示例#1
0
 /** Reverses the tangents and normals associated with this BSpline */
 public void reverseNormalsAndTangents() {
   for (CubicBezier b : approximationCurves) {
     for (Vector2 p : b.getNormalReferences()) p.mul(-1);
     for (Vector2 p : b.getTangentReferences()) p.mul(-1);
   }
 }
  public static void main(String args[]) {

    // create the document

    SBMLDocument document = new SBMLDocument(2, 1);

    // ensure the layout api is enabled
    document.enablePackage(LayoutExtension.getXmlnsL2(), "layout", true);

    // create the Model

    Model model = document.createModel("TestModel");

    // create the Compartment

    Compartment compartment = model.createCompartment();
    compartment.setId("Compartment_1");

    // create the Species

    Species species1 = model.createSpecies();
    species1.setId("Species_1");
    species1.setCompartment(compartment.getId());

    Species species2 = model.createSpecies();
    species2.setId("Species_2");
    species2.setCompartment(compartment.getId());

    // create the Reactions

    Reaction reaction1 = model.createReaction();
    reaction1.setId("Reaction_1");

    SpeciesReference reference1 = reaction1.createReactant();
    reference1.setSpecies(species1.getId());
    reference1.setId("SpeciesReference_1");

    reaction1.setReversible(false);

    SpeciesReference reference2 = reaction1.createProduct();
    reference2.setSpecies(species2.getId());
    reference2.setId("SpeciesReference_2");

    Reaction reaction2 = model.createReaction();
    reaction2.setId("Reaction_2");
    reaction2.setReversible(false);

    SpeciesReference reference3 = reaction2.createReactant();
    reference3.setSpecies(species2.getId());
    reference3.setId("SpeciesReference_3");

    SpeciesReference reference4 = reaction2.createProduct();
    reference4.setSpecies(species1.getId());
    reference4.setId("SpeciesReference_4");

    // create the Layout

    LayoutModelPlugin mplugin = (LayoutModelPlugin) (model.getPlugin("layout"));
    Layout layout = mplugin.createLayout();

    layout.setId("Layout_1");
    layout.setDimensions(createDimensions(400, 220));

    // create the CompartmentGlyph

    CompartmentGlyph compartmentGlyph = layout.createCompartmentGlyph();
    compartmentGlyph.setId("CompartmentGlyph_1");
    compartmentGlyph.setCompartmentId(compartment.getId());
    compartmentGlyph.setBoundingBox(createBoundingBox("bb1", 5, 5, 390, 210));

    // create the SpeciesGlyphs

    SpeciesGlyph speciesGlyph1 = layout.createSpeciesGlyph();
    speciesGlyph1.setId("SpeciesGlyph_1");
    speciesGlyph1.setSpeciesId(species1.getId());
    speciesGlyph1.setBoundingBox(createBoundingBox("bb2", 80, 26, 240, 24));

    TextGlyph textGlyph1 = layout.createTextGlyph();
    textGlyph1.setId("TextGlyph_01");
    textGlyph1.setBoundingBox(createBoundingBox("bbA", 92, 26, 228, 24));
    textGlyph1.setOriginOfTextId(speciesGlyph1.getId());
    textGlyph1.setGraphicalObjectId(speciesGlyph1.getId());

    SpeciesGlyph speciesGlyph2 = layout.createSpeciesGlyph();
    speciesGlyph2.setId("SpeciesGlyph_2");
    speciesGlyph2.setSpeciesId(species2.getId());
    speciesGlyph2.setBoundingBox(createBoundingBox("bb3", 80, 170, 240, 24));

    TextGlyph textGlyph2 = layout.createTextGlyph();
    textGlyph2.setId("TextGlyph_02");
    textGlyph2.setBoundingBox(createBoundingBox("bbB", 92, 170, 228, 24));
    textGlyph2.setOriginOfTextId(speciesGlyph2.getId());
    textGlyph2.setGraphicalObjectId(speciesGlyph2.getId());

    // create the ReactionGlyphs

    ReactionGlyph reactionGlyph1 = layout.createReactionGlyph();
    reactionGlyph1.setId("ReactionGlyph_1");
    reactionGlyph1.setReactionId(reaction1.getId());

    Curve reactionCurve1 = reactionGlyph1.getCurve();
    LineSegment ls = reactionCurve1.createLineSegment();
    ls.setStart(createPoint(165, 105));
    ls.setEnd(createPoint(165, 115));

    ReactionGlyph reactionGlyph2 = layout.createReactionGlyph();
    reactionGlyph2.setId("ReactionGlyph_1");
    reactionGlyph2.setReactionId(reaction2.getId());

    Curve reactionCurve2 = reactionGlyph2.getCurve();
    ls = reactionCurve2.createLineSegment();
    ls.setStart(createPoint(235, 105));
    ls.setEnd(createPoint(235, 115));

    // add the SpeciesReferenceGlyphs

    SpeciesReferenceGlyph speciesReferenceGlyph1 = reactionGlyph1.createSpeciesReferenceGlyph();
    speciesReferenceGlyph1.setId("SpeciesReferenceGlyph_1");
    speciesReferenceGlyph1.setSpeciesGlyphId(speciesGlyph1.getId());
    speciesReferenceGlyph1.setSpeciesReferenceId(reference1.getId());
    speciesReferenceGlyph1.setRole(libsbmlConstants.SPECIES_ROLE_SUBSTRATE);

    Curve speciesReferenceCurve1 = speciesReferenceGlyph1.getCurve();
    CubicBezier cb = speciesReferenceCurve1.createCubicBezier();
    cb.setStart(createPoint(165.0, 105.0));
    cb.setBasePoint1(createPoint(165.0, 90.0));
    cb.setBasePoint2(createPoint(165.0, 90.0));
    cb.setEnd(createPoint(195.0, 60.0));

    SpeciesReferenceGlyph speciesReferenceGlyph2 = reactionGlyph1.createSpeciesReferenceGlyph();
    speciesReferenceGlyph2.setId("SpeciesReferenceGlyph_2");
    speciesReferenceGlyph2.setSpeciesGlyphId(speciesGlyph2.getId());
    speciesReferenceGlyph2.setSpeciesReferenceId(reference2.getId());
    speciesReferenceGlyph2.setRole(libsbmlConstants.SPECIES_ROLE_PRODUCT);

    Curve speciesReferenceCurve2 = speciesReferenceGlyph2.getCurve();
    cb = speciesReferenceCurve2.createCubicBezier();
    cb.setStart(createPoint(165.0, 115.0));
    cb.setBasePoint1(createPoint(165.0, 130.0));
    cb.setBasePoint2(createPoint(165.0, 130.0));
    cb.setEnd(createPoint(195.0, 160.0));

    SpeciesReferenceGlyph speciesReferenceGlyph3 = reactionGlyph2.createSpeciesReferenceGlyph();
    speciesReferenceGlyph3.setId("SpeciesReferenceGlyph_3");
    speciesReferenceGlyph3.setSpeciesGlyphId(speciesGlyph2.getId());
    speciesReferenceGlyph3.setSpeciesReferenceId(reference3.getId());
    speciesReferenceGlyph3.setRole(libsbmlConstants.SPECIES_ROLE_SUBSTRATE);

    Curve speciesReferenceCurve3 = speciesReferenceGlyph3.getCurve();
    cb = speciesReferenceCurve3.createCubicBezier();
    cb.setStart(createPoint(235.0, 115.0));
    cb.setBasePoint1(createPoint(235.0, 130.0));
    cb.setBasePoint2(createPoint(235.0, 130.0));
    cb.setEnd(createPoint(205.0, 160.0));

    SpeciesReferenceGlyph speciesReferenceGlyph4 = reactionGlyph2.createSpeciesReferenceGlyph();
    speciesReferenceGlyph4.setId("SpeciesReferenceGlyph_4");
    speciesReferenceGlyph4.setSpeciesGlyphId(speciesGlyph1.getId());
    speciesReferenceGlyph4.setSpeciesReferenceId(reference4.getId());
    speciesReferenceGlyph4.setRole(libsbmlConstants.SPECIES_ROLE_PRODUCT);

    Curve speciesReferenceCurve4 = speciesReferenceGlyph4.getCurve();
    cb = speciesReferenceCurve4.createCubicBezier();
    cb.setStart(createPoint(235.0, 105.0));
    cb.setBasePoint1(createPoint(235.0, 90.0));
    cb.setBasePoint2(createPoint(235.0, 90.0));
    cb.setEnd(createPoint(205.0, 60.0));

    libsbml.writeSBML(document, "TestModel1-java.xml");

    System.gc();
  }
示例#3
0
 /**
  * Returns the sequence of normals on this BSpline specified by the sequence of approximation
  * curves
  */
 public ArrayList<Vector2> getTangents() {
   ArrayList<Vector2> returnList = new ArrayList<Vector2>();
   for (CubicBezier b : approximationCurves)
     for (Vector2 p : b.getTangents()) returnList.add(p.clone());
   return returnList;
 }