Examples of org.sbml.jsbml.SBase

org.sbml.jsbml.SBase
The interface to implement for each SBML component. @author Andreas Dräger @author Marine Dumousseau @since 0.8 @version $Rev: 1533 $

  @Override
  public void writeElement(SBMLObjectForXML xmlObject,
    Object sbmlElementToWrite)
  {
    if (sbmlElementToWrite instanceof SBase) {
      SBase sbase = (SBase) sbmlElementToWrite;


      if (log4jLogger.isDebugEnabled())
      {
        log4jLogger.debug(MessageFormat.format("{0} ", sbase.getElementName()));
      }


      if (!xmlObject.isSetName()) {
        xmlObject.setName(sbase.getElementName());
      }
      if (!xmlObject.isSetPrefix()) {
        xmlObject.setPrefix("layout");
      }
      xmlObject.setNamespace(namespaceURI);

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    boolean isAttributeRead = false;


    if (contextObject instanceof SBase) {


      SBase sbase = (SBase) contextObject;


      log4jLogger.debug("processAttribute: level, version = "
          + sbase.getLevel() + ", " + sbase.getVersion());


      try {
        isAttributeRead = sbase.readAttribute(attributeName, prefix,
          value);
      } catch (Throwable exc) {
        System.err.println(exc.getMessage());
      }
    } else if (contextObject instanceof Annotation) {

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   * @param newContextObject
   * @param parent
   */
  private void setLevelAndVersionFor(Object newContextObject, SBase parent) {
    if (newContextObject instanceof SBase) {
      SBase sb = (SBase) newContextObject;
      // Level and version will be -1 if not set, so we don't
      // have to check.
      sb.setLevel(parent.getLevel());
      sb.setVersion(parent.getVersion());
    }
  }

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        ListOf<SBase> listOf = (ListOf<SBase>) sbase;


        if (!listOf.isEmpty()) {
          listOfElementsToWrite = new ArrayList<Object>();
          for (int i = 0; i < listOf.size(); i++) {
            SBase element = listOf.get(i);


            if (element != null) {
              listOfElementsToWrite.add(element);
            }
          }

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  public void processAttribute(String elementName, String attributeName,
      String value, String prefix, boolean isLastAttribute,
      Object contextObject) {
    boolean isAttributeRead = false;
    if (contextObject instanceof SBase) {
      SBase sbase = (SBase) contextObject;
      try {
        isAttributeRead = sbase.readAttribute(attributeName, prefix,
            value);
      } catch (Throwable exc) {
        System.err.println(exc.getMessage());
      }
    } else if (contextObject instanceof Annotation) {

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        Object newContextObject = SBMLCoreElements.get(elementName)
            .newInstance();
        
        if (elementName.equals("notes")
            && contextObject instanceof SBase) {
          SBase sbase = (SBase) contextObject;
          sbase.setNotes(new XMLNode(new XMLTriple("notes", null, null), new XMLAttributes()));
        } else if (elementName.equals("annotation")
            && contextObject instanceof SBase) {
          SBase sbase = (SBase) contextObject;
          Annotation annotation = (Annotation) newContextObject;
          sbase.setAnnotation(annotation);


          return annotation;
        } else if (contextObject instanceof SBMLDocument) {
          SBMLDocument sbmlDocument = (SBMLDocument) contextObject;
          if (elementName.equals("model")) {

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   * xml.stax.SBMLObjectForXML, java.lang.Object)
   */
  public void writeAttributes(SBMLObjectForXML xmlObject,
      Object sbmlElementToWrite) {
    if (sbmlElementToWrite instanceof SBase) {
      SBase sbase = (SBase) sbmlElementToWrite;


      xmlObject.addAttributes(sbase.writeXMLAttributes());
    }
  }

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   */
  public void writeElement(SBMLObjectForXML xmlObject,
      Object sbmlElementToWrite) {


    if (sbmlElementToWrite instanceof SBase) {
      SBase sbase = (SBase) sbmlElementToWrite;
      if (!xmlObject.isSetName()) {
        if (sbase.getElementName().equals("species")) {
          xmlObject.setName("specie");
        } else if (sbase.getElementName().equals("speciesReference")) {
          xmlObject.setName("specieReference");
        } else if (sbase.getElementName().equals("assignementRule")) {
          AssignmentRule assignmentRule = (AssignmentRule) sbase;
          Variable variable = assignmentRule.getVariableInstance();


          if (variable instanceof Species) {
            xmlObject.setName("specieConcentrationRule");
          } else if (variable instanceof Compartment) {
            xmlObject.setName("compartmentVolumeRule");
          } else if (variable instanceof Parameter) {
            xmlObject.setName("parameterRule");
          }
        } else {
          xmlObject.setName(sbase.getElementName());
        }
      }
    }
  }

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   *            nodes already visited in the path
   */
  @SuppressWarnings("unchecked")
  private void findShortestPath(int i, Node<SBase> node,
      List<Node<SBase>> path) {
    SBase value;
    // Path has reached the desired length -> store it in the list
    if (path.size() == i * 2) {
      paths.add(path);
    } else {
      value = matching.get(node.getValue());

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        }
      } else if (pattern != null) {
        return cvt.filterResources(pattern).size() > 0;
      }
    } else if (o instanceof SBase) {
      SBase sbase = (SBase) o;
      if (qualifier != null) {
        if (pattern != null) {
          if (sbase.filterCVTerms(qualifier, pattern).size() > 0) {
            return true;
          }
        } else if (sbase.filterCVTerms(qualifier).size() > 0) {
          return true;
        }
      }
    }
    return false;

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org.sbml.jsbml.ext.groups.Member

org.sbml.jsbml.ext.render.RenderLayoutPlugin

org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler

org.sbml.jsbml.util.filters.CVTermFilter

org.sbml.jsbml.util.filters.SBOFilter

org.sbml.jsbml.validator.OverdeterminationValidator

org.sbml.jsbml.xml.parsers.AbstractReaderWriter

org.sbml.jsbml.xml.parsers.CompParser

org.sbml.jsbml.xml.parsers.FBCParser

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