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.xml.stax.SBMLReader

    {
      DATA_FOLDER = System.getProperty("user.dir") + "/extensions/layout/test/org/sbml/jsbml/xml/test/data";
    }
    String fileName = DATA_FOLDER + "/layout/GlycolysisLayout_small.xml";


    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();


    System.out.println("Model extension objects: " + model.getExtension(LAYOUT_NAMESPACE));
    LayoutModelPlugin extendedModel = (LayoutModelPlugin) model.getExtension(LAYOUT_NAMESPACE);

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

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

   * @throws InvalidPropertiesFormatException 
   */
  @Test public void readL1V1Units() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-units.xml";
    
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
    
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 1);
    
    assertTrue(model.getLevel() == 1 && model.getVersion() == 1);

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

   */
  @Test public void readL1V1Rules() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {


    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-rules.xml";
    
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
    
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 1);
    
    assertTrue(model.getLevel() == 1 && model.getVersion() == 1);

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

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

   * @throws InvalidPropertiesFormatException 
   */
  @Test public void readL1V1Units() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {
    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-units.xml";
    
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
    
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 1);
    
    assertTrue(model.getLevel() == 1 && model.getVersion() == 1);

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

   */
  @Test public void readL1V1Rules() throws XMLStreamException, InvalidPropertiesFormatException, IOException, ClassNotFoundException {


    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-rules.xml";
    
    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
    Model model = doc.getModel();
    
    assertTrue(doc.getLevel() == 1 && doc.getVersion() == 1);
    
    assertTrue(model.getLevel() == 1 && model.getVersion() == 1);

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

    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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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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