Examples of org.sbml.jsbml.ext.layout.BoundingBox

org.sbml.jsbml.ext.layout.BoundingBox
@author Nicolas Rodriguez @author Sebastian Frölich @author Andreas Dräger @author Clemens Wrzodek @since 1.0 @version $Rev: 1639 $

      }
    }
  }
  private void setMissingQTransitionBoundingBoxes(){
    Map<String, BoundingBox> boxes = reactionBoundingBoxes;
    BoundingBox genericBox = createGenericBoundingBox();
    String key;
    Model model = document.getModel();
    QualitativeModel qModel = (QualitativeModel) model.getExtension(QualConstant.namespaceURI);
    if (qModel != null){
      for (Transition qtransition : qModel.getListOfTransitions()){

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  private void setCyNodeAttributesForMap(CyAttributes attrs, Map<String, BoundingBox> map){
    for (String id : map.keySet()) {
      CyNode node = Cytoscape.getCyNode(id, false);
      if (node != null){
        BoundingBox box = map.get(id);
        attrs.setAttribute(id, ATT_LAYOUT_HEIGHT,
            new Double(box.getDimensions().getHeight()));
        attrs.setAttribute(id, ATT_LAYOUT_WIDTH,
            new Double(box.getDimensions().getWidth()));
      }
    }
  }

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   */
  public void applyLayoutPositionsToNetwork(CyNetwork network){
    
    CyNetworkView view = Cytoscape.getNetworkView(network.getIdentifier());
      String key;
      BoundingBox box; 
      Point point;
      
      double offset = 80.0;
      double current_x = min_x;
      double current_y = min_y - 2.0*offset;
      
      double x;
      double y;
      
    @SuppressWarnings("unchecked")
    List<Node> nodes = network.nodesList();
      for (Node node : nodes){
        key = node.getIdentifier();
        if (speciesBoundingBoxes.containsKey(key)){
          box = speciesBoundingBoxes.get(key);
        } else {
          box = reactionBoundingBoxes.get(key);
        }
        
        // set the position of the node
        giny.view.NodeView nodeView = view.getNodeView(node);
        
        point = box.getPosition();
        x = point.getX();
        y = point.getY();
        
        // layout generic nodes in grid
        if (x == GENERIC_X && y == GENERIC_Y){

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  }
  
  public void applyLayoutPositionsToLayoutNetwork(CyNetwork network){
    CyNetworkView view = Cytoscape.getNetworkView(network.getIdentifier());
      String key;
      BoundingBox box; 
      Point point;
      
      double offset = 80.0;
      double current_x = min_x;
      double current_y = min_y - 2.0*offset;
      
      double x;
      double y;
      
    @SuppressWarnings("unchecked")
    List<Node> nodes = network.nodesList();
      for (Node node : nodes){
        key = node.getIdentifier();
        if (speciesGlyphBoundingBoxes.containsKey(key)){
          box = speciesGlyphBoundingBoxes.get(key);
        } else {
          box = reactionGlyphBoundingBoxes.get(key);
        }
        
        // set the position of the node
        giny.view.NodeView nodeView = view.getNodeView(node);
        
        point = box.getPosition();
        x = point.getX();
        y = point.getY();
        
        // layout generic nodes in grid
        if (x == GENERIC_X && y == GENERIC_Y){

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  /**
   * Set the value of boundingBox
   */
  public void setBoundingBox(BoundingBox boundingBox) {
    BoundingBox oldBoundingBox = this.boundingBox;
    this.boundingBox = boundingBox;
    firePropertyChange(RenderConstants.boundingBox, oldBoundingBox, this.boundingBox);
  }

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   * @return {@code true}, if boundingBox was set before,
   *         otherwise {@code false}
   */
  public boolean unsetBoundingBox() {
    if (isSetBoundingBox()) {
      BoundingBox oldBoundingBox = boundingBox;
      boundingBox = null;
      firePropertyChange(RenderConstants.boundingBox, oldBoundingBox, boundingBox);
      return true;
    }
    return false;

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    }


    else if (contextObject instanceof LineEnding) {
      LineEnding lineEnding = (LineEnding) contextObject;
      if (elementName.equals(RenderConstants.boundingBox)) {
        BoundingBox bbox = new BoundingBox();
        lineEnding.setBoundingBox(bbox);


        return bbox;
      }
      else if (elementName.equals(RenderConstants.group)) {

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    }
    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) {

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              groupList = LayoutList.listOfReactionGlyphs;
              return reactionGlyph;
            } else if (elementName.equals("boundingBox")
                && groupList.equals(LayoutList.listOfCompartmentGlyphs)) {
              CompartmentGlyph compartmentGlyph = (CompartmentGlyph) contextObject;
              BoundingBox boundingBox = (BoundingBox) newContextObject;
              setNamespace(boundingBox, namespaceURI);
              compartmentGlyph.setBoundingBox(boundingBox);
              return boundingBox;
            }
          } else if (listOf.getParentSBMLObject() instanceof ReactionGlyph) {
            if (elementName.equals("speciesReferenceGlyph")
                && groupList.equals(LayoutList.listOfSpeciesReferenceGlyphs)) {
              SpeciesReferenceGlyph speciesReferenceGlyph = (SpeciesReferenceGlyph) newContextObject;
              setNamespace(speciesReferenceGlyph, namespaceURI);
              ListOf<SpeciesReferenceGlyph> listOfSpeciesReferenceGlyph = (ListOf<SpeciesReferenceGlyph>) contextObject;
              listOfSpeciesReferenceGlyph
              .add(speciesReferenceGlyph);
              return speciesReferenceGlyph;
            }
          } else if (elementName.equals("curveSegment")
              && groupList.equals(LayoutList.listOfCurveSegments)) {
            ListOf<CurveSegment> listOfLineSegment = (ListOf<CurveSegment>) contextObject;
            CubicBezier lineSegment = (CubicBezier) newContextObject;
            setNamespace(lineSegment, namespaceURI);
            listOfLineSegment.add(lineSegment);
            groupList = LayoutList.listOfCurveSegments;
            return lineSegment;
          } else if (listOf.getParentSBMLObject() instanceof Curve) {


            if (elementName.equals("curveSegment") || elementName.equals("cubicBezier")
                || elementName.equals("lineSegment"))
            {
              ListOf<CurveSegment> listOfLineSegment = (ListOf<CurveSegment>) contextObject;
              CubicBezier lineSegment = (CubicBezier) newContextObject;
              setNamespace(lineSegment, namespaceURI);
              listOfLineSegment.add(lineSegment);
              return lineSegment;
            }
          }


        } else if (contextObject instanceof Layout) {
          Layout layout = (Layout) contextObject;
          groupList = LayoutList.listOfLayouts;
          if (elementName.equals("dimensions")
              && groupList.equals(LayoutList.listOfLayouts)) {
            Dimensions dimensions = (Dimensions) newContextObject;
            setNamespace(dimensions, namespaceURI);
            layout.setDimensions(dimensions);
            return dimensions;
          } else if (elementName.equals("listOfCompartmentGlyphs")
              && groupList.equals(LayoutList.listOfLayouts)) {
            ListOf<CompartmentGlyph> listOfCompartmentGlyphs = (ListOf<CompartmentGlyph>) newContextObject;
            listOfCompartmentGlyphs.setSBaseListType(ListOf.Type.other);
            layout.setListOfCompartmentGlyphs(listOfCompartmentGlyphs);
            groupList = LayoutList.listOfCompartmentGlyphs;
            return listOfCompartmentGlyphs;
          } else if (elementName.equals("listOfSpeciesGlyphs")
              && groupList.equals(LayoutList.listOfLayouts)) {
            ListOf<SpeciesGlyph> listofSpeciesGlyph = (ListOf<SpeciesGlyph>) newContextObject;
            listofSpeciesGlyph.setSBaseListType(ListOf.Type.other);
            layout.setListOfSpeciesGlyphs(listofSpeciesGlyph);
            groupList = LayoutList.listOfSpeciesGlyphs;
            return listofSpeciesGlyph;
          } else if (elementName.equals("listOfReactionGlyphs")
              && groupList.equals(LayoutList.listOfLayouts)) {
            ListOf<ReactionGlyph> listOfReactionGlyphs = (ListOf<ReactionGlyph>) newContextObject;
            listOfReactionGlyphs.setSBaseListType(ListOf.Type.other);
            layout.setListOfReactionGlyphs(listOfReactionGlyphs);
            groupList = LayoutList.listOfReactionGlyphs;
            return listOfReactionGlyphs;
          } else if (elementName.equals("listOfTextGlyphs")
              && groupList.equals(LayoutList.listOfLayouts)) {
            ListOf<TextGlyph> listOfTextGlyphs = (ListOf<TextGlyph>) newContextObject;
            listOfTextGlyphs.setSBaseListType(ListOf.Type.other);
            layout.setListOfTextGlyphs(listOfTextGlyphs);
            groupList = LayoutList.listOfTextGlyphs;
            return listOfTextGlyphs;
          }
        } else if (contextObject instanceof ReactionGlyph) {
          ReactionGlyph reactionGlyph = (ReactionGlyph) contextObject;
          if (elementName.equals("curve")
              && groupList.equals(LayoutList.listOfReactionGlyphs)) {
            Curve curve = (Curve) newContextObject;
            setNamespace(curve, namespaceURI);
            reactionGlyph.setCurve(curve);
            return curve;
          } else if (elementName
              .equals("listOfSpeciesReferenceGlyphs")
              && groupList.equals(LayoutList.listOfReactionGlyphs)) {
            ListOf<SpeciesReferenceGlyph> listOfSpeciesReferenceGlyphs = (ListOf<SpeciesReferenceGlyph>) newContextObject;
            listOfSpeciesReferenceGlyphs.setSBaseListType(ListOf.Type.other);
            reactionGlyph.setListOfSpeciesReferencesGlyph(listOfSpeciesReferenceGlyphs);
            groupList = LayoutList.listOfSpeciesReferenceGlyphs;
            return listOfSpeciesReferenceGlyphs;
          } else if (elementName.equals("boundingBox")) {
            BoundingBox boundingBox = (BoundingBox) newContextObject;
            setNamespace(boundingBox, namespaceURI);
            reactionGlyph.setBoundingBox(boundingBox);
            return boundingBox;
          }
        } else if (contextObject instanceof SpeciesGlyph) {
          SpeciesGlyph speciesGlyph = (SpeciesGlyph) contextObject;
          if (elementName.equals("boundingBox")) {
            BoundingBox boundingBox = (BoundingBox) newContextObject;
            setNamespace(boundingBox, namespaceURI);
            speciesGlyph.setBoundingBox(boundingBox);
            return boundingBox;
          }
        } else if (contextObject instanceof CompartmentGlyph) {
          if (elementName.equals("boundingBox")
              && groupList.equals(LayoutList.listOfCompartmentGlyphs)) {
            CompartmentGlyph compartmentGlyph = (CompartmentGlyph) contextObject;
            BoundingBox boundingBox = (BoundingBox) newContextObject;
            setNamespace(boundingBox, namespaceURI);
            compartmentGlyph.setBoundingBox(boundingBox);
            return boundingBox;
          }
        } else if (contextObject instanceof TextGlyph) {
          if (elementName.equals("boundingBox")
              && groupList.equals(LayoutList.listOfTextGlyphs)) {
            TextGlyph textGlyph = (TextGlyph) contextObject;
            BoundingBox boundingBox = (BoundingBox) newContextObject;
            setNamespace(boundingBox, namespaceURI);
            textGlyph.setBoundingBox(boundingBox);
            return boundingBox;
          }
        } else if (contextObject instanceof Curve) {
          if (elementName.equals("listOfCurveSegments")
              && groupList.equals(LayoutList.listOfReactionGlyphs)) {
            Curve curve = (Curve) contextObject;
            ListOf<CurveSegment> listOfCurveSegments = (ListOf<CurveSegment>) newContextObject;
            listOfCurveSegments.setSBaseListType(ListOf.Type.other);
            setNamespace(listOfCurveSegments, namespaceURI);
            curve.setListOfCurveSegments(listOfCurveSegments);
            groupList = LayoutList.listOfReactionGlyphs;
            return listOfCurveSegments;
          } else if (elementName.equals("listOfCurveSegments")
              && groupList.equals(LayoutList.listOfSpeciesReferenceGlyphs)) {
            Curve curve = (Curve) contextObject;
            ListOf<CurveSegment> listOfCurveSegments = (ListOf<CurveSegment>) newContextObject;
            listOfCurveSegments.setSBaseListType(ListOf.Type.other);
            setNamespace(listOfCurveSegments, namespaceURI);
            curve.setListOfCurveSegments(listOfCurveSegments);
            groupList = LayoutList.listOfSpeciesReferenceGlyphs;
            return listOfCurveSegments;
          }
        } else if (contextObject instanceof BoundingBox) {
          BoundingBox boundingBox = (BoundingBox) contextObject;
          if (elementName.equals("position")) {
            Point point = (Point) newContextObject;
            setNamespace(point, namespaceURI);
            boundingBox.setPosition(point);
            return point;
          } else if (elementName.equals("dimensions")) {
            Dimensions dimensions = (Dimensions) newContextObject;
            setNamespace(dimensions, namespaceURI);
            boundingBox.setDimensions(dimensions);
            return dimensions;
          }
        } else if (contextObject instanceof CurveSegment) {
          if (elementName.equals("start")) {
            CurveSegment lineSegment = (CurveSegment) contextObject;
            Point start = (Point) newContextObject;
            lineSegment.setStart(start);
            setNamespace(start, namespaceURI);
            return start;
          } else if (elementName.equals("end")) {
            CurveSegment lineSegment = (CurveSegment) contextObject;
            Point end = (Point) newContextObject;
            lineSegment.setEnd(end);
            setNamespace(end, namespaceURI);
            return end;
          } else if (elementName.equals("basePoint1")) {
            CubicBezier lineSegment = (CubicBezier) contextObject;


            BasePoint1 basePoint1 = (BasePoint1) newContextObject;
            lineSegment.setBasePoint1(basePoint1);
            setNamespace(basePoint1, namespaceURI);
            return basePoint1;
          } else if (elementName.equals("basePoint2")) {
            CubicBezier lineSegment = (CubicBezier) contextObject;
            BasePoint2 basePoint2 = (BasePoint2) newContextObject;
            lineSegment.setBasePoint2(basePoint2);
            setNamespace(basePoint2, namespaceURI);
            return basePoint2;
          }
        } else if (contextObject instanceof SpeciesReferenceGlyph
            && groupList.equals(LayoutList.listOfSpeciesReferenceGlyphs)) {
          SpeciesReferenceGlyph speciesReferenceGlyph = (SpeciesReferenceGlyph) contextObject;
          if (elementName.equals("curve")) {
            Curve curve = (Curve) newContextObject;
            speciesReferenceGlyph.setCurve(curve);
            setNamespace(curve, namespaceURI);
            return curve;
          } else if (elementName.equals("boundingBox")) {
            BoundingBox boundingBox = (BoundingBox) newContextObject;
            setNamespace(boundingBox, namespaceURI);
            speciesReferenceGlyph.setBoundingBox(boundingBox);
            return boundingBox;
          }
        } else {

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Related Classes of org.sbml.jsbml.ext.layout.BoundingBox

cysbml.layout.CytoscapeLayoutTools

cysbml.layout.NetworkLayout

org.sbml.jsbml.ext.render.LineEnding

org.sbml.jsbml.xml.parsers.L3LayoutParser

org.sbml.jsbml.xml.parsers.LayoutParser

org.sbml.jsbml.xml.parsers.RenderParser

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