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);
}
public void dealData(Sphere shape) {
String userData = shape.getName();
String[] str = userData.split(",");
int state = Integer.parseInt(str[3]);
float x = Float.parseFloat(str[0]);
float y = Float.parseFloat(str[1]);
float z = Float.parseFloat(str[2]);
if (state == 0) {
data[getXintValue(x)][getYintValue(y)] =
data[getXintValue(x)][getYintValue(y)] | getZintValue(z);
shape.setName(str[0] + "," + str[1] + "," + str[2] + "," + 1);
Appearance appear = new Appearance();
Material mater = new Material();
mater.setDiffuseColor(new Color3f(Color.red));
appear.setMaterial(mater);
shape.setAppearance(appear);
jta.setText(getDataString());
} else {
data[getXintValue(x)][getYintValue(y)] =
data[getXintValue(x)][getYintValue(y)] & (~getZintValue(z));
shape.setName(str[0] + "," + str[1] + "," + str[2] + "," + 0);
Appearance appear = new Appearance();
Material mater = new Material();
mater.setDiffuseColor(new Color3f(Color.black));
appear.setMaterial(mater);
shape.setAppearance(appear);
jta.setText(getDataString());
}
}
/**
* Method to set color in 3D. Since it must set 3 different colors, it is a function called by
* setOtherAppearanceValues.
*
* @param material material to change if available
* @param color
*/
public void set3DColor(Object material, Color color) {
Material mat = (material == null) ? getMaterial() : (Material) material;
Color3f objColor = new Color3f(color);
mat.setDiffuseColor(objColor);
// mat.setSpecularColor(objColor);
mat.setAmbientColor(objColor);
if (getColoringAttributes() != null) getColoringAttributes().setColor(objColor);
}
private static Appearance getAparencia() {
if (ap == null) {
ap = new Appearance();
// Copper
Material mat = new Material();
mat.setAmbientColor(0.19125f, 0.0735f, 0.0225f);
mat.setDiffuseColor(0.7038f, 0.27048f, 0.0828f);
mat.setSpecularColor(0.256777f, 0.137622f, 0.086014f);
mat.setShininess(12.8f);
ap.setMaterial(mat);
}
return ap;
}
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);
}
@Override
protected Appearance createAppearance() {
Appearance appearance = new Appearance();
appearance.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_READ);
appearance.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
LineAttributes lineAttrib = new LineAttributes();
lineAttrib.setCapability(LineAttributes.ALLOW_ANTIALIASING_WRITE);
lineAttrib.setCapability(LineAttributes.ALLOW_PATTERN_WRITE);
lineAttrib.setCapability(LineAttributes.ALLOW_WIDTH_WRITE);
lineAttrib.setLineWidth(linewidth);
lineAttrib.setLinePattern(pattern);
appearance.setLineAttributes(lineAttrib);
PolygonAttributes polyAttrib = new PolygonAttributes();
polyAttrib.setCapability(PolygonAttributes.ALLOW_MODE_WRITE);
polyAttrib.setPolygonMode(PolygonAttributes.POLYGON_FILL);
polyAttrib.setCullFace(PolygonAttributes.CULL_NONE);
polyAttrib.setBackFaceNormalFlip(true);
appearance.setPolygonAttributes(polyAttrib);
ColoringAttributes colorAttrib = new ColoringAttributes();
colorAttrib.setShadeModel(ColoringAttributes.SHADE_GOURAUD);
colorAttrib.setColor(color);
appearance.setColoringAttributes(colorAttrib);
TransparencyAttributes tr = new TransparencyAttributes();
int mode = transparency == 0f ? TransparencyAttributes.NONE : TransparencyAttributes.FASTEST;
tr.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE);
tr.setCapability(TransparencyAttributes.ALLOW_MODE_WRITE);
tr.setTransparencyMode(mode);
tr.setTransparency(transparency);
appearance.setTransparencyAttributes(tr);
Material material = new Material();
material.setCapability(Material.ALLOW_COMPONENT_WRITE);
material.setAmbientColor(0.1f, 0.1f, 0.1f);
material.setSpecularColor(0.1f, 0.1f, 0.1f);
material.setDiffuseColor(0.1f, 0.1f, 0.1f);
appearance.setMaterial(material);
return appearance;
}
public MyMousePickBehavior(Canvas3D canvas, BranchGroup root, Bounds bounds, JTextArea jta) {
super(canvas, root, bounds);
this.jta = jta;
this.setSchedulingBounds(bounds);
root.addChild(this);
pickCanvas.setMode(PickTool.GEOMETRY);
appear = new Appearance();
mater = new Material();
mater.setDiffuseColor(new Color3f(Color.red));
appear.setMaterial(mater);
}
@Override
protected Appearance createAppearance() {
final Appearance appearance = new Appearance();
appearance.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_READ);
appearance.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
final PointAttributes pointAttrib = new PointAttributes();
pointAttrib.setCapability(PointAttributes.ALLOW_ANTIALIASING_WRITE);
pointAttrib.setCapability(PointAttributes.ALLOW_SIZE_WRITE);
pointAttrib.setPointSize(pointsize);
appearance.setPointAttributes(pointAttrib);
final PolygonAttributes polyAttrib = new PolygonAttributes();
polyAttrib.setCapability(PolygonAttributes.ALLOW_MODE_WRITE);
polyAttrib.setPolygonMode(PolygonAttributes.POLYGON_FILL);
polyAttrib.setCullFace(PolygonAttributes.CULL_BACK);
polyAttrib.setBackFaceNormalFlip(false);
appearance.setPolygonAttributes(polyAttrib);
final ColoringAttributes colorAttrib = new ColoringAttributes();
colorAttrib.setShadeModel(ColoringAttributes.SHADE_GOURAUD);
colorAttrib.setColor(color);
appearance.setColoringAttributes(colorAttrib);
final TransparencyAttributes tr = new TransparencyAttributes();
final int mode =
transparency == 0f ? TransparencyAttributes.NONE : TransparencyAttributes.FASTEST;
tr.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE);
tr.setCapability(TransparencyAttributes.ALLOW_MODE_WRITE);
tr.setTransparencyMode(mode);
tr.setTransparency(transparency);
appearance.setTransparencyAttributes(tr);
final Material material = new Material();
material.setCapability(Material.ALLOW_COMPONENT_WRITE);
material.setAmbientColor(0.1f, 0.1f, 0.1f);
material.setSpecularColor(0.1f, 0.1f, 0.1f);
material.setDiffuseColor(0.1f, 0.1f, 0.1f);
appearance.setMaterial(material);
return appearance;
}
private void createTriangle() {
int[] stripCount = {3};
GeometryInfo gi = new GeometryInfo(GeometryInfo.POLYGON_ARRAY);
gi.setCoordinates(points);
gi.setStripCounts(stripCount);
NormalGenerator ng = new NormalGenerator();
ng.generateNormals(gi);
gi.recomputeIndices();
Stripifier st = new Stripifier();
st.stripify(gi);
gi.recomputeIndices();
Appearance appearance = new Appearance();
Material material = new Material();
material.setAmbientColor(new Color3f(Color.GREEN));
appearance.setMaterial(material);
shape3D = new Shape3D();
shape3D.setGeometry(gi.getGeometryArray());
shape3D.setAppearance(appearance);
}
public static void writeMeshToObj(String objPath, String mtlPath, Mesh mesh) throws IOException {
// obj
PrintWriter writer = new PrintWriter(new FileWriter(objPath));
Vector3d[] vertices = mesh.getLocalVertices();
Triangle[] triangles = mesh.getLocalTriangles();
writer.println("mtllib " + mtlPath.substring(mtlPath.lastIndexOf(File.separator) + 1));
for (Vector3d vertex : vertices) {
writer.println("v " + vertex.x + " " + vertex.y + " " + vertex.z);
}
writer.println("usemtl Material");
for (Triangle triangle : triangles) {
writer.println("f " + (triangle.v0 + 1) + " " + (triangle.v1 + 1) + " " + (triangle.v2 + 1));
}
writer.close();
// mtl
writer = new PrintWriter(new FileWriter(mtlPath));
Material material = mesh.getShape().getAppearance().getMaterial();
Color3f ambientColour = new Color3f();
material.getAmbientColor(ambientColour);
Color3f diffuseColour = new Color3f();
material.getDiffuseColor(diffuseColour);
Color3f specularColour = new Color3f();
material.getSpecularColor(specularColour);
Color3f emissiveColour = new Color3f();
material.getEmissiveColor(emissiveColour);
float shininess = material.getShininess();
writer.println("newmtl Material");
writer.println("Ns " + shininess);
writer.println("Ka " + ambientColour.x + " " + ambientColour.y + " " + ambientColour.z);
writer.println("Kd " + diffuseColour.x + " " + diffuseColour.y + " " + diffuseColour.z);
writer.println("Ks " + specularColour.x + " " + specularColour.y + " " + specularColour.z);
writer.close();
}
/** Creates the objects on the scene, adds behavior effects and so on. */
public void addChildren() {
BranchGroup group = new BranchGroup(); // Root group of the applet.
Appearance ap = new Appearance(); // Configurate a material for the branch.
Material mat = new Material();
mat.setAmbientColor(new Color3f(43 / 255f, 23 / 255f, 5 / 255f)); // Brown.
ap.setMaterial(mat);
TransformGroup tg =
new TransformGroup(); // This will actually store all leaf nodes because we want them to
// rotate with mouse movements.
tg.setCapability(TransformGroup.ALLOW_TRANSFORM_READ);
tg.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
BranchShape bs =
new BranchShape(
new Branch(
6,
0f,
-0f,
0.9f,
new Random(1253312432),
6,
0.1f,
new Point3f(0, -2, 0),
new Vector3f(0, 1, 0),
0),
ap,
0,
10);
bs.addChildren(10, 0.5f, 0.2f, 0.3f, 0.3f, 0.5f, 4, -0.3f, 0.3f, 0.1f, 1.2f, ap);
tg.addChild(bs);
bs =
new BranchShape(
new Branch(
6,
0.0f,
-0.0f,
0.9f,
new Random(125462432),
6,
0.1f,
new Point3f(0, -2, 0),
new Vector3f(0, 1, 0),
0),
ap,
0,
10);
bs.addChildren(10, 0.5f, 0.2f, 0.3f, 0.3f, 0.5f, 4, -0.3f, 0.3f, 0.1f, 1.2f, ap);
tg.addChild(bs);
bs =
new BranchShape(
new Branch(
6,
0.0f,
-0.0f,
0.9f,
new Random(3755678),
6,
0.1f,
new Point3f(0, -2, 0),
new Vector3f(0, 1, 0),
0),
ap,
0,
10);
bs.addChildren(10, 0.5f, 0.2f, 0.3f, 0.3f, 0.5f, 4, -0.3f, 0.3f, 0.1f, 1.2f, ap);
tg.addChild(bs);
bs =
new BranchShape(
new Branch(
6,
0.0f,
-0.0f,
0.9f,
new Random(8765683),
6,
0.1f,
new Point3f(0, -2, 0),
new Vector3f(0, 1, 0),
0),
ap,
0,
10);
bs.addChildren(10, 0.5f, 0.2f, 0.3f, 0.3f, 0.5f, 4, -0.3f, 0.3f, 0.1f, 1.2f, ap);
tg.addChild(bs);
// Four branches initialized by three different roots for Random.
MouseRotate mr = new MouseRotate(tg);
mr.setSchedulingBounds(new BoundingSphere(new Point3d(), 100));
mr.setFactor(0.005, 0.001); // Slow rotation.
tg.addChild(mr);
group.addChild(tg);
Color3f light1Color =
new Color3f(1f, 1f, 1f); // Just to see the model, as a temporary solution.
BoundingSphere bounds = new BoundingSphere(new Point3d(), 100);
AmbientLight light1 = new AmbientLight(light1Color);
light1.setInfluencingBounds(bounds); // Some more j3d magic.
group.addChild(light1);
universe.addBranchGraph(group);
}
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);
}
}
private void readNode(Node node) {
EnvironmentDom dom;
NamedNodeMap attrs = node.getAttributes();
try {
dom = EnvironmentDom.valueOf(node.getNodeName());
} catch (java.lang.IllegalArgumentException ex) {
return;
}
switch (dom) {
case background:
String type = attrs.getNamedItem("type").getTextContent();
if (type.equals("color"))
mainScene.setBackgroundColor(
new Color3f(Converter.stringToFloatArray(node.getTextContent())));
else if (type.equals("image")) {
try {
File bgFile = new File(attrs.getNamedItem("src").getTextContent());
mainScene.setBackgroundFile(bgFile);
} catch (NullPointerException ex) {
System.err.println(ex.getMessage());
}
}
break;
case limits:
float width = Float.parseFloat(attrs.getNamedItem("width").getTextContent());
float height = Float.parseFloat(attrs.getNamedItem("height").getTextContent());
float deepness = Float.parseFloat(attrs.getNamedItem("deepness").getTextContent());
float thickness = Float.parseFloat(attrs.getNamedItem("thickness").getTextContent());
mainScene.getEnvironmentLimits().updateLimits(width, height, deepness, thickness);
// mainScene.getEnvironmentLimits().calculateUniverseBounds();
break;
case light:
type = attrs.getNamedItem("type").getTextContent();
sceneLight = new SceneLight(LightType.valueOf(type));
scene.addLightNode(sceneLight.getLight());
mainScene.addLight(sceneLight);
break;
case object:
type = attrs.getNamedItem("type").getTextContent();
String src = attrs.getNamedItem("src").getTextContent();
String id = attrs.getNamedItem("id").getTextContent();
object =
new MainSceneComponent(
Integer.parseInt(id), ComponentType.valueOf(type), new File(src));
object.loadType();
if (attrs.getNamedItem("scale") != null) {
String sca = attrs.getNamedItem("scale").getTextContent();
object.setScale(Double.valueOf(sca));
}
if (attrs.getNamedItem("name") != null) {
String name = attrs.getNamedItem("name").getTextContent();
object.setComponentName(name);
}
scene.addViewGroup(object.getTransformGroup());
mainScene.addComponent(object);
break;
case appearance:
limitApp = new Appearance();
break;
case material:
material = new Material();
break;
case texture:
// TextureLoader textureLoad = new
// TextureLoader(attrs.getNamedItem("src").getTextContent(), null);
// ImageComponent2D textureIm = textureLoad.getScaledImage(128, 128);
// texture = new Texture2D(Texture2D.BASE_LEVEL, Texture2D.RGB,
// textureIm.getWidth(), textureIm.getHeight());
// texture.setImage(0, textureIm);
// limitApp.setTexture(texture);
// TextureAttributes textureAttr = new TextureAttributes();
// textureAttr.setTextureMode(TextureAttributes.REPLACE);
// limitApp.setTextureAttributes(textureAttr);
// TexCoordGeneration tcg = new
// TexCoordGeneration(TexCoordGeneration.OBJECT_LINEAR,
//
// TexCoordGeneration.TEXTURE_COORDINATE_2);
// limitApp.setTexCoordGeneration(tcg);
//// limitApp.setTransparencyAttributes(new
// TransparencyAttributes(TransparencyAttributes.NICEST, 0.7f));
//// mainScene.getEnvironmentLimits().setAppearance(EnvironmentLimits.RIGHT,
// limitApp);
// mainScene.getEnvironmentLimits().setAppearance(limitApp);
mainScene
.getEnvironmentLimits()
.setTexture(new File(attrs.getNamedItem("src").getTextContent()));
boolean enabled = Boolean.parseBoolean(attrs.getNamedItem("enabled").getTextContent());
mainScene.getEnvironmentLimits().setTextureFlag(enabled);
break;
case ambient:
material.setAmbientColor(new Color3f(Converter.stringToFloatArray(node.getTextContent())));
break;
case emissive:
material.setEmissiveColor(new Color3f(Converter.stringToFloatArray(node.getTextContent())));
break;
case diffuse:
material.setDiffuseColor(new Color3f(Converter.stringToFloatArray(node.getTextContent())));
break;
case specular:
material.setSpecularColor(new Color3f(Converter.stringToFloatArray(node.getTextContent())));
break;
case shininess:
material.setShininess(Float.parseFloat(node.getTextContent()));
limitApp.setMaterial(material);
// mainScene.getEnvironmentLimits().setAppearance(limitApp);
break;
case color:
sceneLight.setColor(new Color3f(Converter.stringToFloatArray(node.getTextContent())));
break;
case position:
sceneLight.setPosition(new Point3f(Converter.stringToFloatArray(node.getTextContent())));
// if(sceneLight instanceof PointLight){
// PointLight pl = (PointLight)sceneLight;
// pl.setPosition(new Point3f(Converter.stringToFloatArray
// (node.getTextContent())));
// } else if(sceneLight instanceof DirectionalLight){
// DirectionalLight dl = (DirectionalLight)sceneLight;
// dl.setDirection(new Vector3f(Converter.stringToFloatArray
// (node.getTextContent())));
// }
break;
case direction:
sceneLight.setDirection(new Vector3f(Converter.stringToFloatArray(node.getTextContent())));
case atenuation:
// PointLight pl = (PointLight)sceneLight;
// pl.setAttenuation(new Point3f(Converter.stringToFloatArray(
// node.getTextContent())));
sceneLight.setAttenuation(new Point3f(Converter.stringToFloatArray(node.getTextContent())));
break;
case objPos:
object.setPosition(Converter.stringToDoubleArray(node.getTextContent()));
break;
case angles:
double rotation[] = Converter.stringToDoubleArray(node.getTextContent());
object.setRotation(rotation);
break;
}
}
/**
* 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);
}