private void setVis(Map<?, Ellipsoid> ellipsoids, BS bs, Atom[] atoms) {
for (Ellipsoid e : ellipsoids.values()) {
Tensor t = e.tensor;
boolean isOK = (t != null && e.isValid && e.isOn);
if (isOK && t.atomIndex1 >= 0) {
if (t.iType == Tensor.TYPE_ADP) {
boolean isModTensor = t.isModulated;
boolean isUnmodTensor = t.isUnmodulated;
boolean isModAtom = ms.isModulated(t.atomIndex1);
isOK = (!isModTensor && !isUnmodTensor || isModTensor == isModAtom);
}
atoms[t.atomIndex1].setShapeVisibility(vf, true);
}
e.visible = isOK && (e.modelIndex < 0 || bs.get(e.modelIndex));
}
}
/**
* needed for XmlPersistable
*
* @param encoder encoder for encoding
* @return this as an encoded Element
*/
public Element createElement(XmlEncoder encoder) {
List arguments =
Misc.newList(
ellipsoid, new Integer(onezone), new Boolean(onehemiflag), getDefaultMapArea());
List types =
Misc.newList(ellipsoid.getClass(), Integer.TYPE, Boolean.TYPE, Rectangle2D.Double.class);
Element result = encoder.createObjectElement(getClass());
Element ctorElement = encoder.createConstructorElement(arguments, types);
result.appendChild(ctorElement);
return result;
}
@Override
protected void setSize(int size, BS bsSelected) {
if (ms.at == null || size == 0 && ms.atomTensors == null) return;
boolean isAll = (bsSelected == null);
if (!isAll && selectedAtoms != null) bsSelected = selectedAtoms;
Lst<Object> tensors = vwr.ms.getAllAtomTensors(typeSelected);
if (tensors == null) return;
Atom[] atoms = ms.at;
for (int i = tensors.size(); --i >= 0; ) {
Tensor t = (Tensor) tensors.get(i);
if (isAll || t.isSelected(bsSelected, -1)) {
Ellipsoid e = atomEllipsoids.get(t);
boolean isNew = (size != 0 && e == null);
if (isNew)
atomEllipsoids.put(t, e = Ellipsoid.getEllipsoidForAtomTensor(t, atoms[t.atomIndex1]));
if (e != null && (isNew || size != Integer.MAX_VALUE)) { // MAX_VALUE --> "create only"
e.setScale(size, true);
}
}
}
}
private void setProp(Ellipsoid e, int mode, Object value) {
// "ax ce co de eq mo on op sc tr"
// 0 1 2 3 4 5 6 7 8 9
switch (mode) {
case 0: // axes
e.setTensor(
((Tensor) Interface.getUtil("Tensor", vwr, "script")).setFromAxes((V3[]) value));
return;
case 1: // center
e.setCenter((P3) value);
return;
case 2: // color
e.colix = C.getColixO(value);
return;
case 3: // delete
simpleEllipsoids.remove(e.id);
return;
case 4: // equation
e.setTensor(
((Tensor) Interface.getUtil("Tensor", vwr, "script"))
.setFromThermalEquation((double[]) value, null));
return;
case 5: // modelindex
e.tensor.modelIndex = ((Integer) value).intValue();
return;
case 6: // on
e.isOn = ((Boolean) value).booleanValue();
return;
case 7: // options
e.options = ((String) value).toLowerCase();
return;
case 8: // scale
e.setScale(((Float) value).floatValue(), false);
return;
case 9: // translucency
e.colix = C.getColixTranslucent3(e.colix, value.equals("translucent"), translucentLevel);
return;
}
return;
}
@Override
public void setProperty(String propertyName, Object value, BS bs) {
// System.out.println(propertyName + " " + value + " " + bs);
if (propertyName == "thisID") {
if (initEllipsoids(value) && ellipsoidSet.size() == 0) {
String id = (String) value;
Ellipsoid e = Ellipsoid.getEmptyEllipsoid(id, vwr.am.cmi);
ellipsoidSet.addLast(e);
simpleEllipsoids.put(id, e);
}
return;
}
if ("atoms" == propertyName) {
selectedAtoms = (BS) value;
return;
}
if (propertyName == "deleteModelAtoms") {
int modelIndex = ((int[]) ((Object[]) value)[2])[0];
Iterator<Ellipsoid> e = simpleEllipsoids.values().iterator();
while (e.hasNext()) if (e.next().tensor.modelIndex == modelIndex) e.remove();
e = atomEllipsoids.values().iterator();
while (e.hasNext()) if (e.next().modelIndex == modelIndex) e.remove();
ellipsoidSet.clear();
return;
}
int mode = PROPERTY_MODES.indexOf((propertyName + " ").substring(0, 2));
if (ellipsoidSet.size() > 0) {
if ("translucentLevel" == propertyName) {
setPropS(propertyName, value, bs);
return;
}
if (mode >= 0)
for (int i = ellipsoidSet.size(); --i >= 0; ) setProp(ellipsoidSet.get(i), mode / 3, value);
return;
}
if ("color" == propertyName) {
short colix = C.getColixO(value);
byte pid = PAL.pidOf(value);
if (selectedAtoms != null) bs = selectedAtoms;
for (Ellipsoid e : atomEllipsoids.values())
if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1)) {
e.colix = getColixI(colix, pid, e.tensor.atomIndex1);
e.pid = pid;
}
return;
}
if ("on" == propertyName) {
boolean isOn = ((Boolean) value).booleanValue();
if (selectedAtoms != null) bs = selectedAtoms;
if (isOn) setSize(Integer.MAX_VALUE, bs);
for (Ellipsoid e : atomEllipsoids.values()) {
Tensor t = e.tensor;
if ((t.type.equals(typeSelected) || typeSelected.equals(t.altType))
&& t.isSelected(bs, -1)) {
e.isOn = isOn;
}
}
return;
}
if ("options" == propertyName) {
String options = ((String) value).toLowerCase().trim();
if (options.length() == 0) options = null;
if (selectedAtoms != null) bs = selectedAtoms;
if (options != null) setSize(Integer.MAX_VALUE, bs);
for (Ellipsoid e : atomEllipsoids.values())
if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1)) e.options = options;
return;
}
if ("params" == propertyName) {
Object[] data = (Object[]) value;
data[2] = null; // Jmol does not allow setting sizes this way from PyMOL yet
typeSelected = "0";
setSize(50, bs);
// onward...
}
if ("points" == propertyName) {
// Object[] o = (Object[]) value;
// setPoints((P3[]) o[1], (BS) o[2]);
return;
}
if ("scale" == propertyName) {
setSize((int) (((Float) value).floatValue() * 100), bs);
return;
}
if ("select" == propertyName) {
typeSelected = ((String) value).toLowerCase();
return;
}
if ("translucency" == propertyName) {
boolean isTranslucent = (value.equals("translucent"));
for (Ellipsoid e : atomEllipsoids.values())
if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1))
e.colix = C.getColixTranslucent3(e.colix, isTranslucent, translucentLevel);
return;
}
setPropS(propertyName, value, bs);
}
protected void makeShapes() {
RenderableLayer layer = new RenderableLayer();
layer.setName("Rigid Shapes");
// Create and set an attribute bundle.
ShapeAttributes attrs = new BasicShapeAttributes();
attrs.setInteriorMaterial(Material.YELLOW);
attrs.setInteriorOpacity(0.7);
attrs.setEnableLighting(true);
attrs.setOutlineMaterial(Material.RED);
attrs.setOutlineWidth(2d);
attrs.setDrawInterior(true);
attrs.setDrawOutline(false);
// Create and set a second attribute bundle.
ShapeAttributes attrs2 = new BasicShapeAttributes();
attrs2.setInteriorMaterial(Material.PINK);
attrs2.setInteriorOpacity(1);
attrs2.setEnableLighting(true);
attrs2.setOutlineMaterial(Material.WHITE);
attrs2.setOutlineWidth(2d);
attrs2.setDrawOutline(false);
// Pyramid with equal axes, ABSOLUTE altitude mode.
Pyramid pyramid = new Pyramid(Position.fromDegrees(40, -120, 220000), 200000, 200000, 200000);
pyramid.setAltitudeMode(WorldWind.ABSOLUTE);
pyramid.setAttributes(attrs);
pyramid.setValue(AVKey.DISPLAY_NAME, "Pyramid with equal axes, ABSOLUTE altitude mode");
layer.addRenderable(pyramid);
// Cone with equal axes, RELATIVE_TO_GROUND.
Cone cone = new Cone(Position.fromDegrees(37.5, -115, 200000), 200000, 200000, 200000);
cone.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
cone.setAttributes(attrs);
cone.setValue(AVKey.DISPLAY_NAME, "Cone with equal axes, RELATIVE_TO_GROUND altitude mode");
layer.addRenderable(cone);
// Wedge with equal axes, CLAMP_TO_GROUND.
Wedge wedge =
new Wedge(
Position.fromDegrees(35, -110, 200000),
Angle.fromDegrees(225),
200000,
200000,
200000);
wedge.setAltitudeMode(WorldWind.CLAMP_TO_GROUND);
wedge.setAttributes(attrs);
wedge.setValue(AVKey.DISPLAY_NAME, "Wedge with equal axes, CLAMP_TO_GROUND altitude mode");
layer.addRenderable(wedge);
// Box with a texture.
Box box = new Box(Position.fromDegrees(0, -90, 600000), 600000, 600000, 600000);
box.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
ArrayList<Object> imageSources = new ArrayList<Object>();
imageSources.add("images/32x32-icon-nasa.png");
imageSources.add(null);
imageSources.add("gov/nasa/worldwindx/examples/images/500px-Checkerboard_pattern.png");
imageSources.add(null);
imageSources.add("images/64x64-crosshair.png");
imageSources.add(null);
box.setImageSources(imageSources);
box.setAttributes(attrs);
box.setValue(AVKey.DISPLAY_NAME, "Box with a texture");
layer.addRenderable(box);
// Sphere with a texture.
Ellipsoid sphere =
new Ellipsoid(Position.fromDegrees(0, -110, 600000), 600000, 600000, 600000);
sphere.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
sphere.setImageSources("gov/nasa/worldwindx/examples/images/500px-Checkerboard_pattern.png");
sphere.setAttributes(attrs);
sphere.setValue(AVKey.DISPLAY_NAME, "Sphere with a texture");
layer.addRenderable(sphere);
// Cylinder with a texture.
Cylinder cylinder =
new Cylinder(Position.fromDegrees(0, -130, 600000), 600000, 600000, 600000);
cylinder.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
cylinder.setImageSources(
"gov/nasa/worldwindx/examples/images/500px-Checkerboard_pattern.png");
cylinder.setAttributes(attrs);
cylinder.setValue(AVKey.DISPLAY_NAME, "Cylinder with a texture");
layer.addRenderable(cylinder);
// Cylinder with default orientation.
cylinder = new Cylinder(Position.ZERO, 600000, 500000, 300000);
cylinder.setAltitudeMode(WorldWind.ABSOLUTE);
cylinder.setAttributes(attrs);
cylinder.setValue(AVKey.DISPLAY_NAME, "Cylinder with default orientation");
layer.addRenderable(cylinder);
// Ellipsoid with a pre-set orientation.
Ellipsoid ellipsoid =
new Ellipsoid(
Position.fromDegrees(0, 30, 750000),
1000000,
500000,
100000,
Angle.fromDegrees(90),
Angle.fromDegrees(45),
Angle.fromDegrees(30));
ellipsoid.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
ellipsoid.setAttributes(attrs2);
ellipsoid.setValue(AVKey.DISPLAY_NAME, "Ellipsoid with a pre-set orientation");
layer.addRenderable(ellipsoid);
// Ellipsoid with a pre-set orientation.
ellipsoid =
new Ellipsoid(
Position.fromDegrees(30, 30, 750000),
1000000,
500000,
100000,
Angle.fromDegrees(90),
Angle.fromDegrees(45),
Angle.fromDegrees(30));
ellipsoid.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
ellipsoid.setImageSources(
"gov/nasa/worldwindx/examples/images/500px-Checkerboard_pattern.png");
ellipsoid.setAttributes(attrs2);
ellipsoid.setValue(AVKey.DISPLAY_NAME, "Ellipsoid with a pre-set orientation");
layer.addRenderable(ellipsoid);
// Ellipsoid with a pre-set orientation.
ellipsoid =
new Ellipsoid(
Position.fromDegrees(60, 30, 750000),
1000000,
500000,
100000,
Angle.fromDegrees(90),
Angle.fromDegrees(45),
Angle.fromDegrees(30));
ellipsoid.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
ellipsoid.setAttributes(attrs2);
ellipsoid.setValue(AVKey.DISPLAY_NAME, "Ellipsoid with a pre-set orientation");
layer.addRenderable(ellipsoid);
// Ellipsoid oriented in 3rd "quadrant" (-X, -Y, -Z).
ellipsoid =
new Ellipsoid(
Position.fromDegrees(-45, -180, 750000),
1000000,
500000,
100000,
Angle.fromDegrees(90),
Angle.fromDegrees(45),
Angle.fromDegrees(30));
ellipsoid.setAltitudeMode(WorldWind.RELATIVE_TO_GROUND);
ellipsoid.setAttributes(attrs2);
ellipsoid.setValue(AVKey.DISPLAY_NAME, "Ellipsoid oriented in 3rd \"quadrant\" (-X, -Y, -Z)");
layer.addRenderable(ellipsoid);
// Add the layer to the model and update the layer panel.
insertBeforePlacenames(getWwd(), layer);
}
