Package org.sbml.jsbml

Examples of org.sbml.jsbml.ASTNode

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      logger.debug("processAttribute : !!!!!!!!! context is not an ASTNode ( " +
          contextObject.getClass());
      return;
    }
   
    ASTNode astNode = (ASTNode) contextObject;
   
    // System.out.println("MathMLStaxParser : processAttribute called");
    // System.out.println("MathMLStaxParser : processAttribute : element name = " + elementName + ", attribute name = " + attributeName +
    // ", value = " + value + ", prefix = " + prefix + ", " + isLastAttribute + ", " + contextObject);
   
    // Possible value : type, id, style, class, encoding, definitionURL ...
    if (attributeName.equals("type")) {
      astNode.setIsSetNumberType(true);
    }
    if (attributeName.equals("definitionURL")) {
      astNode.setDefinitionURL(value);
    }
   
    if (attributeName.equals("type") || attributeName.equals("definitionURL")) {
      astNode.setType(value);
      // System.out.println("MathMLStaxParser : processAttribute : astNode Type = " + astNode.getType());
    } else if (attributeName.equals("id")) {
      astNode.setId(value);
    } else if (attributeName.equals("style")) {
      astNode.setStyle(value);
    } else if (attributeName.equals("class")) {
      astNode.setClassName(value);
    } else if (attributeName.equals("encoding")) {
      astNode.setEncoding(value);
    }
   
   
  }
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  }

  @Test
  public void test_ASTNode_setName_override()
  {
    ASTNode node = new  ASTNode(ASTNode.Type.FUNCTION_SIN);
    assertTrue(node.getName().equals( "sin"));
    assertTrue( node.getType() == ASTNode.Type.FUNCTION_SIN );
    node.setName( "MySinFunc");
    assertTrue(node.getName().equals( "MySinFunc"));
    assertTrue( node.getType() == ASTNode.Type.FUNCTION_SIN );
    node.setName(null);
    assertTrue(node.getName().equals( "sin"));
    assertTrue( node.getType() == ASTNode.Type.FUNCTION_SIN );
    node = null;
  }
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  }

  @Test
  public void test_ASTNode_setReal()
  {
    ASTNode node = new  ASTNode();

    node.setValue(32.1);
    assertTrue( node.getType() == ASTNode.Type.REAL );

    // assertTrue( node.getInteger() == 0 ); // Exception thrown   
    // assertTrue( node.getName() == null ); // Exception thrown   
    // assertTrue( node.getCharacter() == '\0' );  // Exception thrown
    assertTrue( node.getReal() == 32.1 );
    assertTrue( node.getExponent() == 0 );
    // assertTrue( node.getDenominator() == 1 );  // Exception thrown
    assertTrue( node.getMantissa() == 32.1 );

    node.setValue(45,90);
   
    assertTrue( node.getType() == ASTNode.Type.RATIONAL );
    // assertTrue( node.getInteger() == 45 );
    // assertTrue( node.getName() == null );
    // assertTrue( node.getCharacter() == '\0' );
    assertTrue( node.getReal() == 0.5 );
    // assertTrue( node.getExponent() == 0 ); // Exception thrown
    assertTrue( node.getDenominator() == 90 );
    // assertTrue( node.getMantissa() == 0 ); // Exception thrown
   
    node.setValue(32.0,4);
   
    assertTrue( node.getType() == ASTNode.Type.REAL_E );
    // assertTrue( node.getInteger() == 0 );
    // assertTrue( node.getName() == null );
    // assertTrue( node.getCharacter() == '\0' );
    assertTrue( node.getReal() == 320000 );
    assertTrue( node.getExponent() == 4 );
    // assertTrue( node.getDenominator() == 1 );
    assertTrue( node.getMantissa() == 32 );
    node = null;
  }
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  public static void main(String[] args) throws Exception {
   
    IFormulaParser parser = new FormulaParserLL3(new StringReader(""));
   
    ASTNode node = ASTNode.parseFormula("true || false", parser);
   
    System.out.println(node.toFormula());
   
    node = ASTNode.parseFormula("true && false", parser);   
    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("and(true,false)", parser);   
    System.out.println(node.toFormula());
   
    node = ASTNode.parseFormula("! true", parser);   
    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("not(true)", parser);   
    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("NOT(true)", parser);   
    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("NOT true", parser);   
    System.out.println(node.toFormula());
   
//    node = ASTNode.parseFormula("true and false", parser);    // Not supported anymore by the new parser     
//    System.out.println(node.toFormula());
   
//    node = ASTNode.parseFormula("not true", parser); // Not supported anymore by the new parser   
//    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("and(or(gt(x,2), lt(S1, 4)),and(x >= 2, (S1 AND true) || (true && true)))", parser);   
    System.out.println(node.toFormula());

//    node = ASTNode.parseFormula("4!", parser);  // Not supported anymore by the new parser   
//    System.out.println(node.toFormula());
   
    node = ASTNode.parseFormula("selector(S, 1)", parser);   
    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("selector(S, 1, 5)", parser);   
    System.out.println(node.toFormula());
   
    String mathMLSelector = node.toMathML();
   
    System.out.println(mathMLSelector);

    node = JSBML.readMathMLFromString(mathMLSelector);
   
    System.out.println(node.toFormula());
   
    mathMLSelector = node.toMathML();
    System.out.println(mathMLSelector);
   
    node = ASTNode.parseFormula("plus(1, 2, 3, 4)", parser);   
    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("minus(1, 2, 3, 4)", parser);   
    System.out.println(node.toFormula());

    node = ASTNode.parseFormula("times(1, 2, 3, 4)", parser);   
    System.out.println(node.toFormula());
   
    node = ASTNode.parseFormula("divide(2, 4)", parser);   
    System.out.println(node.toFormula());
   
    node = ASTNode.parseFormula("modulo(13, 5)", parser);       
    System.out.println(node.toFormula());
    System.out.println(node.toMathML());

    node = ASTNode.parseFormula("18 % 5", parser);   
    System.out.println(node.toFormula());
}
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  }

  @Test
  public void test_ASTNode_setType()
  {
    ASTNode node = new  ASTNode(Type.NAME);
    node.setName( "foo");
    assertTrue( node.getType() == ASTNode.Type.NAME );
    node.setType(ASTNode.Type.FUNCTION);
    assertTrue( node.getType() == ASTNode.Type.FUNCTION );
    assertTrue(node.getName().equals( "foo"));
    node.setType(ASTNode.Type.NAME);
    assertTrue( node.getType() == ASTNode.Type.NAME );
    assertTrue(node.getName() == null); // in jsbml setType will reset the name !! assertTrue(node.getName().equals( "foo"));
    node.setType(ASTNode.Type.INTEGER);
    assertTrue( node.getType() == ASTNode.Type.INTEGER );
    node.setType(ASTNode.Type.REAL);
    assertTrue( node.getType() == ASTNode.Type.REAL );
    node.setType(ASTNode.Type.UNKNOWN);
    assertTrue( node.getType() == ASTNode.Type.UNKNOWN );
    node.setType(ASTNode.Type.PLUS);
    assertTrue( node.getType() == ASTNode.Type.PLUS );
    assertTrue( node.getCharacter() ==  '+'       );
    node.setType(ASTNode.Type.MINUS);
    assertTrue( node.getType() == ASTNode.Type.MINUS );
    assertTrue( node.getCharacter() ==  '-'        );
    node.setType(ASTNode.Type.TIMES);
    assertTrue( node.getType() == ASTNode.Type.TIMES );
    assertTrue( node.getCharacter() ==  '*'        );
    node.setType(ASTNode.Type.DIVIDE);
    assertTrue( node.getType() == ASTNode.Type.DIVIDE );
    assertTrue( node.getCharacter() ==  '/'         );
    node.setType(ASTNode.Type.POWER);
    assertTrue( node.getType() == ASTNode.Type.POWER );
    assertTrue( node.getCharacter() ==  '^'        );
    node = null;
  }
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  @SuppressWarnings("deprecation")
  @Test
public void test_ASTNode_swapChildren()
  {
    ASTNode node = new  ASTNode();
    ASTNode c1 = new  ASTNode(Type.NAME);
    ASTNode c2 = new  ASTNode(Type.NAME);
    ASTNode node_1 = new  ASTNode();
    ASTNode c1_1 = new  ASTNode(Type.NAME);
    ASTNode c2_1 = new  ASTNode(Type.NAME);

    node.setType(ASTNode.Type.LOGICAL_AND);
    c1.setName( "a");
    c2.setName( "b");
    node.addChild(c1);
    node.addChild(c2);
    assertTrue( node.getNumChildren() == 2 );
    assertTrue(JSBML.formulaToString(node).equals( "a and b"));
    node_1.setType(ASTNode.Type.LOGICAL_AND);
    c1_1.setName( "d");
    c2_1.setName( "f");
    node_1.addChild(c1_1);
    node_1.addChild(c2_1);
    assertTrue( node_1.getNumChildren() == 2 );
    assertTrue(JSBML.formulaToString(node_1).equals( "d and f"));
    node.swapChildren(node_1);
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  @SuppressWarnings("deprecation")
  @Test
public void test_ASTNode_deepCopy_2()
  {
    ASTNode node = new  ASTNode(Type.NAME); // TODO: setName will assign Type.FUNCTION if type and variable are not defined !!!
    ASTNode copy;
    node.setName( "Foo");
    assertTrue( node.getType() == ASTNode.Type.NAME );
    assertTrue(node.getName().equals( "Foo"));
    assertTrue( node.getNumChildren() == 0 );
    copy = node.clone();
    assertTrue( copy.equals(node) );
    assertTrue( copy.getType() == ASTNode.Type.NAME );
    assertTrue(copy.getName().equals( "Foo"));
    assertTrue( copy.getNumChildren() == 0 );
    node = null;
    copy = null;
  }
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  @SuppressWarnings("deprecation")
  @Test
public void test_ASTNode_deepCopy_3()
  {
    ASTNode node = new  ASTNode(ASTNode.Type.FUNCTION);
    ASTNode copy;
    node.setName( "Foo");
    assertTrue( node.getType() == ASTNode.Type.FUNCTION );
    assertTrue(node.getName().equals( "Foo"));
    assertTrue( node.getNumChildren() == 0 );
    copy = node.clone();
    assertTrue( copy.equals(node) );
    assertTrue( copy.getType() == ASTNode.Type.FUNCTION );
    assertTrue(copy.getName().equals( "Foo"));
    assertTrue( copy.getNumChildren() == 0 );
    node = null;
    copy = null;
  }
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  @SuppressWarnings("deprecation")
  @Test
public void test_ASTNode_deepCopy_4()
  {
    ASTNode node = new  ASTNode(ASTNode.Type.FUNCTION_ABS);
    ASTNode copy;
    node.setName( "ABS"); // TODO setName() is changing the type of the node to Type.Function ??
    assertTrue( node.getType() == ASTNode.Type.FUNCTION_ABS );
    assertTrue(node.getName().equals( "ABS"));
    assertTrue( node.getNumChildren() == 0 );
    copy = node.clone();
    assertTrue( copy.equals(node) );
    assertTrue( copy.getType() == ASTNode.Type.FUNCTION_ABS );
    assertTrue(copy.getName().equals( "ABS"));
    assertTrue( copy.getNumChildren() == 0 );
    node = null;
    copy = null;
  }
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  // freeName does not exist in jsbml
  @Test
  public void test_ASTNode_freeName()
  {
    ASTNode node = new  ASTNode(Type.NAME);
    node.setName( "a");
    assertTrue(JSBML.formulaToString(node).equals( "a"));
    assertTrue(node.getName().equals( "a"));
    node.setName(null);
    assertTrue( node.getName() == null );
    node.setType(ASTNode.Type.UNKNOWN);
    assertTrue( node.getName() == null );
    node = null;
  }
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Related Classes of org.sbml.jsbml.ASTNode

  • org.sbml.jsbml.ext.qual.BuildToyModelTest
  • org.sbml.jsbml.test.EventTest
  • org.sbml.jsbml.test.FormulaTest
  • org.sbml.jsbml.test.MathMLSpecialTest
  • org.sbml.jsbml.test.PriorityTest
  • org.sbml.jsbml.test.sbml.TestASTNode
  • org.sbml.jsbml.test.sbml.TestEvent
  • org.sbml.jsbml.test.sbml.TestIncompatibilities
  • org.sbml.jsbml.test.sbml.TestModel
  • org.sbml.jsbml.test.Test
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