Examples with Color3f javax.vecmath.Color3f used on opensource projects

Example 6 with Color3f

use of javax.vecmath.Color3f 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 7 with Color3f

use of javax.vecmath.Color3f in project ffx by mjschnie.

the class RendererCache method getColor.

/**
 * <p>
 * getColor</p>
 *
 * @param a a {@link ffx.potential.bonded.Atom} object.
 * @param mode a {@link ffx.potential.bonded.RendererCache.ColorModel}
 * object.
 * @return a {@link javax.vecmath.Color3f} object.
 */
public static final Color3f getColor(Atom a, ColorModel mode) {
    switch(mode) {
        case CPK:
            return Atom.AtomColor.get(a.getAtomicNumber());
        case PICK:
            return pickingColor;
        case SELECT:
            return selectionColor;
        case PARTIALCHARGE:
            int index = 0;
            double charge = a.getCharge();
            if (charge < 0.0d) {
                float c = (float) (charge * 1000.0);
                index = -1 * Math.round(c);
                if (index > 999) {
                    index = 999;
                }
                if (negCharge[index] == null) {
                    float value = index * 0.001f;
                    negCharge[index] = new Color3f(1.0f, 1.0f - value, 1.0f - value);
                }
                return negCharge[index];
            } else if (charge == 0) {
                return WHITE;
            } else {
                float c = (float) (charge * 1000.0);
                index = Math.round(c);
                if (index > 999) {
                    index = 999;
                }
                if (posCharge[index] == null) {
                    float value = index * 0.001f;
                    posCharge[index] = new Color3f(1.0f - value, 1.0f - value, 1.0f);
                }
                return posCharge[index];
            }
        default:
            return NULLColor;
    }
}

Example 8 with Color3f

use of javax.vecmath.Color3f in project ffx by mjschnie.

the class GraphicsAxis method createAxis.

/**
 * <p>
 * createAxis</p>
 */
public void createAxis() {
    Appearance ap = new Appearance();
    Color3f col = new Color3f(Color.lightGray);
    Color3f black = new Color3f(Color.black);
    Color3f white = new Color3f(Color.white);
    Material mat = new Material(col, black, col, white, 50.0f);
    mat.setLightingEnable(true);
    ap.setMaterial(mat);
    // X-Axis
    Cone xcone = new Cone(2.0f, 3.0f, ap);
    xcone.setUserData(this);
    Transform3D xconeT3d = new Transform3D();
    xconeT3d.setTranslation(new Vector3d(10.0f, 0.0f, 0.0f));
    xconeT3d.setRotation(new AxisAngle4f(0.0f, 0.0f, 1.0f, (float) Math.PI / -2.0f));
    TransformGroup xconeTG = new TransformGroup(xconeT3d);
    xconeTG.addChild(xcone);
    Cylinder xcylinder = new Cylinder(1.0f, 9.0f, ap);
    xcylinder.setUserData(this);
    Transform3D xcyT3d = new Transform3D();
    xcyT3d.setTranslation(new Vector3d(4.5, 0.0, 0.0));
    xcyT3d.setRotation(new AxisAngle4f(0.0f, 0.0f, 1.0f, (float) Math.PI / 2.0f));
    TransformGroup xcyTG = new TransformGroup(xcyT3d);
    xcyTG.addChild(xcylinder);
    setCapabilities(xcone, xcylinder);
    addChild(xconeTG);
    addChild(xcyTG);
    // Y-Axis
    Cone ycone = new Cone(2.0f, 3.0f, ap);
    ycone.setUserData(this);
    Transform3D yconeT3d = new Transform3D();
    yconeT3d.setTranslation(new Vector3d(0.0f, 10.0f, 0.0f));
    TransformGroup yconeTG = new TransformGroup(yconeT3d);
    yconeTG.addChild(ycone);
    Cylinder ycylinder = new Cylinder(1.0f, 9.0f, ap);
    ycylinder.setUserData(this);
    Transform3D ycyT3d = new Transform3D();
    ycyT3d.setTranslation(new Vector3d(0.0, 4.5, 0.0));
    TransformGroup ycyTG = new TransformGroup(ycyT3d);
    ycyTG.addChild(ycylinder);
    setCapabilities(ycone, ycylinder);
    addChild(yconeTG);
    addChild(ycyTG);
    // Z-Axis
    Cone zcone = new Cone(2.0f, 3.0f, ap);
    zcone.setUserData(this);
    Transform3D zconeT3d = new Transform3D();
    zconeT3d.setTranslation(new Vector3d(0.0f, 0.0f, 10.0f));
    zconeT3d.setRotation(new AxisAngle4f(1.0f, 0.0f, 0.0f, (float) Math.PI / 2.0f));
    TransformGroup zconeTG = new TransformGroup(zconeT3d);
    zconeTG.addChild(zcone);
    Cylinder zcylinder = new Cylinder(1.0f, 9.0f, ap);
    zcylinder.setUserData(this);
    Transform3D zcyT3d = new Transform3D();
    zcyT3d.setTranslation(new Vector3d(0.0, 0.0, 4.5));
    zcyT3d.setRotation(new AxisAngle4f(1.0f, 0.0f, 0.0f, (float) Math.PI / 2.0f));
    TransformGroup zcyTG = new TransformGroup(zcyT3d);
    zcyTG.addChild(zcylinder);
    setCapabilities(zcone, zcylinder);
    addChild(zconeTG);
    addChild(zcyTG);
    Sphere sphere = new Sphere(1.0f, ap);
    if (!sphere.getShape().getGeometry(0).isCompiled() && !sphere.getShape().getGeometry(0).isLive()) {
        PickTool.setCapabilities(sphere.getShape(), PickTool.INTERSECT_COORD);
    }
    addChild(sphere);
    // Labels
    ap = new Appearance();
    col = new Color3f(Color.green);
    mat = new Material(col, black, col, white, 50.0f);
    mat.setLightingEnable(true);
    ap.setMaterial(mat);
    Font font = new Font("Arial", Font.PLAIN, 4);
    Font3D font3d = new Font3D(font, new FontExtrusion());
    addChild(createAxisLabel("X", font3d, ap, 11.0, 0.0, 0.0));
    addChild(createAxisLabel("Y", font3d, ap, 0.0, 11.0, 0.0));
    addChild(createAxisLabel("Z", font3d, ap, 0.0, 0.0, 11.0));
}

Example 9 with Color3f

use of javax.vecmath.Color3f in project ffx by mjschnie.

the class GraphicsCanvas method setBackgroundColor.

/**
 * <p>
 * setBackgroundColor</p>
 */
public void setBackgroundColor() {
    Color3f col = new Color3f();
    background.getColor(col);
    Color newcolor = JColorChooser.showDialog(this, "Choose Background Color", col.get());
    if (newcolor != null && newcolor != col.get()) {
        background.setColor(new Color3f(newcolor));
    }
}

Example 10 with Color3f

use of javax.vecmath.Color3f 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);
}