private void createLoaderSceneGraph() {
loaderBranchGroup = new BranchGroup();
loaderBranchGroup.setCapability(BranchGroup.ALLOW_DETACH);
loaderTransformGroup = new TransformGroup();
loaderTransformGroup.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
addLights(loaderBranchGroup);
Appearance loaderAppearance = new Appearance();
Color3f loaderColor = new Color3f(0.5f, 0.5f, 0.5f);
Material loaderMaterial =
new Material(loaderColor, new Color3f(), loaderColor, loaderColor, 10);
loaderMaterial.setLightingEnable(true);
loaderAppearance.setMaterial(loaderMaterial);
for (int i = 0; i < 20; i++) {
Transform3D translate3d = new Transform3D();
translate3d.setTranslation(new Vector3f(0f, 0f, 0.9f));
TransformGroup translate = new TransformGroup(translate3d);
Transform3D rotationY3d = new Transform3D();
rotationY3d.rotY((Math.PI * 2 * i) / 20);
TransformGroup rotateY = new TransformGroup(rotationY3d);
rotateY.addChild(translate);
Box box = new Box(0.1f, 0.1f, 0.1f, loaderAppearance);
translate.addChild(box);
loaderTransformGroup.addChild(rotateY);
}
loaderBranchGroup.addChild(loaderTransformGroup);
sceneBranchGroup.addChild(loaderBranchGroup);
}
private Appearance makeMaterial(float r, float g, float b, float transparency) {
Appearance appearance = new Appearance();
Color3f color3f = new Color3f(r, g, b);
Material material = new Material(color3f, new Color3f(0f, 0f, 0f), color3f, color3f, 10f);
material.setLightingEnable(true);
appearance.setMaterial(material);
if (!Float.isNaN(transparency)) {
TransparencyAttributes ta = new TransparencyAttributes();
ta.setTransparencyMode(TransparencyAttributes.NICEST);
ta.setTransparency(transparency);
appearance.setTransparencyAttributes(ta);
}
return appearance;
}
public MoonSphere() {
Color3f eColor = new Color3f(1.0f, 1.0f, 1.0f);
Transform3D t3d = new Transform3D();
t3d.setTranslation(new Vector3d(0, -100, 0));
pos.setTransform(t3d);
addChild(pos);
// Create a Sphere object, generate one copy of the sphere,
// and add it into the scene graph.
Material m = new Material(new Color3f(), eColor, new Color3f(), new Color3f(), 1.0f);
Appearance a = new Appearance();
m.setLightingEnable(true);
a.setMaterial(m);
Sphere sph = new Sphere(2.0f, Primitive.GENERATE_NORMALS, 80, a);
pos.addChild(sph);
pos.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
}
private void setOtherAppearanceValues(int mode, float factor, Color color, boolean visible) {
// Transparency values
TransparencyAttributes ta = new TransparencyAttributes(mode, factor);
ta.setCapability(TransparencyAttributes.ALLOW_VALUE_READ);
ta.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE);
ta.setCapability(TransparencyAttributes.ALLOW_MODE_READ);
ta.setCapability(TransparencyAttributes.ALLOW_MODE_WRITE);
setTransparencyAttributes(ta);
setCapability(ALLOW_TRANSPARENCY_ATTRIBUTES_READ);
setCapability(ALLOW_TRANSPARENCY_ATTRIBUTES_WRITE);
// For highlight
setCapability(ALLOW_MATERIAL_READ);
setCapability(ALLOW_MATERIAL_WRITE);
// For visibility
setCapability(ALLOW_RENDERING_ATTRIBUTES_READ);
setCapability(ALLOW_RENDERING_ATTRIBUTES_WRITE);
// Color
setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_READ);
setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_WRITE);
// Adding Rendering attributes to access visibility flag if layer is available
if (layer != null) {
RenderingAttributes ra = new RenderingAttributes();
ra.setCapability(RenderingAttributes.ALLOW_VISIBLE_READ);
ra.setCapability(RenderingAttributes.ALLOW_VISIBLE_WRITE);
ra.setCapability(RenderingAttributes.ALLOW_DEPTH_ENABLE_READ);
ra.setCapability(RenderingAttributes.ALLOW_DEPTH_ENABLE_WRITE);
ra.setVisible(visible);
setRenderingAttributes(ra);
if (mode != TransparencyAttributes.NONE) ra.setDepthBufferEnable(true);
}
// Set up the polygon attributes
// PolygonAttributes pa = new PolygonAttributes();
// pa.setCullFace(PolygonAttributes.CULL_NONE);
// pa.setPolygonMode(PolygonAttributes.POLYGON_LINE);
// setPolygonAttributes(pa);
// TextureAttributes texAttr = new TextureAttributes();
// texAttr.setTextureMode(TextureAttributes.MODULATE);
// texAttr.setTextureColorTable(pattern);
// setTextureAttributes(texAttr);
// LineAttributes lineAttr = new LineAttributes();
// lineAttr.setLineAntialiasingEnable(true);
// setLineAttributes(lineAttr);
// Adding to internal material
// Material mat = new Material(objColor, black, objColor, white, 70.0f);
if (color != null) {
Color3f objColor = new Color3f(color);
// Emissive is black and specular is plastic!
// Color3f specular = new Color3f(color.brighter());
Material mat =
new Material(objColor, J3DUtils.black, objColor, J3DUtils.plastic /*J3DUtils.white*/, 17);
mat.setLightingEnable(true);
mat.setCapability(Material.ALLOW_COMPONENT_READ);
mat.setCapability(Material.ALLOW_COMPONENT_WRITE);
mat.setCapability(Material.AMBIENT_AND_DIFFUSE);
setMaterial(mat);
}
}
/**
* Build the 3D scene on a Java3D enabled draw.
*
* @param objRot the transform object
*/
@Override
public void buildJava3DScene(TransformGroup objRot) {
if (objRot == null) return;
AtomInfo ai = AtomInfo.getInstance();
double xMin = gridProperty.getBoundingBox().getUpperLeft().getX(),
yMin = gridProperty.getBoundingBox().getUpperLeft().getY(),
zMin = gridProperty.getBoundingBox().getUpperLeft().getZ();
double f1, f2, f3;
double[] functionValues = gridProperty.getFunctionValues();
double incInX = gridProperty.getXIncrement(),
incInY = gridProperty.getYIncrement(),
incInZ = gridProperty.getZIncrement();
int pointsAlongX = gridProperty.getNoOfPointsAlongX(),
pointsAlongY = gridProperty.getNoOfPointsAlongY(),
pointsAlongZ = gridProperty.getNoOfPointsAlongZ();
int i, j, k;
Atom atom;
String symbol;
SphereTriSetGenerator stsg;
Point3DI point1, point2, point3;
int noOfAtoms = molecule.getNumberOfAtoms();
int pointsAlongSlice = pointsAlongY * pointsAlongZ;
HashMap<String, SphereTriSetGenerator> triSetTableTmp =
new HashMap<String, SphereTriSetGenerator>(5);
if (noOfAtoms > largeMoleculeSize) triSetTableTmp = triSetTable;
Matrix3D tmat = new Matrix3D();
tmat.unit();
TransformGroup surfaceScene = new TransformGroup();
for (int atomIndex = 0; atomIndex < noOfAtoms; atomIndex++) {
atom = molecule.getAtom(atomIndex);
// check to see if we are with in the bounding box?
if (!gridProperty.getBoundingBox().contains(atom.getAtomCenter())) continue;
symbol = atom.getSymbol();
if ((stsg = triSetTableTmp.get(symbol)) == null) {
stsg =
new SphereTriSetGenerator(
atom.getAtomCenter(), ai.getVdwRadius(symbol), numberOfSphereDivisions);
triSetTableTmp.put(symbol, stsg);
} // end if
// setup color
Color3f eColor = new Color3f(0.0f, 0.0f, 0.0f);
Color3f sColor = new Color3f(1.0f, 1.0f, 1.0f);
Color3f objColor = new Color3f(colorMap.getInterpolatedColor(currentFunctionValue));
Appearance app = new Appearance();
Material mm = new Material(objColor, eColor, objColor, sColor, 100.0f);
mm.setLightingEnable(true);
app.setMaterial(mm);
if (fillTransperency > 0) {
app.setTransparencyAttributes(
new TransparencyAttributes(
TransparencyAttributes.NICEST, (float) (fillTransperency / 255.0)));
} // end if
int idx = 0;
stsg.setTransform(tmat);
stsg.setCenter(atom.getAtomCenter());
ArrayList<Point3d> validPoints = new ArrayList<Point3d>();
ArrayList<Color3f> validColors = new ArrayList<Color3f>();
while (true) {
Triangle t = stsg.nextVisibleTriSet();
if (t == null) break;
// first point
point1 = t.getPoint1();
i = (int) Math.round(Math.abs((point1.getX() - xMin) / incInX));
j = (int) Math.round(Math.abs((point1.getY() - yMin) / incInY));
k = (int) Math.round(Math.abs((point1.getZ() - zMin) / incInZ));
if (i > pointsAlongX - 1) i = pointsAlongX - 1;
if (j > pointsAlongY - 1) j = pointsAlongY - 1;
if (k > pointsAlongZ - 1) k = pointsAlongZ - 1;
f1 = functionValues[(i * pointsAlongSlice) + (j * pointsAlongZ) + k];
// second point
point2 = t.getPoint2();
i = (int) Math.round(Math.abs((point2.getX() - xMin) / incInX));
j = (int) Math.round(Math.abs((point2.getY() - yMin) / incInY));
k = (int) Math.round(Math.abs((point2.getZ() - zMin) / incInZ));
if (i > pointsAlongX - 1) i = pointsAlongX - 1;
if (j > pointsAlongY - 1) j = pointsAlongY - 1;
if (k > pointsAlongZ - 1) k = pointsAlongZ - 1;
f2 = functionValues[(i * pointsAlongSlice) + (j * pointsAlongZ) + k];
// third point
point3 = t.getPoint3();
i = (int) Math.round(Math.abs((point3.getX() - xMin) / incInX));
j = (int) Math.round(Math.abs((point3.getY() - yMin) / incInY));
k = (int) Math.round(Math.abs((point3.getZ() - zMin) / incInZ));
if (i > pointsAlongX - 1) i = pointsAlongX - 1;
if (j > pointsAlongY - 1) j = pointsAlongY - 1;
if (k > pointsAlongZ - 1) k = pointsAlongZ - 1;
f3 = functionValues[(i * pointsAlongSlice) + (j * pointsAlongZ) + k];
validPoints.add(new Point3d(point1.getX(), point1.getY(), point1.getZ()));
validColors.add(new Color3f(colorMap.getInterpolatedColor(f1)));
validPoints.add(new Point3d(point2.getX(), point2.getY(), point2.getZ()));
validColors.add(new Color3f(colorMap.getInterpolatedColor(f2)));
validPoints.add(new Point3d(point3.getX(), point3.getY(), point3.getZ()));
validColors.add(new Color3f(colorMap.getInterpolatedColor(f3)));
} // end while
TriangleArray ta =
new TriangleArray(validPoints.size(), GeometryArray.COORDINATES | GeometryArray.COLOR_3);
for (idx = 0; idx < validPoints.size(); idx++) {
ta.setCoordinate(idx, validPoints.get(idx));
ta.setColor(idx, validColors.get(idx));
}
validColors = null;
validPoints = null;
GeometryInfo gi = new GeometryInfo(ta);
gi.compact();
gi.recomputeIndices();
// generate normals
NormalGenerator ng = new NormalGenerator();
ng.generateNormals(gi);
// stripify
Stripifier st = new Stripifier();
st.stripify(gi);
surfaceScene.addChild(new Shape3D(gi.getGeometryArray(), app));
} // end for
if (showBoundingBox) {
boundingBox.setTransform(transform);
boundingBox.applyTransforms();
(new ScreenCuboidJ3D(boundingBox)).buildJava3DScene(surfaceScene);
} // end if
objRot.addChild(surfaceScene);
}
