Package org.sbml.jsbml.xml.stax

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

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        new ASTNode(10)));
    ev.createPriority(ASTNode.parseFormula("25"));
    ev.createDelay(ASTNode.parseFormula("2"));
    ev.createEventAssignment("s1", ASTNode.parseFormula("s2"));
    System.out.println("==================================");
    new SBMLWriter().write(doc, System.out);
    System.out.println("\n==================================");
    doc.setLevelAndVersion(2, 4);
    System.out.println("==================================");
    new SBMLWriter().write(doc, System.out);
  }
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  ClassNotFoundException, SBMLException, SAXException {
    String fileName = DATA_FOLDER + "/groups/groups1.xml";

    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);

    new SBMLWriter().write(doc, DATA_FOLDER + "/groups/groups1_write.xml");
  }
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        .setNotes("<body>A senseless test model with a senseless notes element.</body>");

    m.getUnitDefinition("substance").getUnit(0).setScale(-3);

    try {
      new SBMLWriter().write(doc, new BufferedOutputStream(System.out),
          "SBMLWriterTest", "");
    } catch (XMLStreamException e) {
      e.printStackTrace();
    } catch (SBMLException e) {
      e.printStackTrace();
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    r.setKineticLaw(kl);
   
    System.out.println(math.toMathML());

    try {
      new SBMLWriter().write(doc, System.out);
    } catch (XMLStreamException e) {
      e.printStackTrace();
    } catch (SBMLException e) {
      e.printStackTrace();
    }
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    EventAssignment assignment2 = event.createEventAssignment();
    assignment2.setVariable(k2);
    assignment2.setMath(new ASTNode(k1));
   
    new SBMLWriter().write(doc, System.out);
  }
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        .setNotes("<body>A senseless test model with a senseless notes element.</body>");

    m.getUnitDefinition("substance").getUnit(0).setScale(-3);

    try {
      new SBMLWriter().write(doc, new BufferedOutputStream(System.out),
          "SBMLWriterTest", "");
    } catch (XMLStreamException e) {
      e.printStackTrace();
    } catch (SBMLException e) {
      e.printStackTrace();
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    // s1.getAnnotation().addRDFAnnotationNamespace("bqbiol", "",
    // "http://biomodels.net/biology-qualifiers/");
    s1.addCVTerm(new CVTerm(CVTerm.Type.BIOLOGICAL_QUALIFIER,
        CVTerm.Qualifier.BQB_HAS_PART, "urn:miriam:obo.chebi:CHEBI:15422"));
    System.out.println("==================================");
    new SBMLWriter().write(doc, System.out);
    new JTreeOfSBML(doc);
  }
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   * @return the {@link Annotation} of this SBML object as a {@link String} or
   *         an empty {@link String} if there are no {@link Annotation}.
   *
   */
  public String getAnnotationString() {
    return isSetAnnotation() ? (new SBMLWriter()).writeAnnotation(this) : "";
  }
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    s1.setValue(23.7);
    model.removeSpecies(s1);

    try {
      System.out.println();
      new SBMLWriter().write(doc, System.out);
    } catch (Exception exc) {
      exc.printStackTrace();
    }
  }
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    SBMLDocument doc = new SBMLReader().readSBMLFile(fileName);
   
    String resultFileName = "biomd-025.xml";
   
    new SBMLWriter().write(doc, resultFileName);
  }
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Related Classes of org.sbml.jsbml.xml.stax.SBMLWriter

  • org.apache.log4j.Logger
  • org.codehaus.stax2.XMLStreamWriter2
  • org.codehaus.staxmate.dom.DOMConverter
  • org.codehaus.staxmate.out.SMNamespace
  • org.codehaus.staxmate.out.SMOutputContext
  • org.codehaus.staxmate.out.SMOutputDocument
  • org.codehaus.staxmate.out.SMOutputElement
  • org.codehaus.staxmate.out.SMRootFragment
  • org.codehaus.staxmate.SMOutputFactory
  • org.sbml.jsbml.AbstractSBase
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