Examples of SBMLWriter

org.sbml.jsbml.SBMLWriter
Provides methods for writing SBML to files, text strings or streams.
This {@link SBMLWriter} is just a wrapper for the actual implementation in{@link org.sbml.jsbml.xml.stax.SBMLWriter}.
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.SBMLWriter}. The {@link SBMLWriter} class is the converse of {@link SBMLReader}, and provides the main interface for serializing SBML models into XML and writing the result to files and text strings. The methods for writing SBML all take an {@link SBMLDocument} object and a destination. @author Andreas Dräger @author Nicolas Rodriguez @since 0.8 @version $Rev: 1524 $
org.sbml.jsbml.xml.stax.SBMLWriter
A SBMLWriter provides the methods to write a SBML file. @author Marine Dumousseau @author Nicolas Rodriguez @author Andreas Dräger @since 0.8 @version $Rev: 1533 $

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

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

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

    
    EventAssignment assignment2 = event.createEventAssignment();
    assignment2.setVariable(k2);
    assignment2.setMath(new ASTNode(k1));
    
    new SBMLWriter().write(doc, System.out);
  }

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

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

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

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

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

  
    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.SBMLWriter

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

    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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