Examples with BoundingSphere javax.media.j3d.BoundingSphere used on opensource projects

Example 1 with BoundingSphere

use of javax.media.j3d.BoundingSphere in project ffx by mjschnie.

the class MolecularAssembly method createBox.

/**
 * <p>
 * createBox</p>
 */
public void createBox() {
    int vertices = 8;
    LineArray la = new LineArray(4 * vertices, GeometryArray.COORDINATES | GeometryArray.COLOR_4 | GeometryArray.NORMALS);
    la.setCapability(LineArray.ALLOW_COORDINATE_WRITE);
    la.setCapability(LineArray.ALLOW_COORDINATE_READ);
    la.setCapability(LineArray.ALLOW_COLOR_WRITE);
    la.setCapability(LineArray.ALLOW_COUNT_READ);
    la.setCapability(LineArray.ALLOW_INTERSECT);
    la.setCapability(LineArray.ALLOW_FORMAT_READ);
    // Create a normal
    // for (ListIterator<MSNode> li = bondlist.listIterator(); li.hasNext(); ){
    // la.setCoordinate(i, a1);
    // la.setColor(i, col);
    // la.setNormal(i++, a1);
    // }
    ColoringAttributes cola = new ColoringAttributes(new Color3f(), ColoringAttributes.SHADE_GOURAUD);
    Appearance app = new Appearance();
    lineAttributes = new LineAttributes();
    lineAttributes.setLineWidth(RendererCache.bondwidth);
    lineAttributes.setCapability(LineAttributes.ALLOW_WIDTH_WRITE);
    lineAttributes.setLineAntialiasingEnable(true);
    app.setLineAttributes(lineAttributes);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE);
    RenderingAttributes ra = new RenderingAttributes();
    ra.setAlphaTestValue(0.1f);
    ra.setAlphaTestFunction(RenderingAttributes.GREATER);
    ra.setDepthBufferEnable(true);
    ra.setDepthBufferWriteEnable(true);
    app.setRenderingAttributes(ra);
    app.setColoringAttributes(cola);
    Shape3D wireframe = new Shape3D(la, app);
    // PickTool.setCapabilities(wire, PickTool.INTERSECT_COORD);
    wireframe.setUserData(this);
    wireframe.setBounds(new BoundingSphere(new Point3d(0, 0, 0), 10.0));
    try {
        wireframe.setBoundsAutoCompute(false);
    } catch (Exception e) {
        e.printStackTrace();
    }
    wireframe.setCapability(Shape3D.ALLOW_GEOMETRY_READ);
    wireframe.setCapability(Shape3D.ALLOW_APPEARANCE_READ);
// return wire;
}

Example 2 with BoundingSphere

use of javax.media.j3d.BoundingSphere in project ffx by mjschnie.

the class MolecularAssembly method renderWire.

private Shape3D renderWire() {
    ArrayList<ROLS> bonds = getBondList();
    int numbonds = bonds.size();
    if (numbonds < 1) {
        return null;
    }
    Vector3d bondmidpoint = new Vector3d();
    double[] mid = { 0, 0, 0 };
    Vector3d v1 = new Vector3d();
    Vector3d v2 = new Vector3d();
    float[] a1 = { 0, 0, 0 };
    float[] a2 = { 0, 0, 0 };
    float[] col = new float[4];
    Bond bond;
    Atom atom1, atom2;
    LineArray la = new LineArray(4 * numbonds, GeometryArray.COORDINATES | GeometryArray.COLOR_4 | GeometryArray.NORMALS);
    la.setCapability(LineArray.ALLOW_COORDINATE_WRITE);
    la.setCapability(LineArray.ALLOW_COORDINATE_READ);
    la.setCapability(LineArray.ALLOW_COLOR_WRITE);
    la.setCapability(LineArray.ALLOW_COUNT_READ);
    la.setCapability(LineArray.ALLOW_INTERSECT);
    la.setCapability(LineArray.ALLOW_FORMAT_READ);
    atomLookUp = new Atom[4 * numbonds];
    int i = 0;
    col[3] = 0.9f;
    for (ListIterator<ROLS> li = bonds.listIterator(); li.hasNext(); ) {
        bond = (Bond) li.next();
        bond.setWire(la, i);
        atom1 = bond.getAtom(0);
        atom2 = bond.getAtom(1);
        atom1.getV3D(v1);
        atom2.getV3D(v2);
        a1[0] = (float) v1.x;
        a1[1] = (float) v1.y;
        a1[2] = (float) v1.z;
        a2[0] = (float) v2.x;
        a2[1] = (float) v2.y;
        a2[2] = (float) v2.z;
        // Find the bond center
        bondmidpoint.add(v1, v2);
        bondmidpoint.scale(0.5d);
        bondmidpoint.get(mid);
        // Atom #1
        Atom.AtomColor.get(atom1.getAtomicNumber()).get(col);
        atomLookUp[i] = atom1;
        la.setCoordinate(i, a1);
        la.setColor(i, col);
        la.setNormal(i, a2);
        i++;
        atomLookUp[i] = atom1;
        la.setCoordinate(i, mid);
        la.setColor(i, col);
        la.setNormal(i, a2);
        i++;
        // Atom #2
        Atom.AtomColor.get(atom2.getAtomicNumber()).get(col);
        atomLookUp[i] = atom2;
        la.setCoordinate(i, a2);
        la.setColor(i, col);
        la.setNormal(i, a1);
        i++;
        atomLookUp[i] = atom2;
        la.setCoordinate(i, mid);
        la.setColor(i, col);
        la.setNormal(i, a1);
        i++;
    }
    ColoringAttributes cola = new ColoringAttributes(new Color3f(), ColoringAttributes.SHADE_GOURAUD);
    Appearance app = new Appearance();
    lineAttributes = new LineAttributes();
    lineAttributes.setLineWidth(RendererCache.bondwidth);
    lineAttributes.setCapability(LineAttributes.ALLOW_WIDTH_WRITE);
    lineAttributes.setLineAntialiasingEnable(true);
    app.setLineAttributes(lineAttributes);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE);
    RenderingAttributes ra = new RenderingAttributes();
    ra.setAlphaTestValue(0.1f);
    ra.setAlphaTestFunction(RenderingAttributes.GREATER);
    ra.setDepthBufferEnable(true);
    ra.setDepthBufferWriteEnable(true);
    app.setRenderingAttributes(ra);
    app.setColoringAttributes(cola);
    Shape3D wireframe = new Shape3D(la, app);
    // PickTool.setCapabilities(wire, PickTool.INTERSECT_COORD);
    wireframe.setUserData(this);
    wireframe.setBounds(new BoundingSphere(new Point3d(0, 0, 0), 1000.0));
    try {
        wireframe.setBoundsAutoCompute(false);
    } catch (Exception e) {
        e.printStackTrace();
    }
    wireframe.setCapability(Shape3D.ALLOW_GEOMETRY_READ);
    wireframe.setCapability(Shape3D.ALLOW_APPEARANCE_READ);
    wireframe.setCapability(Shape3D.ALLOW_LOCAL_TO_VWORLD_READ);
    return wireframe;
}

Example 3 with BoundingSphere

use of javax.media.j3d.BoundingSphere in project ffx by mjschnie.

the class GraphicsCanvas method initialize.

/**
 * Initialization of the GraphisCanvas.
 */
private void initialize() {
    setBackground(Color.black);
    universe = new SimpleUniverse(this);
    SimpleUniverse.setJ3DThreadPriority(Thread.MAX_PRIORITY);
    universe.getViewingPlatform().setNominalViewingTransform();
    // Create the Scene Root BranchGroup
    BranchGroup objRoot = new BranchGroup();
    baseTransformGroup = new TransformGroup();
    Transform3D t3d = new Transform3D();
    t3d.setScale(0.1d);
    baseTransformGroup.setTransform(t3d);
    baseTransformGroup.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
    baseTransformGroup.setCapability(TransformGroup.ALLOW_TRANSFORM_READ);
    // Set the Background
    Color3f bgColor = new Color3f(RendererCache.BLACK);
    background = new Background(bgColor);
    background.setCapability(Background.ALLOW_COLOR_READ);
    background.setCapability(Background.ALLOW_COLOR_WRITE);
    bounds = new BoundingSphere(new Point3d(0.0, 0.0, 0.0), 2000.0);
    background.setApplicationBounds(bounds);
    // Create lights
    AmbientLight aLgt = new AmbientLight(new Color3f(Color.darkGray));
    aLgt.setInfluencingBounds(bounds);
    Vector3f dir = new Vector3f(0.0f, -1.0f, -1.0f);
    Color3f dLgtColor = new Color3f(Color.lightGray);
    DirectionalLight dLgt = new DirectionalLight(dLgtColor, dir);
    dLgt.setInfluencingBounds(bounds);
    dir = new Vector3f(0.0f, 1.0f, -1.0f);
    dLgtColor = new Color3f(0.1f, 0.1f, 0.1f);
    DirectionalLight dLgt2 = new DirectionalLight(dLgtColor, dir);
    dLgt2.setInfluencingBounds(bounds);
    // Create the Base of the Molecular Scene
    baseBranchGroup = new BranchGroup();
    baseBranchGroup.setCapability(BranchGroup.ALLOW_CHILDREN_EXTEND);
    baseBranchGroup.setCapability(BranchGroup.ALLOW_CHILDREN_READ);
    baseBranchGroup.setCapability(BranchGroup.ALLOW_CHILDREN_WRITE);
    baseBranchGroup.setCapability(BranchGroup.ALLOW_BOUNDS_READ);
    // Add children created above to the base TransformGroup
    baseTransformGroup.addChild(background);
    baseTransformGroup.addChild(baseBranchGroup);
    objRoot.addChild(baseTransformGroup);
    // Position the view platmform and add lights
    View v = universe.getViewer().getView();
    v.setProjectionPolicy(View.PARALLEL_PROJECTION);
    v.setFrontClipPolicy(View.VIRTUAL_EYE);
    v.setFrontClipDistance(1.0);
    v.setBackClipPolicy(View.VIRTUAL_EYE);
    v.setBackClipDistance(10.0);
    v.setTransparencySortingPolicy(View.TRANSPARENCY_SORT_NONE);
    Transform3D trans = new Transform3D();
    trans.set(new Vector3d(0.0d, 0.0d, 2.0d));
    TransformGroup vptg = universe.getViewingPlatform().getViewPlatformTransform();
    vptg.setTransform(trans);
    BranchGroup viewBranch = new BranchGroup();
    viewBranch.addChild(aLgt);
    viewBranch.addChild(dLgt);
    viewBranch.addChild(dLgt2);
    vptg.addChild(viewBranch);
    // Initialize Behaviors
    graphicsAxis = new GraphicsAxis(universe.getViewingPlatform(), this, bounds);
    graphicsEvents = new GraphicsEvents(mainPanel, this, graphicsAxis, universe, bounds, baseBranchGroup, baseTransformGroup);
    baseBranchGroup.addChild(graphicsEvents);
    rendererPicking = new GraphicsPicking(baseBranchGroup, bounds, this, mainPanel);
    baseBranchGroup.addChild(rendererPicking);
    renderer = new ffx.potential.Renderer(bounds, mainPanel.getStatusBar());
    baseBranchGroup.addChild(renderer);
    // Compile the Root BranchGroup and add it to the Universe
    objRoot.compile();
    universe.addBranchGraph(objRoot);
}