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.SBMLWriter

    Trigger t = e.createTrigger();
    t.setFormula("time == 1");
    EventAssignment ea = e.createEventAssignment(p, ASTNode
        .parseFormula("3"));
    e.addEventAssignment(ea);
    System.out.println((new SBMLWriter()).writeSBMLToString(doc));
  }

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Examples of org.sbml.jsbml.SBMLWriter

    // sbmlModel.addDeclaredNamespace("toto:ns2", "http://www.test.com");
    sbmlModel.addDeclaredNamespace("xmlns:ns3", "http://www.test.com");


    // but it is not working. In the output file written with:
    
    SBMLWriter ttt = new SBMLWriter();
    System.out.println( ttt.writeSBMLToString(sbmlDoc) );


    // the "html" namespace is missing (no line with xmlns:html="http://www.w3.org/1999/xhtml")
    // Could you please tell me if it is a bug or if I am doing something wrong?


  }

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Examples of org.sbml.jsbml.SBMLWriter

    Rule r = model.createAlgebraicRule();
    r.setMath(ASTNode.parseFormula("sin(3) + 1"));
    
    SBMLDocument doc2 = doc1.clone();
    try {
      (new SBMLWriter()).write(doc1, System.out);
      System.out.println("\n==================");
      (new SBMLWriter()).write(doc2, System.out);
    } catch (SBMLException e) {
      e.printStackTrace();
    } catch (XMLStreamException e) {
      e.printStackTrace();
    }

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Examples of org.sbml.jsbml.SBMLWriter

    Trigger t = e.createTrigger();
    t.setFormula("time == 1");
    EventAssignment ea = e.createEventAssignment(p, ASTNode
        .parseFormula("3"));
    e.addEventAssignment(ea);
    System.out.println((new SBMLWriter()).writeSBMLToString(doc));
  }

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Examples of org.sbml.jsbml.SBMLWriter

        }




        System.out.printf("Starting writing\n");


        new SBMLWriter().write(testDocument.clone(), jsbmlWriteFileName);
      }
      catch (XMLStreamException e)
      {
        e.printStackTrace();
      }

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Examples of org.sbml.jsbml.SBMLWriter

    Trigger t = e.createTrigger();
    t.setFormula("time == 1");
    EventAssignment ea = e.createEventAssignment(p, ASTNode
        .parseFormula("3"));
    e.addEventAssignment(ea);
    System.out.println((new SBMLWriter()).writeSBMLToString(doc));
  }

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Examples of org.sbml.jsbml.SBMLWriter

    
    // calling the generateSubModel with the selected reaction ids.
    // We do not care about any specific compartments, species, rules or events so we can pass null for these.
    SBMLDocument subModel = SubModel.generateSubModel(model, null, null, selectedReactionIds, null, null);
    
    new SBMLWriter().write(subModel, args[1]);
    
  }

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Examples of org.sbml.jsbml.SBMLWriter

    
    // calling the generateSubModel with the selected reaction ids.
    // We do not care about any specific compartments, species, rules or events so we can pass null for these.
    SBMLDocument subModel = SubModel.generateSubModel(model, null, null, selectedReactionIds, null, null);
    
    new SBMLWriter().write(subModel, args[1]);
    
  }

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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

    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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