Package org.sbml.jsbml.ext.layout

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


      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;
      }
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          return o instanceof Curve;
        }
      });

      for (TreeNode curveNode : curveElements) {
        Curve curve = (Curve) curveNode;

        // transform the CubicBezier into LineSegment when needed
        int i = 0;
        for (CurveSegment curveSegment : curve.getListOfCurveSegments().clone())
        {
          if (! curveSegment.isSetType())
          {
            if (((CubicBezier) curveSegment).isSetBasePoint1() || ((CubicBezier) curveSegment).isSetBasePoint2())
            {
              // trick to set the 'type' attribute, although the setType method is not visible.
              curveSegment.readAttribute("type", "", CurveSegment.Type.CUBIC_BEZIER.toString());
            }
            else
            {
              curveSegment.readAttribute("type", "", CurveSegment.Type.LINE_SEGMENT.toString());
            }
          }

          if (curveSegment.getType().equals(CurveSegment.Type.LINE_SEGMENT))
          {
            LineSegment realCurveSegment = new LineSegment(curveSegment);
            logger.debug("Transformed CubicBezier: " + curveSegment + " into a LineSegment.");
            curve.getListOfCurveSegments().remove(i);
            curve.getListOfCurveSegments().add(i, realCurveSegment);
          }

          if (logger.isDebugEnabled())
          {
            logger.debug("CurveSegment = " + curve.getListOfCurveSegments().get(i));
          }

          i++;
        }
      }
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        }
      });

      for (TreeNode curveNode : curveElements)
      {
        Curve curve = (Curve) curveNode;

        // transform the CubicBezier into LineSegment
        int i = 0;
        for (CurveSegment curveSegment : curve.getListOfCurveSegments().clone())
        {
          // Making sure the type attribute is set
          if (! curveSegment.isSetType())
          {
            if (((CubicBezier) curveSegment).isSetBasePoint1() || ((CubicBezier) curveSegment).isSetBasePoint2())
            {
              // trick to set the 'type' attribute, although the setType method is not visible.
              curveSegment.readAttribute("type", "", CurveSegment.Type.CUBIC_BEZIER.toString());
            }
            else
            {
              curveSegment.readAttribute("type", "", CurveSegment.Type.LINE_SEGMENT.toString());
            }
          }

          if (curveSegment.getType().equals(CurveSegment.Type.LINE_SEGMENT))
          {
            LineSegment realCurveSegment = new LineSegment(curveSegment);
            setNamespace(realCurveSegment, namespaceURI);
            logger.debug("Transformed CubicBezier: " + curveSegment + " into LineSegment.");
            curve.getListOfCurveSegments().remove(i);
            curve.getListOfCurveSegments().add(i, realCurveSegment);
          }

          if (logger.isDebugEnabled())
          {
            logger.debug("Transformed CurveSegment: realCurveSegment = " + curve.getListOfCurveSegments().get(i));
          }

          i++;
        }
      }
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          }
        } 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;
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