Examples of SBMLReader

org.sbml.jsbml.SBMLReader
Provides methods for reading SBML from files, text strings or streams.
This {@link SBMLReader} is just a wrapper for the actual implementationin {@link org.sbml.jsbml.xml.stax.SBMLReader}.
This class is provided for compatibility with libSBML and to avoid problems if the internal of jsbml change, so it is preferable to use it instead of directly using {@link org.sbml.jsbml.xml.stax.SBMLReader}.
The {@link SBMLReader} class provides the main interface for reading SBMLcontent from files and strings. The methods for reading SBML all return an {@link SBMLDocument} object representing the results.
In the case of failures (such as if the SBML contains errors), the errors will be recorded with the {@link SBMLErrorLog}object kept in the {@link SBMLDocument} returned by {@link SBMLReader}. Consequently, immediately after calling a method on {@link SBMLReader}, callers should always check for errors and warnings using the methods for this purpose provided by {@link SBMLDocument}. @author Andreas Dräger @author Nicolas Rodriguez @since 0.8 @version $Rev: 1524 $
org.sbml.jsbml.xml.stax.SBMLReader
Provides all the methods to read a SBML file. @author Marine Dumousseau @author Andreas Dräger @author Nicolas Rodriguez @author Clemens Wrzodek @since 0.8 @version $Rev: 1533 $

Examples of org.sbml.jsbml.SBMLReader

   * Tries to validate biomodels file with id 228. 
   */
  @Test public void checkConsistency228() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v4/BIOMD0000000228.xml";
    
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
    try {
      int nbErrors = doc.checkConsistency();


      System.out.println("Found " + nbErrors + " errors on Biomodels 228 with the unit checking turned off.");

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Examples of org.sbml.jsbml.SBMLReader

   * Tries to validate biomodels file with id 228. 
   */
  @Test public void checkConsistency025() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v1/BIOMD0000000025.xml";
    
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
    try {
      int nbErrors = doc.checkConsistency();


      System.out.println("Found " + nbErrors + " errors on Biomodels 025 with the unit checking turned off.");

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Examples of org.sbml.jsbml.SBMLReader

  }
  
  /** @param args Expects a valid path to an SBML file. */ 
  public static void main(String[] args) throws Exception {
    UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
    new JSBMLvisualizer((new SBMLReader()).readSBML(args[0]));
  }

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

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

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

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

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

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

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

   *            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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