Package org.sbml.jsbml

Examples of org.sbml.jsbml.SBMLReader

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   * 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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   * 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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  }
 
  /** @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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   * Tries to use getNotesString on a model without a notes element.
   */
  @Test public void getNotesStringOnModel() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-minimal.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
        assertNotNull(doc.getModel().getNotesString());
    assertTrue(doc.getModel().getNotesString() == "");
  }
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    // Getting the sbml file name from the arguments passed to the java program
    String fileName = args[0];

    // Reading the file and creating the jsbml objects structure
    SBMLDocument testDocument = new SBMLReader().readSBML(fileName);
   
    // Getting the model
    Model model = testDocument.getModel();
 
    // creating a variable to store all the ids of the reactions we want to keep
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    // Getting the sbml file name from the arguments passed to the java program
    String fileName = args[0];

    // Reading the file and creating the jsbml objects structure
    SBMLDocument testDocument = new SBMLReader().readSBML(fileName);
   
    // Getting the model
    Model model = testDocument.getModel();
 
    // creating a variable to store all the ids of the reactions we want to keep
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   * Tries to use getNotesString on a model without a notes element.
   */
  @Test public void getNotesStringOnModel() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/libsbml-test-data/l1v1-minimal.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
        assertNotNull(doc.getModel().getNotesString());
    assertTrue(doc.getModel().getNotesString() == "");
  }
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Related Classes of org.sbml.jsbml.SBMLReader

  • cysbml.SBMLGraphReader
  • org.sbml.jsbml.test.gui.JSBMLvisualizer
  • org.sbml.jsbml.test.sbml.TestReadFromFile5
  • org.sbml.jsbml.test.SubModelTest
  • org.sbml.jsbml.test.TestLocalParameterIdentification
  • org.sbml.jsbml.test.ValidateSBML
  • org.sbml.jsbml.util.SimpleTreeNodeChangeListener
  • org.sbml.jsbml.xml.parsers.FBCParser
  • org.sbml.jsbml.xml.test.CheckConsistencyTests
  • org.sbml.jsbml.xml.test.GetNotesStringTests
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