Package org.sbml.jsbml.xml.stax

Examples of org.sbml.jsbml.xml.stax.SBMLReader

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  @SuppressWarnings("deprecation")
  @Test public void read1() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    // URL fileUrl = this.getClass().getResource("./data/BIOMD0000000025.xml");
    String fileName = DATA_FOLDER + "/l2v1/BIOMD0000000025.xml";
   
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
   
    assertTrue(doc.getLevel() == 2 && doc.getVersion() == 1);
   
    // TODO: assertTrue(model.getLevel() == 2 && model.getVersion() == 1);
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   * @throws InvalidPropertiesFormatException
   */
  @Test public void read2() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/l2v1/BIOMD0000000227.xml";
   
    new SBMLReader().readSBMLFile(fileName);
  }
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   * @throws InvalidPropertiesFormatException
   */
  @Test public void read3() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/l2v4/BIOMD0000000228.xml"; // l2v4
   
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
   
    assertTrue(doc.getLevel() == 2 && doc.getVersion() == 4);
   
    assertTrue(model.getId().equals(""));
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   * @throws InvalidPropertiesFormatException
   */
  @Test public void read4() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/l2v4/BIOMD0000000229.xml"; // l2v4
   
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
   
    assertTrue(doc.getLevel() == 2 && doc.getVersion() == 4);
   
    assertTrue(model.getId().equals("Ma2002_cAMP_oscillations"));
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   * @throws InvalidPropertiesFormatException
   */
  @Test public void read5() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/l2v3/BIOMD0000000191.xml"; // l2v3
   
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
   
    assertTrue(doc.getLevel() == 2 && doc.getVersion() == 3);
   
    assertTrue(model.getUnitDefinitionCount() == 4);
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   * @throws SAXException
   */
  @Test public void write1() throws XMLStreamException, InstantiationException, IllegalAccessException, InvalidPropertiesFormatException, IOException, ClassNotFoundException, SBMLException, SAXException{
    String fileName = DATA_FOLDER + "/l2v1/BIOMD0000000025.xml";
 
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
   
    String resultFileName = "biomd-025.xml";
   
    new SBMLWriter().write(doc, resultFileName);
  }
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   *            The path to an SBML file.
   */
  public JTreeOfSBML(String fileName) {
    super();
    try {
      SBMLDocument doc = new SBMLReader().readSBML(fileName);
      showGUI(doc);
    } catch (Exception exc) {
      exc.printStackTrace();
      JOptionPane.showMessageDialog(this, exc.getMessage(), exc
          .getClass().getSimpleName(), JOptionPane.ERROR_MESSAGE);
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   *            the MathML XML string.
   * @return an {@link ASTNode}
   */
  public static ASTNode readMathMLFromString(String xml) {
    try {
      return new SBMLReader().readMathML(xml);
    } catch (XMLStreamException e) {
      e.printStackTrace();
    }

    return null;
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    Reaction r;
    Species s;
    SpeciesReference sr;
    UnitDefinition ud;
    String filename = DATA_FOLDER + "/libsbml-test-data/l1v1-branch.xml";
    d = new SBMLReader().readSBML(filename);
    if (d == null)
      ;
    {
    }
    assertTrue(d.getLevel() == 1);
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   */
  @SuppressWarnings("deprecation")
  @Test public void readL1V2Branch() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v2-branch.xml";
   
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
   
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 2);
   
    assertTrue(model.getLevel() == 1 && model.getVersion() == 2);
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Related Classes of org.sbml.jsbml.xml.stax.SBMLReader

  • com.ctc.wstx.stax.WstxInputFactory
  • org.apache.log4j.Logger
  • org.sbml.jsbml.ASTNode
  • org.sbml.jsbml.Constraint
  • org.sbml.jsbml.ext.groups.TestL3groups
  • org.sbml.jsbml.ext.layout.TestL3Layout
  • org.sbml.jsbml.SBase
  • org.sbml.jsbml.SBMLDocument
  • org.sbml.jsbml.test.gui.JTreeOfSBML
  • org.sbml.jsbml.test.sbml.TestReadFromFile1
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