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 $

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


      if (sbase instanceof SBMLDocument) {
        SBMLDocument sbmlDocument = (SBMLDocument) sbmlElementToWrite;


        xmlObject.addAttributes(sbmlDocument

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      XMLNode xmlNode = (XMLNode) contextObject;


      xmlNode.addChild(textNode);
      
    } else if (contextObject instanceof SBase) {
      SBase parentSBMLElement = (SBase) contextObject;
      
      XMLNode xmlNode = null;


      if (parentSBMLElement.isSetNotes() && typeOfNotes.equals("notes")) 
      {
        xmlNode = parentSBMLElement.getNotes(); 
      }
      else if (typeOfNotes.equals("message") && parentSBMLElement instanceof Constraint
          && ((Constraint) parentSBMLElement).isSetMessage())
      {
        xmlNode = ((Constraint) parentSBMLElement).getMessage();
      } 
      else 
      {
        logger.warn("The type of String " + typeOfNotes + " on the element " + 
            parentSBMLElement.getElementName() + " is unknown !! Some data might be lost");
        return;
      }


      xmlNode.addChild(textNode);

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  {
    logger.debug("processStartElement : element name = " + elementName);
    
    if (elementName.equals("notes")
        && (contextObject instanceof SBase)) {
      SBase sbase = (SBase) contextObject;
      sbase.setNotes(new XMLNode(new XMLTriple("notes", null, null), new XMLAttributes()));
      return contextObject;
    }
    
    // Creating a StartElement XMLNode !!  
    XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, null, prefix), new XMLAttributes(), new XMLNamespaces());
    
    if (contextObject instanceof SBase) {
      SBase parentSBMLElement = (SBase) contextObject;
      
      if (typeOfNotes.equals("notes")) {
        parentSBMLElement.getNotes().addChild(xmlNode);
      } else if (typeOfNotes.equals("message") && parentSBMLElement instanceof Constraint) {
        ((Constraint) parentSBMLElement).getMessage().addChild(xmlNode);
      } else {
        logger.warn("The type of String " + typeOfNotes + " on the element " + 
            parentSBMLElement.getElementName() + " is unknown !! Some data might be lost");
      }
      
    } else if (contextObject instanceof XMLNode) {
      XMLNode parentNode = (XMLNode) contextObject;

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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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   * 
   * @see org.sbml.jsbml.util.Filter#accepts(java.lang.Object)
   */
  public boolean accepts(Object o) {
    if (o instanceof SBase) {
      SBase sbase = (SBase) o;
      if (sbase.isSetSBOTerm() && (SBO.isChildOf(sbase.getSBOTerm(), term))) {
        return true;
      }
    }
    return false;
  }

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    Object sbmlElementToWrite) {


    logger.debug("FBCParser: writeElement");


    if (sbmlElementToWrite instanceof SBase) {
      SBase sbase = (SBase) sbmlElementToWrite;


      if (!xmlObject.isSetName()) {
        if (sbase instanceof ListOf<?>) {
          ListOf<?> listOf = (ListOf<?>) sbase;


          if (listOf.size() > 0) {
            if (listOf.get(0) instanceof FluxBound) {
              xmlObject.setName(FBCList.listOfFluxBounds.toString());
            } else if (listOf.get(0) instanceof Objective) {
              xmlObject.setName(FBCList.listOfObjectives.toString());
            } else if (listOf.get(0) instanceof FluxObjective) {
              xmlObject.setName(FBCList.listOfFluxObjectives.toString());
            }
          }
        } else {
          xmlObject.setName(sbase.getElementName());
        }
      }
      //      if (!xmlObject.isSetPrefix()) {
      //        xmlObject.setPrefix(FBCConstants.shortLabel);
      //      }

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        return layoutModel.getListOfLayouts();
      }
    }
    else if (contextObject instanceof Layout) {
      Layout layout = (Layout) contextObject;
      SBase newElement = null;


      if (elementName.equals(listOfCompartmentGlyphs)) {


        newElement = layout.getListOfCompartmentGlyphs();
      }
      else if (elementName.equals(listOfSpeciesGlyphs)) {


        newElement = layout.getListOfSpeciesGlyphs();
      }
      else if (elementName.equals(listOfReactionGlyphs)) {


        newElement = layout.getListOfReactionGlyphs();
      }
      else if (elementName.equals(listOfTextGlyphs)) {


        newElement = layout.getListOfTextGlyphs();
      }
      else if (elementName.equals(listOfAdditionalGraphicalObjects)) {


        newElement = layout.getListOfAdditionalGraphicalObjects();
      }
      else if (elementName.equals(dimensions)) {
        Dimensions dimension = new Dimensions();
        layout.setDimensions(dimension);


        newElement = dimension;
      }


      if (newElement != null) {
        return newElement;
      }
    }
    else if (contextObject instanceof GraphicalObject) {
      GraphicalObject graphicalObject = (GraphicalObject) contextObject;


      if (elementName.equals(boundingBox)) {
        BoundingBox bbox = new BoundingBox();
        graphicalObject.setBoundingBox(bbox);


        return bbox;
      }


      if (graphicalObject instanceof ReactionGlyph)
      {
        ReactionGlyph reactionGlyph = (ReactionGlyph) graphicalObject;


        if (elementName.equals(curve)) {
          Curve curve = new Curve();
          reactionGlyph.setCurve(curve);


          return curve;
        }
        else if (elementName.equals(listOfSpeciesReferenceGlyphs))
        {
          ListOf<SpeciesReferenceGlyph> list = reactionGlyph.getListOfSpeciesReferenceGlyphs();
          return list;
        }


      }
      else if (graphicalObject instanceof SpeciesReferenceGlyph)
      {
        SpeciesReferenceGlyph speciesRefGlyph = (SpeciesReferenceGlyph) contextObject;


        if (elementName.equals(curve)) {
          Curve curve = new Curve();
          speciesRefGlyph.setCurve(curve);


          return curve;
        }


      }
      else if (graphicalObject instanceof GeneralGlyph)
      {
        GeneralGlyph generalGlyph = (GeneralGlyph) graphicalObject;


        if (elementName.equals(curve)) {
          Curve curve = new Curve();
          generalGlyph.setCurve(curve);


          return curve;
        }
        else if (elementName.equals(listOfSubGlyphs))
        {
          ListOf<GraphicalObject> list = generalGlyph.getListOfSubGlyphs();
          return list;
        }
        else if (elementName.equals(listOfReferenceGlyphs))
        {
          ListOf<ReferenceGlyph> list = generalGlyph.getListOfReferenceGlyphs();
          return list;
        }


      }
      else if (graphicalObject instanceof ReferenceGlyph)
      {
        ReferenceGlyph refGlyph = (ReferenceGlyph) contextObject;


        if (elementName.equals(curve)) {
          Curve curve = new Curve();
          refGlyph.setCurve(curve);


          return curve;
        }
      }


    }
    else if (contextObject instanceof BoundingBox)
    {
      BoundingBox bbox = (BoundingBox) contextObject;


      if (elementName.equals(position)) {
        Position position = new Position();
        bbox.setPosition(position);


        return position;
      }
      else if (elementName.equals(dimensions)) {
        Dimensions dimension = new Dimensions();
        bbox.setDimensions(dimension);


        return dimension;
      }
    }
    else if (contextObject instanceof Curve) {
      Curve curve = (Curve) contextObject;
      SBase newElement = null;


      if (elementName.equals(listOfCurveSegments)) {


        newElement = curve.getListOfCurveSegments();
      }


      if (newElement != null) {
        return newElement;
      }
    }
    else if (contextObject instanceof CurveSegment) {
      CubicBezier curveSegment = (CubicBezier) contextObject;


      if (elementName.equals(start)) {
        Start point = new Start();
        curveSegment.setStart(point);


        return point;
      }
      else if (elementName.equals(end)) {
        End point = new End();
        curveSegment.setEnd(point);


        return point;
      }
      else if (elementName.equals(basePoint1)) {
        BasePoint1 point = new BasePoint1();
        curveSegment.setBasePoint1(point);


        return point;
      }
      else if (elementName.equals(basePoint2)) {
        BasePoint2 point = new BasePoint2();
        curveSegment.setBasePoint2(point);


        return point;
      }


    }
    else if (contextObject instanceof ListOf<?>) {
      ListOf<SBase> listOf = (ListOf<SBase>) contextObject;
      SBase newElement = null;


      if (elementName.equals(layout)) {
        newElement = new Layout();
      }
      else if (elementName.equals(compartmentGlyph)) {

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    Set<String> packageNamespaces = null;


    // logger.debug("getInitializedParsers : name space, object = " + name space + ", " + object);


    if (object instanceof SBase) {
      SBase sbase = (SBase) object;
      packageNamespaces = sbase.getNamespaces();
    } else if (object instanceof Annotation) {
      Annotation annotation = (Annotation) object;
      packageNamespaces = annotation.getNamespaces();
    } else {
      logger.warn("getInitializedParsers : I don't know what to do with " + object);

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      // TODO : add all other namespaces !!


      if (isSBMLNamespaceNeeded) {
        // writing the SBML namespace
        SBMLDocument doc = null;
        SBase sbase = m.getMath().getParentSBMLObject();
        String sbmlNamespace = SBMLDocument.URI_NAMESPACE_L3V1Core;
        
        if (sbase != null) {
          doc = sbase.getSBMLDocument();
          sbmlNamespace = doc.getSBMLDocumentNamespaces().get("xmlns");
          
          if (sbmlNamespace == null) {
            logger.warn("writeMathML : the SBML namespace of this SBMLDocument" +
                " could not be found, using the default namespace (" +

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           * and Version).
           */
          if (nextObjectToWrite instanceof ListOf<?>) {
            ListOf<?> list = (ListOf<?>) nextObjectToWrite;
            if (list.size() > 0) {
              SBase sb = list.getFirst();
              if ((sb instanceof UnitDefinition) && (parser
                      .getListOfSBMLElementsToWrite(nextObjectToWrite) == null)) {
                streamWriter.writeCharacters(whiteSpaces.substring(0, indent - indentCount));
                continue;
              }
            } else {
              streamWriter.writeCharacters(whiteSpaces.substring(0, indent - indentCount));
              continue;
            }
          }


          parentXmlObject.clear();


          /*
           * The following containers are all optional in a
           * <reaction>, but if any is present, it must not be empty:
           * <listOfReactants>, <listOfProducts>, <listOfModifiers>,
           * <kineticLaw>. (References: L2V2 Section 4.13; L2V3
           * Section 4.13; L2V4 Section 4.13)
           */
          if (nextObjectToWrite instanceof ListOf<?>) {
            ListOf<?> toTest = (ListOf<?>) nextObjectToWrite;
            
            if (toTest.size() > 0) {
              elementIsNested = true;
            }
            
            Type listType = toTest.getSBaseListType();
            if (listType == Type.none) {
              // Prevent writing invalid SBML if list types are
              // not set appropriately.
              throw new SBMLException(String.format(
                  "Unknown ListOf type \"%s\".",
                  toTest.getElementName()));
            }
            if (listType.equals(ListOf.Type.listOfReactants)
                || listType.equals(ListOf.Type.listOfProducts)
                || listType.equals(ListOf.Type.listOfModifiers)) {
              if (toTest.size() < 1) {
                continue; // Skip these, see reference in
                // comment above.
              }
            }
          } else if (nextObjectToWrite instanceof KineticLaw) {
            // TODO: Is there any chance, that an KineticLaw get's
            // an empty XML entity?
          }
          
          // Writing the element, starting by the indent
          streamWriter.writeCharacters(whiteSpaces);
          parser.writeElement(parentXmlObject, nextObjectToWrite);
          parser.writeNamespaces(parentXmlObject, nextObjectToWrite);
          parser.writeAttributes(parentXmlObject, nextObjectToWrite);
          
          
          SMOutputElement newOutPutElement = null;
          if (parentXmlObject.isSetName()) {
            boolean isClosedMathContainer = false, isClosedAnnotation = false;
            
            if (parentXmlObject.isSetNamespace()) {
              SMNamespace namespaceContext = smOutputParentElement
                  .getNamespace(
                      parentXmlObject.getNamespace(),
                      parentXmlObject.getPrefix());
              newOutPutElement = smOutputParentElement
                  .addElement(namespaceContext,
                      parentXmlObject.getName());
            } else {
              newOutPutElement = smOutputParentElement
                  .addElement(smOutputParentElement
                      .getNamespace(), parentXmlObject
                      .getName());
            }


            Iterator<Entry<String, String>> it = parentXmlObject
                .getAttributes().entrySet().iterator();
            while (it.hasNext()) {
              Entry<String, String> entry = it.next();
              newOutPutElement.addAttribute(entry.getKey(),
                  entry.getValue());
            }
            if (nextObjectToWrite instanceof SBase) {
              SBase s = (SBase) nextObjectToWrite;
              if (s.isSetNotes()) {
                writeNotes(s, newOutPutElement, streamWriter,
                    newOutPutElement.getNamespace()
                        .getURI(), indent + indentCount);
                elementIsNested = isClosedAnnotation = true;
              }
              if (s.isSetAnnotation()) {
                writeAnnotation(s, newOutPutElement,
                    streamWriter,
                    indent + indentCount, false);
                elementIsNested = true;
              }
              if (s.getChildCount() > 0) {
                // make sure that we'll have line breaks if an element has any sub elements.
                elementIsNested = true;
              }
            }
            if (nextObjectToWrite instanceof Constraint) {

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org.sbml.jsbml.util.filters.CVTermFilter

org.sbml.jsbml.util.filters.SBOFilter

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org.sbml.jsbml.xml.parsers.AbstractReaderWriter

org.sbml.jsbml.xml.parsers.CompParser

org.sbml.jsbml.xml.parsers.FBCParser

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