fd.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_FunctionDefinition_withSBO()
    {
      string expected = wrapXML("<functionDefinition id=\"pow3\" sboTerm=\"SBO:0000064\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <lambda>\n" + 
    "      <bvar>\n" + 
    "        <ci> x </ci>\n" + 
    "      </bvar>\n" + 
    "      <apply>\n" + 
    "        <power/>\n" + 
    "        <ci> x </ci>\n" + 
    "        <cn type=\"integer\"> 3 </cn>\n" + 
    "      </apply>\n" + 
    "    </lambda>\n" + 
    "  </math>\n" + 
    "</functionDefinition>");
      FunctionDefinition fd = new FunctionDefinition( "pow3", "lambda(x, x^3)" );
      fd.setSBOTerm(64);
      fd.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_INF()
    {
      string expected = wrapXML("<parameter id=\"p\" value=\"INF\"/>");
      Parameter p = new Parameter( "p", util_PosInf() );
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_InitialAssignment()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<initialAssignment symbol=\"c\" sboTerm=\"SBO:0000064\"/>");
      InitialAssignment ia = new InitialAssignment();
      ia.setSBOTerm(64);
      ia.setSymbol("c");
      ia.setSBMLDocument(D);
      ia.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_InitialAssignment_math()
    {
      string expected = wrapXML("<initialAssignment symbol=\"c\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <plus/>\n" + 
    "      <ci> a </ci>\n" + 
    "      <ci> b </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</initialAssignment>");
      InitialAssignment ia = new InitialAssignment();
      ASTNode node = libsbml.parseFormula("a + b");
      ia.setMath(node);
      ia.setSymbol("c");
      ia.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_KineticLaw()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<kineticLaw formula=\"k * e\" timeUnits=\"second\" " + "substanceUnits=\"item\"/>");
      KineticLaw kl = new KineticLaw( "k * e", "second", "item" );
      kl.setSBMLDocument(D);
      kl.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_KineticLaw_ListOfParameters()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<kineticLaw formula=\"nk * e\" timeUnits=\"second\" " + 
    "substanceUnits=\"item\">\n" + 
    "  <listOfParameters>\n" + 
    "    <parameter name=\"n\" value=\"1.2\"/>\n" + 
    "  </listOfParameters>\n" + 
    "</kineticLaw>");
      KineticLaw kl = new KineticLaw( "nk * e", "second", "item" );
      kl.setSBMLDocument(D);
      Parameter p = new Parameter( "n",1.2 );
      kl.addParameter(p);
      kl.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_KineticLaw_l2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<kineticLaw timeUnits=\"second\" substanceUnits=\"item\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <divide/>\n" + 
    "      <apply>\n" + 
    "        <times/>\n" + 
    "        <ci> vm </ci>\n" + 
    "        <ci> s1 </ci>\n" + 
    "      </apply>\n" + 
    "      <apply>\n" + 
    "        <plus/>\n" + 
    "        <ci> km </ci>\n" + 
    "        <ci> s1 </ci>\n" + 
    "      </apply>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</kineticLaw>");
      KineticLaw kl = new KineticLaw();
      kl.setTimeUnits("second");
      kl.setSubstanceUnits("item");
      kl.setFormula("(vm * s1)/(km + s1)");
      kl.setSBMLDocument(D);
      kl.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_KineticLaw_skipOptional()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<kineticLaw formula=\"k * e\"/>");
      KineticLaw kl = new KineticLaw( "k * e" );
      kl.setSBMLDocument(D);
      kl.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_KineticLaw_withSBO()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<kineticLaw sboTerm=\"SBO:0000001\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <divide/>\n" + 
    "      <apply>\n" + 
    "        <times/>\n" + 
    "        <ci> vm </ci>\n" + 
    "        <ci> s1 </ci>\n" + 
    "      </apply>\n" + 
    "      <apply>\n" + 
    "        <plus/>\n" + 
    "        <ci> km </ci>\n" + 
    "        <ci> s1 </ci>\n" + 
    "      </apply>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</kineticLaw>");
      KineticLaw kl = new KineticLaw();
      kl.setFormula("(vm * s1)/(km + s1)");
      kl.setSBOTerm(1);
      kl.setSBMLDocument(D);
      kl.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Model()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapSBML_L1v1("  <model name=\"Branch\"/>\n");
      D.createModel("Branch");
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_Model_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapSBML_L2v1("  <model id=\"Branch\"/>\n");
      D.createModel("Branch");
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_Model_L2v1_skipOptional()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapSBML_L2v1("  <model/>\n");
      D.createModel();
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_Model_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapSBML_L2v2("  <model id=\"Branch\" sboTerm=\"SBO:0000004\"/>\n");
      Model m = D.createModel("Branch");
      m.setSBOTerm(4);
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_Model_skipOptional()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapSBML_L1v2("  <model/>\n");
      D.createModel();
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_NaN()
    {
      string expected = wrapXML("<parameter id=\"p\" value=\"NaN\"/>");
      Parameter p = new Parameter( "p", util_NaN() );
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_NegINF()
    {
      string expected = wrapXML("<parameter id=\"p\" value=\"-INF\"/>");
      Parameter p = new Parameter( "p", util_NegInf() );
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Parameter()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<parameter name=\"Km1\" value=\"2.3\" units=\"second\"/>"  
    );
      Parameter p = new Parameter( "Km1",2.3, "second" );
      p.setSBMLDocument(D);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_ParameterRule()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<parameterRule " + "formula=\"p * t\" type=\"rate\" name=\"p\"/>");
      D.createModel();
      D.getModel().createParameter().setId("p");
      Rule r = D.getModel().createRateRule();
      r.setVariable("p");
      r.setFormula("p * t");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_ParameterRule_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<rateRule variable=\"p\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <times/>\n" + 
    "      <ci> p </ci>\n" + 
    "      <ci> t </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</rateRule>");
      D.createModel();
      D.getModel().createParameter().setId("p");
      Rule r = D.getModel().createRateRule();
      r.setVariable("p");
      r.setFormula("p * t");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_ParameterRule_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<rateRule variable=\"p\" sboTerm=\"SBO:0000007\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <times/>\n" + 
    "      <ci> p </ci>\n" + 
    "      <ci> t </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</rateRule>");
      D.createModel();
      D.getModel().createParameter().setId("p");
      Rule r = D.getModel().createRateRule();
      r.setVariable("p");
      r.setFormula("p * t");
      r.setSBOTerm(7);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_ParameterRule_defaults()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<parameterRule formula=\"p * t\" name=\"p\"/>"  
    );
      D.createModel();
      D.getModel().createParameter().setId("p");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("p");
      r.setFormula("p * t");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Parameter_L1v1_required()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<parameter name=\"Km1\" value=\"NaN\"/>"  
    );
      Parameter p = new Parameter();
      p.setId("Km1");
      p.unsetValue();
      p.setSBMLDocument(D);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Parameter_L1v2_skipOptional()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<parameter name=\"Km1\"/>");
      Parameter p = new Parameter();
      p.setId("Km1");
      p.unsetValue();
      p.setSBMLDocument(D);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Parameter_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<parameter id=\"Km1\" value=\"2.3\" units=\"second\"/>"  
    );
      Parameter p = new Parameter( "Km1",2.3, "second" );
      p.setSBMLDocument(D);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Parameter_L2v1_constant()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<parameter id=\"x\" constant=\"false\"/>");
      Parameter p = new Parameter( "x" );
      p.setConstant(false);
      p.setSBMLDocument(D);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Parameter_L2v1_skipOptional()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<parameter id=\"Km1\"/>");
      Parameter p = new Parameter( "Km1" );
      p.setSBMLDocument(D);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Parameter_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<parameter id=\"Km1\" value=\"2.3\" units=\"second\" sboTerm=\"SBO:0000002\"/>"  
    );
      Parameter p = new Parameter( "Km1",2.3, "second" );
      p.setSBOTerm(2);
      p.setSBMLDocument(D);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Reaction()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<reaction name=\"r\" reversible=\"false\" fast=\"true\"/>"  
    );
      Reaction r = new Reaction( "r", "",null,false );
      r.setFast(true);
      r.setSBMLDocument(D);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Reaction_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<reaction id=\"r\" reversible=\"false\"/>"  
    );
      Reaction r = new Reaction( "r", "",null,false );
      r.setSBMLDocument(D);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Reaction_L2v1_full()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<reaction id=\"v1\">\n" + 
    "  <listOfReactants>\n" + 
    "    <speciesReference species=\"x0\"/>\n" + 
    "  </listOfReactants>\n" + 
    "  <listOfProducts>\n" + 
    "    <speciesReference species=\"s1\"/>\n" + 
    "  </listOfProducts>\n" + 
    "  <listOfModifiers>\n" + 
    "    <modifierSpeciesReference species=\"m1\"/>\n" + 
    "  </listOfModifiers>\n" + 
    "  <kineticLaw>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <apply>\n" + 
    "        <divide/>\n" + 
    "        <apply>\n" + 
    "          <times/>\n" + 
    "          <ci> vm </ci>\n" + 
    "          <ci> s1 </ci>\n" + 
    "        </apply>\n" + 
    "        <apply>\n" + 
    "          <plus/>\n" + 
    "          <ci> km </ci>\n" + 
    "          <ci> s1 </ci>\n" + 
    "        </apply>\n" + 
    "      </apply>\n" + 
    "    </math>\n" + 
    "  </kineticLaw>\n" + 
    "</reaction>");
      D.createModel();
      Reaction r = D.getModel().createReaction();
      r.setId("v1");
      r.setReversible(true);
      r.createReactant().setSpecies("x0");
      r.createProduct().setSpecies("s1");
      r.createModifier().setSpecies("m1");
      r.createKineticLaw().setFormula("(vm * s1)/(km + s1)");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Reaction_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<reaction id=\"r\" name=\"r1\" reversible=\"false\" fast=\"true\" sboTerm=\"SBO:0000064\"/>"  
    );
      Reaction r = new Reaction( "r", "r1",null,false );
      r.setFast(true);
      r.setSBOTerm(64);
      r.setSBMLDocument(D);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Reaction_defaults()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<reaction name=\"r\"/>");
      Reaction r = new Reaction();
      r.setId("r");
      r.setSBMLDocument(D);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Reaction_full()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<reaction name=\"v1\">\n" + 
    "  <listOfReactants>\n" + 
    "    <speciesReference species=\"x0\"/>\n" + 
    "  </listOfReactants>\n" + 
    "  <listOfProducts>\n" + 
    "    <speciesReference species=\"s1\"/>\n" + 
    "  </listOfProducts>\n" + 
    "  <kineticLaw formula=\"(vm * s1)/(km + s1)\"/>\n" + 
    "</reaction>");
      D.createModel();
      Reaction r = D.getModel().createReaction();
      r.setId("v1");
      r.setReversible(true);
      r.createReactant().setSpecies("x0");
      r.createProduct().setSpecies("s1");
      r.createKineticLaw().setFormula("(vm * s1)/(km + s1)");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SBMLDocument_L1v1()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level1\" " + "level=\"1\" version=\"1\"/>\n");
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_SBMLDocument_L1v2()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level1\" " + "level=\"1\" version=\"2\"/>\n");
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_SBMLDocument_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2\" " + "level=\"2\" version=\"1\"/>\n");
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_SBMLDocument_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version2\" " + "level=\"2\" version=\"2\"/>\n");
      S = libsbml.writeSBMLToString(D);
      assertEquals( true, equals(expected,S) );
    }

    public void test_WriteSBML_Species()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<species name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"" + " units=\"mole\" boundaryCondition=\"true\" charge=\"2\"/>");
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setInitialAmount(0.7);
      s.setUnits("mole");
      s.setBoundaryCondition(true);
      s.setCharge(2);
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesConcentrationRule()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<speciesConcentrationRule " + "formula=\"t * s\" type=\"rate\" species=\"s\"/>");
      D.createModel();
      D.getModel().createSpecies().setId("s");
      Rule r = D.getModel().createRateRule();
      r.setVariable("s");
      r.setFormula("t * s");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesConcentrationRule_L1v1()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<specieConcentrationRule formula=\"t * s\" specie=\"s\"/>"  
    );
      D.createModel();
      D.getModel().createSpecies().setId("s");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("s");
      r.setFormula("t * s");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesConcentrationRule_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<assignmentRule variable=\"s\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <times/>\n" + 
    "      <ci> t </ci>\n" + 
    "      <ci> s </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</assignmentRule>");
      D.createModel();
      D.getModel().createSpecies().setId("s");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("s");
      r.setFormula("t * s");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesConcentrationRule_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<assignmentRule variable=\"s\" sboTerm=\"SBO:0000006\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <times/>\n" + 
    "      <ci> t </ci>\n" + 
    "      <ci> s </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</assignmentRule>");
      D.createModel();
      D.getModel().createSpecies().setId("s");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("s");
      r.setFormula("t * s");
      r.setSBOTerm(6);
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesConcentrationRule_defaults()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<speciesConcentrationRule formula=\"t * s\" species=\"s\"/>"  
    );
      D.createModel();
      D.getModel().createSpecies().setId("s");
      Rule r = D.getModel().createAssignmentRule();
      r.setVariable("s");
      r.setFormula("t * s");
      r.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<speciesReference species=\"s\" stoichiometry=\"3\" denominator=\"2\"/>"  
    );
      SpeciesReference sr = new SpeciesReference( "s",3,2 );
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference_L1v1()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<specieReference specie=\"s\" stoichiometry=\"3\" denominator=\"2\"/>"  
    );
      SpeciesReference sr = new SpeciesReference( "s",3,2 );
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference_L2v1_1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<speciesReference species=\"s\">\n" + 
    "  <stoichiometryMath>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <cn type=\"rational\"> 3 <sep/> 2 </cn>\n" + 
    "    </math>\n" + 
    "  </stoichiometryMath>\n" + 
    "</speciesReference>");
      SpeciesReference sr = new SpeciesReference( "s",3,2 );
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference_L2v1_2()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<speciesReference species=\"s\" stoichiometry=\"3.2\"/>"  
    );
      SpeciesReference sr = new SpeciesReference( "s",3.2 );
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference_L2v1_3()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<speciesReference species=\"s\">\n" + 
    "  <stoichiometryMath>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <apply>\n" + 
    "        <divide/>\n" + 
    "        <cn type=\"integer\"> 1 </cn>\n" + 
    "        <ci> d </ci>\n" + 
    "      </apply>\n" + 
    "    </math>\n" + 
    "  </stoichiometryMath>\n" + 
    "</speciesReference>");
      SpeciesReference sr = new SpeciesReference( "s" );
      ASTNode math = libsbml.parseFormula("1/d");
      StoichiometryMath stoich = new StoichiometryMath();
      stoich.setMath(math);
      sr.setStoichiometryMath(stoich);
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference_L2v2_1()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<speciesReference id=\"ss\" name=\"odd\" sboTerm=\"SBO:0000009\" species=\"s\">\n" + 
    "  <stoichiometryMath>\n" + 
    "    <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "      <cn type=\"rational\"> 3 <sep/> 2 </cn>\n" + 
    "    </math>\n" + 
    "  </stoichiometryMath>\n" + 
    "</speciesReference>");
      SpeciesReference sr = new SpeciesReference( "s",3,2 );
      sr.setId("ss");
      sr.setName("odd");
      sr.setSBOTerm(9);
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference_L2v3_1()
    {
      D.setLevelAndVersion(2,3);
      string expected = wrapXML("<speciesReference id=\"ss\" name=\"odd\" sboTerm=\"SBO:0000009\" species=\"s\" stoichiometry=\"3.2\"/>"  
    );
      SpeciesReference sr = new SpeciesReference( "s",3.2 );
      sr.setId("ss");
      sr.setName("odd");
      sr.setSBOTerm(9);
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesReference_defaults()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<speciesReference species=\"s\"/>");
      SpeciesReference sr = new SpeciesReference( "s" );
      sr.setSBMLDocument(D);
      sr.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesType()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<speciesType id=\"st\"/>");
      SpeciesType st = new SpeciesType();
      st.setId("st");
      st.setSBOTerm(4);
      st.setSBMLDocument(D);
      st.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_SpeciesType_withSBO()
    {
      D.setLevelAndVersion(2,3);
      string expected = wrapXML("<speciesType id=\"st\" sboTerm=\"SBO:0000004\"/>");
      SpeciesType st = new SpeciesType();
      st.setId("st");
      st.setSBOTerm(4);
      st.setSBMLDocument(D);
      st.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Species_L1v1()
    {
      D.setLevelAndVersion(1,1);
      string expected = wrapXML("<specie name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"" + " units=\"mole\" boundaryCondition=\"true\" charge=\"2\"/>");
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setInitialAmount(0.7);
      s.setUnits("mole");
      s.setBoundaryCondition(true);
      s.setCharge(2);
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Species_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<species id=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\" " + "substanceUnits=\"mole\" constant=\"true\"/>");
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setInitialAmount(0.7);
      s.setSubstanceUnits("mole");
      s.setConstant(true);
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Species_L2v1_skipOptional()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<species id=\"Ca2\" compartment=\"cell\"/>"  
    );
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Species_L2v2()
    {
      D.setLevelAndVersion(2,2);
      string expected = wrapXML("<species id=\"Ca2\" speciesType=\"st\" compartment=\"cell\" initialAmount=\"0.7\" " + "substanceUnits=\"mole\" constant=\"true\"/>");
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setInitialAmount(0.7);
      s.setSubstanceUnits("mole");
      s.setConstant(true);
      s.setSpeciesType("st");
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Species_L2v3()
    {
      D.setLevelAndVersion(2,3);
      string expected = wrapXML("<species id=\"Ca2\" compartment=\"cell\" sboTerm=\"SBO:0000007\"/>"  
    );
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setSBOTerm(7);
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Species_defaults()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<species name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"" + " units=\"mole\" charge=\"2\"/>");
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setInitialAmount(0.7);
      s.setUnits("mole");
      s.setCharge(2);
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Species_skipOptional()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<species name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"/>"  
    );
      Species s = new Species( "Ca2" );
      s.setCompartment("cell");
      s.setInitialAmount(0.7);
      s.setSBMLDocument(D);
      s.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_StoichiometryMath()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<stoichiometryMath>\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <divide/>\n" + 
    "      <cn type=\"integer\"> 1 </cn>\n" + 
    "      <ci> d </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</stoichiometryMath>");
      ASTNode math = libsbml.parseFormula("1/d");
      StoichiometryMath stoich = new StoichiometryMath(math);
      stoich.setSBMLDocument(D);
      stoich.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_StoichiometryMath_withSBO()
    {
      D.setLevelAndVersion(2,3);
      string expected = wrapXML("<stoichiometryMath sboTerm=\"SBO:0000333\">\n" + 
    "  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" + 
    "    <apply>\n" + 
    "      <divide/>\n" + 
    "      <cn type=\"integer\"> 1 </cn>\n" + 
    "      <ci> d </ci>\n" + 
    "    </apply>\n" + 
    "  </math>\n" + 
    "</stoichiometryMath>");
      ASTNode math = libsbml.parseFormula("1/d");
      StoichiometryMath stoich = new StoichiometryMath(math);
      stoich.setSBOTerm(333);
      stoich.setSBMLDocument(D);
      stoich.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Unit()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<unit kind=\"kilogram\" exponent=\"2\" scale=\"-3\"/>"  
    );
      Unit u = new Unit( "kilogram",2,-3 );
      u.setSBMLDocument(D);
      u.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_UnitDefinition()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<unitDefinition name=\"mmls\"/>");
      UnitDefinition ud = new UnitDefinition( "mmls" );
      ud.setSBMLDocument(D);
      ud.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_UnitDefinition_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<unitDefinition id=\"mmls\"/>");
      UnitDefinition ud = new UnitDefinition( "mmls" );
      ud.setSBMLDocument(D);
      ud.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_UnitDefinition_L2v1_full()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<unitDefinition id=\"Fahrenheit\">\n" + 
    "  <listOfUnits>\n" + 
    "    <unit kind=\"Celsius\" multiplier=\"1.8\" offset=\"32\"/>\n" + 
    "  </listOfUnits>\n" + 
    "</unitDefinition>");
      Unit u1 = new Unit( "Celsius",1,0,1.8 );
      u1.setOffset(32);
      UnitDefinition ud = new UnitDefinition( "Fahrenheit" );
      ud.addUnit(u1);
      ud.setSBMLDocument(D);
      ud.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_UnitDefinition_full()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<unitDefinition name=\"mmls\">\n" + 
    "  <listOfUnits>\n" + 
    "    <unit kind=\"mole\" scale=\"-3\"/>\n" + 
    "    <unit kind=\"liter\" exponent=\"-1\"/>\n" + 
    "    <unit kind=\"second\" exponent=\"-1\"/>\n" + 
    "  </listOfUnits>\n" + 
    "</unitDefinition>");
      UnitDefinition ud = new UnitDefinition( "mmls" );
      Unit u1 = new Unit( "mole"  ,1,-3 );
      Unit u2 = new Unit( "liter" ,-1 );
      Unit u3 = new Unit( "second",-1 );
      ud.addUnit(u1);
      ud.addUnit(u2);
      ud.addUnit(u3);
      ud.setSBMLDocument(D);
      ud.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Unit_L2v1()
    {
      D.setLevelAndVersion(2,1);
      string expected = wrapXML("<unit kind=\"Celsius\" multiplier=\"1.8\" offset=\"32\"/>"  
    );
      Unit u = new Unit( "Celsius",1,0,1.8 );
      u.setOffset(32);
      u.setSBMLDocument(D);
      u.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Unit_defaults()
    {
      D.setLevelAndVersion(1,2);
      string expected = wrapXML("<unit kind=\"kilogram\"/>");
      Unit u = new Unit( "kilogram",1,0 );
      u.setSBMLDocument(D);
      u.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_Unit_l2v3()
    {
      D.setLevelAndVersion(2,3);
      string expected = wrapXML("<unit kind=\"kilogram\" exponent=\"2\" scale=\"-3\"/>"  
    );
      Unit u = new Unit( "kilogram",2,-3 );
      u.setOffset(32);
      u.setSBMLDocument(D);
      u.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_bzip2()
    {
      uint filenum = 12;
      string[] file = {
                        "../../../examples/sample-models/from-spec/level-2/algebraicrules.xml",
                        "../../../examples/sample-models/from-spec/level-2/assignmentrules.xml",
                        "../../../examples/sample-models/from-spec/level-2/boundarycondition.xml",
                        "../../../examples/sample-models/from-spec/level-2/delay.xml",
                        "../../../examples/sample-models/from-spec/level-2/dimerization.xml",
                        "../../../examples/sample-models/from-spec/level-2/enzymekinetics.xml",
                        "../../../examples/sample-models/from-spec/level-2/events.xml",
                        "../../../examples/sample-models/from-spec/level-2/functiondef.xml",
                        "../../../examples/sample-models/from-spec/level-2/multicomp.xml",
                        "../../../examples/sample-models/from-spec/level-2/overdetermined.xml",
                        "../../../examples/sample-models/from-spec/level-2/twodimensional.xml",
                        "../../../examples/sample-models/from-spec/level-2/units.xml"
      };
      string bzfile = "test.xml.bz2";
      for(uint i = 0; i < filenum; i++) 
      { 
        SBMLDocument d = libsbml.readSBML(file[i]); 
        assertTrue( d != null );
        if (! SBMLWriter.hasBzip2())
        {
          assertTrue( libsbml.writeSBML(d, bzfile) == 0 );
          d = null;
          continue;
        }
        int result = libsbml.writeSBML(d, bzfile);
        assertTrue( result != 0);
        SBMLDocument dg = libsbml.readSBML(bzfile);
        assertTrue( dg != null );
        assertTrue( ( dg.toSBML() != d.toSBML() ) == false );
        d = null;
        dg = null;
      }
  }


    public void test_WriteSBML_error()
    {
      SBMLDocument d = new SBMLDocument();
      SBMLWriter w = new SBMLWriter();
      assertEquals( false, w.writeSBML(d, "/tmp/impossible/path/should/fail") );
      assertTrue( d.getNumErrors() == 1 );
      assertTrue( d.getError(0).getErrorId() == libsbml.XMLFileUnwritable );
      d = null;
      w = null;
    }

    public void test_WriteSBML_gzip()
    {
      uint filenum = 12;
      string[] file = {
                        "../../../examples/sample-models/from-spec/level-2/algebraicrules.xml",
                        "../../../examples/sample-models/from-spec/level-2/assignmentrules.xml",
                        "../../../examples/sample-models/from-spec/level-2/boundarycondition.xml",
                        "../../../examples/sample-models/from-spec/level-2/delay.xml",
                        "../../../examples/sample-models/from-spec/level-2/dimerization.xml",
                        "../../../examples/sample-models/from-spec/level-2/enzymekinetics.xml",
                        "../../../examples/sample-models/from-spec/level-2/events.xml",
                        "../../../examples/sample-models/from-spec/level-2/functiondef.xml",
                        "../../../examples/sample-models/from-spec/level-2/multicomp.xml",
                        "../../../examples/sample-models/from-spec/level-2/overdetermined.xml",
                        "../../../examples/sample-models/from-spec/level-2/twodimensional.xml",
                        "../../../examples/sample-models/from-spec/level-2/units.xml"
      };
      string gzfile = "test.xml.gz";
      for(uint i = 0; i < filenum; i++) 
      { 
        SBMLDocument d = libsbml.readSBML(file[i]); 
        assertTrue( d != null );
        if (! SBMLWriter.hasZlib())
        {
          assertTrue( libsbml.writeSBML(d, gzfile) == 0 );
          d = null;
          continue;
        }
        int result = libsbml.writeSBML(d, gzfile);
        assertTrue( result != 0);
        SBMLDocument dg = libsbml.readSBML(gzfile);
        assertTrue( dg != null );
        assertTrue( ( dg.toSBML() != d.toSBML() ) == false );
        d = null;
        dg = null;
      }
  }


    public void test_WriteSBML_locale()
    {
      string expected = wrapXML("<parameter id=\"p\" value=\"3.31\"/>");
      Parameter p = new Parameter("p",3.31);
      p.write(XOS);
      assertEquals( true, equals(expected) );
    }

    public void test_WriteSBML_zip()
    {
      uint filenum = 12;
      string[] file = {
                        "../../../examples/sample-models/from-spec/level-2/algebraicrules.xml",
                        "../../../examples/sample-models/from-spec/level-2/assignmentrules.xml",
                        "../../../examples/sample-models/from-spec/level-2/boundarycondition.xml",
                        "../../../examples/sample-models/from-spec/level-2/delay.xml",
                        "../../../examples/sample-models/from-spec/level-2/dimerization.xml",
                        "../../../examples/sample-models/from-spec/level-2/enzymekinetics.xml",
                        "../../../examples/sample-models/from-spec/level-2/events.xml",
                        "../../../examples/sample-models/from-spec/level-2/functiondef.xml",
                        "../../../examples/sample-models/from-spec/level-2/multicomp.xml",
                        "../../../examples/sample-models/from-spec/level-2/overdetermined.xml",
                        "../../../examples/sample-models/from-spec/level-2/twodimensional.xml",
                        "../../../examples/sample-models/from-spec/level-2/units.xml"
      };
      string zipfile = "test.xml.zip";
      for(uint i = 0; i < filenum; i++) 
      { 
        SBMLDocument d = libsbml.readSBML(file[i]); 
        assertTrue( d != null );
        if (! SBMLWriter.hasZlib())
        {
          assertTrue( libsbml.writeSBML(d, zipfile) == 0 );
          d = null;
          continue;
        }
        int result = libsbml.writeSBML(d, zipfile);
        assertTrue( result != 0);
        SBMLDocument dg = libsbml.readSBML(zipfile);
        assertTrue( dg != null );
        assertTrue( ( dg.toSBML() != d.toSBML() ) == false );
        d = null;
        dg = null;
      }
  }


  }
}