/**
* Gets the parameters from this PickSegment.
*
* @param start the Point3d object into which the start point will be copied.
* @param end the Point3d object into which the end point will be copied.
*/
public void get(Point3d start, Point3d end) {
start.x = this.start.x;
start.y = this.start.y;
start.z = this.start.z;
end.x = this.end.x;
end.y = this.end.y;
end.z = this.end.z;
}
private Point3d getEffectiveCoordinates(IAtomContainer atomContainer, int[] atomIndices) {
Point3d ret = new Point3d(0, 0, 0);
for (int i : atomIndices) {
Point3d coord = atomContainer.getAtom(i).getPoint3d();
ret.x += coord.x;
ret.y += coord.y;
ret.z += coord.z;
}
ret.x /= atomIndices.length;
ret.y /= atomIndices.length;
ret.z /= atomIndices.length;
return ret;
}
private Point3d getEffectiveCoordinates(IAtomContainer atomContainer, List<Integer> atomIndices) {
Point3d ret = new Point3d(0, 0, 0);
for (Object atomIndice : atomIndices) {
int atomIndex = (Integer) atomIndice;
Point3d coord = atomContainer.getAtom(atomIndex).getPoint3d();
ret.x += coord.x;
ret.y += coord.y;
ret.z += coord.z;
}
ret.x /= atomIndices.size();
ret.y /= atomIndices.size();
ret.z /= atomIndices.size();
return ret;
}
public Point3d calcCenterOfRotation() {
List<Integer> line = getLongestLayerLine();
// can't determine center of rotation if there are only 2 points
// TODO does this ever happen??
if (line.size() < 3) {
return subunits.getCentroid();
}
Point3d centerOfRotation = new Point3d();
List<Point3d> centers = subunits.getOriginalCenters();
// calculate helix mid points for each set of 3 adjacent subunits
for (int i = 0; i < line.size() - 2; i++) {
Point3d p1 = new Point3d(centers.get(line.get(i)));
Point3d p2 = new Point3d(centers.get(line.get(i + 1)));
Point3d p3 = new Point3d(centers.get(line.get(i + 2)));
transformationMatrix.transform(p1);
transformationMatrix.transform(p2);
transformationMatrix.transform(p3);
centerOfRotation.add(getMidPoint(p1, p2, p3));
}
// average over all midpoints to find best center of rotation
centerOfRotation.scale(1 / (line.size() - 2));
// since helix is aligned along the y-axis, with an origin at y = 0, place the center of
// rotation there
centerOfRotation.y = 0;
// transform center of rotation to the original coordinate frame
reverseTransformationMatrix.transform(centerOfRotation);
// System.out.println("center of rotation: " + centerOfRotation);
return centerOfRotation;
}
@Override
void update() {
int newEditId;
if ((newEditId = volume.update()) != volumeEditId) {
for (int i = 0; i < 6; i++) {
boxLine[i].setCoordinates(0, volume.facePoints[i], 0, 4);
boxLine[i].setCoordinate(4, volume.facePoints[i][0]);
imageQuad[i].setCoordinates(0, volume.facePoints[i], 0, 4);
}
faceCenter[PLUS_X].set(volume.maxCoord.x, 0.0, 0.0);
faceCenter[PLUS_Y].set(0.0, volume.maxCoord.y, 0.0);
faceCenter[PLUS_Z].set(0.0, 0.0, volume.maxCoord.z);
faceCenter[MINUS_X].set(volume.minCoord.x, 0.0, 0.0);
faceCenter[MINUS_Y].set(0.0, volume.minCoord.y, 0.0);
faceCenter[MINUS_Z].set(0.0, 0.0, volume.minCoord.z);
volCenter.x = (volume.maxCoord.x + volume.minCoord.x) / 2;
volCenter.y = (volume.maxCoord.y + volume.minCoord.y) / 2;
volCenter.z = (volume.maxCoord.z + volume.minCoord.z) / 2;
volumeEditId = newEditId;
}
eyePtChanged();
for (int i = 0; i < 6; i++) {
if (boxAttr[i].getValue() == true) {
boxSwitch[i].setWhichChild(Switch.CHILD_ALL);
} else {
boxSwitch[i].setWhichChild(Switch.CHILD_NONE);
}
String curImageFile = imageAttr[i].getValue();
if (curImageFile != imageFile[i]) {
imageFile[i] = curImageFile;
if (imageFile[i].length() > 0) {
try {
URL imageURL = new URL(context.getCodeBase().toString() + imageFile[i]);
imageTexture[i] = new TextureLoader(imageURL, null).getTexture();
} catch (Exception e) {
System.err.println("Error " + e + " loading image:" + imageFile[i] + ".");
}
}
imageAppearance[i].setTexture(imageTexture[i]);
if (imageTexture[i] != null) {
imageSwitch[i].setWhichChild(Switch.CHILD_ALL);
} else {
imageSwitch[i].setWhichChild(Switch.CHILD_NONE);
}
}
}
}
public static void transformMesh(final TopLoc_Location loc, double[] src, float[] dst) {
double[] matrix = new double[16];
loc.transformation().getValues(matrix);
Matrix4d m4d = new Matrix4d(matrix);
Point3d p3d = new Point3d();
for (int i = 0; i < src.length; i += 3) {
p3d.x = src[i + 0];
p3d.y = src[i + 1];
p3d.z = src[i + 2];
m4d.transform(p3d);
dst[i + 0] = (float) p3d.x;
dst[i + 1] = (float) p3d.y;
dst[i + 2] = (float) p3d.z;
}
}
// Note we set teh locations values up, but process does the work, in case teh world changes
// without us moving (a door opens)
public void locationUpdated(Quat4f rot, Vector3f trans) {
// only update if new things have happened
if (!prevRot.epsilonEquals(rot, 0.0001f) || !prevTrans.epsilonEquals(trans, 0.005f)) {
// set head point
currentAvartarHeadPoint.set(trans);
currentAvartarHeadPoint.y += avatarCollisionInfo.getCameraAbovePelvisHeight();
tempRotTransform.set(rot);
currentCameraMaxVector.set(0, 0, 1); // use a normal
tempRotTransform.transform(currentCameraMaxVector);
// set max camera vector
currentCameraMaxVector.scale(TRAIL_MAX_DIST);
// recall for next iter
prevRot.set(rot);
prevTrans.set(trans);
}
}
// called on the parent object
// Should be synchronized so that the user thread does not modify the
// OrientedShape3D params while computing the transform
synchronized void updateOrientedTransform(Canvas3D canvas, int viewIndex) {
double angle = 0.0;
double sign;
boolean status;
Transform3D orientedxform = getOrientedTransform(viewIndex);
// get viewplatforms's location in virutal world
if (mode == OrientedShape3D.ROTATE_ABOUT_AXIS) { // rotate about axis
canvas.getCenterEyeInImagePlate(viewPosition);
canvas.getImagePlateToVworld(xform); // xform is imagePlateToLocal
xform.transform(viewPosition);
// get billboard's transform
xform.set(getCurrentLocalToVworld());
xform.invert(); // xform is now vWorldToLocal
// transform the eye position into the billboard's coordinate system
xform.transform(viewPosition);
// eyeVec is a vector from the local origin to the eye pt in local
eyeVec.set(viewPosition);
eyeVec.normalize();
// project the eye into the rotation plane
status = projectToPlane(eyeVec, nAxis);
if (status) {
// project the z axis into the rotation plane
zAxis.x = 0.0;
zAxis.y = 0.0;
zAxis.z = 1.0;
status = projectToPlane(zAxis, nAxis);
}
if (status) {
// compute the sign of the angle by checking if the cross product
// of the two vectors is in the same direction as the normal axis
vector.cross(eyeVec, zAxis);
if (vector.dot(nAxis) > 0.0) {
sign = 1.0;
} else {
sign = -1.0;
}
// compute the angle between the projected eye vector and the
// projected z
double dot = eyeVec.dot(zAxis);
if (dot > 1.0f) {
dot = 1.0f;
} else if (dot < -1.0f) {
dot = -1.0f;
}
angle = sign * Math.acos(dot);
// use -angle because xform is to *undo* rotation by angle
aa.x = nAxis.x;
aa.y = nAxis.y;
aa.z = nAxis.z;
aa.angle = -angle;
orientedxform.set(aa);
} else {
orientedxform.setIdentity();
}
} else if (mode == OrientedShape3D.ROTATE_ABOUT_POINT) { // rotate about point
// Need to rotate Z axis to point to eye, and Y axis to be
// parallel to view platform Y axis, rotating around rotation pt
// get the eye point
canvas.getCenterEyeInImagePlate(viewPosition);
// derive the yUp point
yUpPoint.set(viewPosition);
yUpPoint.y += 0.01; // one cm in Physical space
// transform the points to the Billboard's space
canvas.getImagePlateToVworld(xform); // xform is ImagePlateToVworld
xform.transform(viewPosition);
xform.transform(yUpPoint);
// get billboard's transform
xform.set(getCurrentLocalToVworld());
xform.invert(); // xform is vWorldToLocal
// transfom points to local coord sys
xform.transform(viewPosition);
xform.transform(yUpPoint);
// Make a vector from viewPostion to 0,0,0 in the BB coord sys
eyeVec.set(viewPosition);
eyeVec.normalize();
// create a yUp vector
yUp.set(yUpPoint);
yUp.sub(viewPosition);
yUp.normalize();
// find the plane to rotate z
zAxis.x = 0.0;
zAxis.y = 0.0;
zAxis.z = 1.0;
// rotation axis is cross product of eyeVec and zAxis
vector.cross(eyeVec, zAxis); // vector is cross product
// if cross product is non-zero, vector is rotation axis and
// rotation angle is acos(eyeVec.dot(zAxis)));
double length = vector.length();
if (length > 0.0001) {
double dot = eyeVec.dot(zAxis);
if (dot > 1.0f) {
dot = 1.0f;
} else if (dot < -1.0f) {
dot = -1.0f;
}
angle = Math.acos(dot);
aa.x = vector.x;
aa.y = vector.y;
aa.z = vector.z;
aa.angle = -angle;
zRotate.set(aa);
} else {
// no rotation needed, set to identity (scale = 1.0)
zRotate.set(1.0);
}
// Transform the yAxis by zRotate
yAxis.x = 0.0;
yAxis.y = 1.0;
yAxis.z = 0.0;
zRotate.transform(yAxis);
// project the yAxis onto the plane perp to the eyeVec
status = projectToPlane(yAxis, eyeVec);
if (status) {
// project the yUp onto the plane perp to the eyeVec
status = projectToPlane(yUp, eyeVec);
}
if (status) {
// rotation angle is acos(yUp.dot(yAxis));
double dot = yUp.dot(yAxis);
// Fix numerical error, otherwise acos return NULL
if (dot > 1.0f) {
dot = 1.0f;
} else if (dot < -1.0f) {
dot = -1.0f;
}
angle = Math.acos(dot);
// check the sign by looking a the cross product vs the eyeVec
vector.cross(yUp, yAxis); // vector is cross product
if (eyeVec.dot(vector) < 0) {
angle *= -1;
}
aa.x = eyeVec.x;
aa.y = eyeVec.y;
aa.z = eyeVec.z;
aa.angle = -angle;
xform.set(aa); // xform is now yRotate
// rotate around the rotation point
vector.x = rotationPoint.x;
vector.y = rotationPoint.y;
vector.z = rotationPoint.z; // vector to translate to RP
orientedxform.set(vector); // translate to RP
orientedxform.mul(xform); // yRotate
orientedxform.mul(zRotate); // zRotate
vector.scale(-1.0); // vector to translate back
xform.set(vector); // xform to translate back
orientedxform.mul(xform); // translate back
} else {
orientedxform.setIdentity();
}
}
// Scale invariant computation
if (constantScale) {
// Back Xform a unit vector to local world coords
canvas.getInverseVworldProjection(left_xform, right_xform);
// the two endpts of the vector have to be transformed
// individually because the Xform is not affine
im_vec[0].set(0.0, 0.0, 0.0, 1.0);
im_vec[1].set(1.0, 0.0, 0.0, 1.0);
left_xform.transform(im_vec[0]);
left_xform.transform(im_vec[1]);
left_xform.set(getCurrentLocalToVworld());
left_xform.invert();
left_xform.transform(im_vec[0]);
left_xform.transform(im_vec[1]);
lvec.set(im_vec[1]);
lvec.sub(im_vec[0]);
// We simply need the direction of this vector
lvec.normalize();
im_vec[0].set(0.0, 0.0, 0.0, 1.0);
im_vec[1].set(lvec);
im_vec[1].w = 1.0;
// Forward Xfrom to clip coords
left_xform.set(getCurrentLocalToVworld());
left_xform.transform(im_vec[0]);
left_xform.transform(im_vec[1]);
canvas.getVworldProjection(left_xform, right_xform);
left_xform.transform(im_vec[0]);
left_xform.transform(im_vec[1]);
// Perspective division
im_vec[0].x /= im_vec[0].w;
im_vec[0].y /= im_vec[0].w;
im_vec[0].z /= im_vec[0].w;
im_vec[1].x /= im_vec[1].w;
im_vec[1].y /= im_vec[1].w;
im_vec[1].z /= im_vec[1].w;
lvec.set(im_vec[1]);
lvec.sub(im_vec[0]);
// Use the length of this vector to determine the scaling
// factor
double scale = 1 / lvec.length();
// Convert to meters
scale *= scaleFactor * canvas.getPhysicalWidth() / 2;
// Scale object so that it appears the same size
scaleXform.setScale(scale);
orientedxform.mul(scaleXform);
}
}
/**
* Places the value of the "home" center around which the View rotates into the Point3d. The
* default center is (0, 0, 0).
*
* @param homeCenter The Point3d
* @since Version 1.1
*/
public void getHomeRotationCenter(Point3d homeCenter) {
homeCenter.x = homeRotCenter.x;
homeCenter.y = homeRotCenter.y;
homeCenter.z = homeRotCenter.z;
}
/**
* Procedure required by the CDOInterface. This function is only supposed to be called by the JCFL
* library
*/
public void setObjectProperty(String objectType, String propertyType, String propertyValue) {
logger.debug("objectType: " + objectType);
logger.debug("propType: " + propertyType);
logger.debug("property: " + propertyValue);
if (objectType == null) {
logger.error("Cannot add property for null object");
return;
}
if (propertyType == null) {
logger.error("Cannot add property for null property type");
return;
}
if (propertyValue == null) {
logger.warn("Will not add null property");
return;
}
if (objectType.equals("Molecule")) {
if (propertyType.equals("id")) {
currentMolecule.setID(propertyValue);
} else if (propertyType.equals("inchi")) {
currentMolecule.setProperty("iupac.nist.chemical.identifier", propertyValue);
}
} else if (objectType.equals("PseudoAtom")) {
if (propertyType.equals("label")) {
if (!(currentAtom instanceof IPseudoAtom)) {
currentAtom = builder.newPseudoAtom(currentAtom);
}
((IPseudoAtom) currentAtom).setLabel(propertyValue);
}
} else if (objectType.equals("Atom")) {
if (propertyType.equals("type")) {
if (propertyValue.equals("R") && !(currentAtom instanceof IPseudoAtom)) {
currentAtom = builder.newPseudoAtom(currentAtom);
}
currentAtom.setSymbol(propertyValue);
} else if (propertyType.equals("x2")) {
Point2d coord = currentAtom.getPoint2d();
if (coord == null) coord = new Point2d();
coord.x = Double.parseDouble(propertyValue);
currentAtom.setPoint2d(coord);
} else if (propertyType.equals("y2")) {
Point2d coord = currentAtom.getPoint2d();
if (coord == null) coord = new Point2d();
coord.y = Double.parseDouble(propertyValue);
currentAtom.setPoint2d(coord);
} else if (propertyType.equals("x3")) {
Point3d coord = currentAtom.getPoint3d();
if (coord == null) coord = new Point3d();
coord.x = Double.parseDouble(propertyValue);
currentAtom.setPoint3d(coord);
} else if (propertyType.equals("y3")) {
Point3d coord = currentAtom.getPoint3d();
if (coord == null) coord = new Point3d();
coord.y = Double.parseDouble(propertyValue);
currentAtom.setPoint3d(coord);
} else if (propertyType.equals("z3")) {
Point3d coord = currentAtom.getPoint3d();
if (coord == null) coord = new Point3d();
coord.z = Double.parseDouble(propertyValue);
currentAtom.setPoint3d(coord);
} else if (propertyType.equals("xFract")) {
Point3d coord = currentAtom.getFractionalPoint3d();
if (coord == null) coord = new Point3d();
coord.x = Double.parseDouble(propertyValue);
currentAtom.setFractionalPoint3d(coord);
} else if (propertyType.equals("yFract")) {
Point3d coord = currentAtom.getFractionalPoint3d();
if (coord == null) coord = new Point3d();
coord.y = Double.parseDouble(propertyValue);
currentAtom.setFractionalPoint3d(coord);
} else if (propertyType.equals("zFract")) {
Point3d coord = currentAtom.getFractionalPoint3d();
if (coord == null) coord = new Point3d();
coord.z = Double.parseDouble(propertyValue);
currentAtom.setFractionalPoint3d(coord);
} else if (propertyType.equals("formalCharge")) {
currentAtom.setFormalCharge(Integer.parseInt(propertyValue));
} else if (propertyType.equals("charge") || propertyType.equals("partialCharge")) {
currentAtom.setCharge(Double.parseDouble(propertyValue));
} else if (propertyType.equals("hydrogenCount")) {
currentAtom.setHydrogenCount(Integer.parseInt(propertyValue));
} else if (propertyType.equals("dictRef")) {
currentAtom.setProperty("org.openscience.cdk.dict", propertyValue);
} else if (propertyType.equals("atomicNumber")) {
currentAtom.setAtomicNumber(Integer.parseInt(propertyValue));
} else if (propertyType.equals("massNumber")) {
currentAtom.setMassNumber((int) Double.parseDouble(propertyValue));
} else if (propertyType.equals("id")) {
logger.debug("id: ", propertyValue);
currentAtom.setID(propertyValue);
atomEnumeration.put(propertyValue, numberOfAtoms);
}
} else if (objectType.equals("Bond")) {
if (propertyType.equals("atom1")) {
bond_a1 = Integer.parseInt(propertyValue);
} else if (propertyType.equals("atom2")) {
bond_a2 = Integer.parseInt(propertyValue);
} else if (propertyType.equals("id")) {
logger.debug("id: " + propertyValue);
bond_id = propertyValue;
} else if (propertyType.equals("order")) {
try {
Double order = Double.parseDouble(propertyValue);
if (order == 1.0) {
bond_order = IBond.Order.SINGLE;
} else if (order == 2.0) {
bond_order = IBond.Order.DOUBLE;
} else if (order == 3.0) {
bond_order = IBond.Order.TRIPLE;
} else if (order == 4.0) {
bond_order = IBond.Order.QUADRUPLE;
} else {
bond_order = IBond.Order.SINGLE;
}
} catch (Exception e) {
logger.error("Cannot convert to double: " + propertyValue);
bond_order = IBond.Order.SINGLE;
}
} else if (propertyType.equals("stereo")) {
if (propertyValue.equals("H")) {
bond_stereo = CDKConstants.STEREO_BOND_DOWN;
} else if (propertyValue.equals("W")) {
bond_stereo = CDKConstants.STEREO_BOND_UP;
}
}
}
logger.debug("Object property set...");
}
@Override
boolean intersect(
PickShape pickShape,
PickInfo pickInfo,
int flags,
Point3d iPnt,
GeometryRetained geom,
int geomIndex) {
Point3d pnts[] = new Point3d[4];
double sdist[] = new double[1];
double minDist = Double.MAX_VALUE;
double x = 0, y = 0, z = 0;
int[] vtxIndexArr = new int[4];
int i =
((vertexFormat & GeometryArray.BY_REFERENCE) == 0 ? initialVertexIndex : initialCoordIndex);
pnts[0] = new Point3d();
pnts[1] = new Point3d();
pnts[2] = new Point3d();
pnts[3] = new Point3d();
switch (pickShape.getPickType()) {
case PickShape.PICKRAY:
PickRay pickRay = (PickRay) pickShape;
while (i < validVertexCount) {
for (int j = 0; j < 4; j++) {
vtxIndexArr[j] = i;
getVertexData(i++, pnts[j]);
}
if (intersectRay(pnts, pickRay, sdist, iPnt)) {
if (flags == 0) {
return true;
}
if (sdist[0] < minDist) {
minDist = sdist[0];
x = iPnt.x;
y = iPnt.y;
z = iPnt.z;
if ((flags & PickInfo.CLOSEST_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
if ((flags & PickInfo.ALL_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
}
break;
case PickShape.PICKSEGMENT:
PickSegment pickSegment = (PickSegment) pickShape;
while (i < validVertexCount) {
for (int j = 0; j < 4; j++) {
vtxIndexArr[j] = i;
getVertexData(i++, pnts[j]);
}
if (intersectSegment(pnts, pickSegment.start, pickSegment.end, sdist, iPnt)) {
if (flags == 0) {
return true;
}
if (sdist[0] < minDist) {
minDist = sdist[0];
x = iPnt.x;
y = iPnt.y;
z = iPnt.z;
if ((flags & PickInfo.CLOSEST_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
if ((flags & PickInfo.ALL_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
}
break;
case PickShape.PICKBOUNDINGBOX:
BoundingBox bbox = (BoundingBox) ((PickBounds) pickShape).bounds;
while (i < validVertexCount) {
for (int j = 0; j < 4; j++) {
vtxIndexArr[j] = i;
getVertexData(i++, pnts[j]);
}
if (intersectBoundingBox(pnts, bbox, sdist, iPnt)) {
if (flags == 0) {
return true;
}
if (sdist[0] < minDist) {
minDist = sdist[0];
x = iPnt.x;
y = iPnt.y;
z = iPnt.z;
if ((flags & PickInfo.CLOSEST_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
if ((flags & PickInfo.ALL_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
}
break;
case PickShape.PICKBOUNDINGSPHERE:
BoundingSphere bsphere = (BoundingSphere) ((PickBounds) pickShape).bounds;
while (i < validVertexCount) {
for (int j = 0; j < 4; j++) {
vtxIndexArr[j] = i;
getVertexData(i++, pnts[j]);
}
if (intersectBoundingSphere(pnts, bsphere, sdist, iPnt)) {
if (flags == 0) {
return true;
}
if (sdist[0] < minDist) {
minDist = sdist[0];
x = iPnt.x;
y = iPnt.y;
z = iPnt.z;
if ((flags & PickInfo.CLOSEST_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
if ((flags & PickInfo.ALL_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
}
break;
case PickShape.PICKBOUNDINGPOLYTOPE:
BoundingPolytope bpolytope = (BoundingPolytope) ((PickBounds) pickShape).bounds;
while (i < validVertexCount) {
for (int j = 0; j < 4; j++) {
vtxIndexArr[j] = i;
getVertexData(i++, pnts[j]);
}
if (intersectBoundingPolytope(pnts, bpolytope, sdist, iPnt)) {
if (flags == 0) {
return true;
}
if (sdist[0] < minDist) {
minDist = sdist[0];
x = iPnt.x;
y = iPnt.y;
z = iPnt.z;
if ((flags & PickInfo.CLOSEST_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
if ((flags & PickInfo.ALL_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
}
break;
case PickShape.PICKCYLINDER:
PickCylinder pickCylinder = (PickCylinder) pickShape;
while (i < validVertexCount) {
for (int j = 0; j < 4; j++) {
vtxIndexArr[j] = i;
getVertexData(i++, pnts[j]);
}
if (intersectCylinder(pnts, pickCylinder, sdist, iPnt)) {
if (flags == 0) {
return true;
}
if (sdist[0] < minDist) {
minDist = sdist[0];
x = iPnt.x;
y = iPnt.y;
z = iPnt.z;
if ((flags & PickInfo.CLOSEST_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
if ((flags & PickInfo.ALL_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
}
break;
case PickShape.PICKCONE:
PickCone pickCone = (PickCone) pickShape;
while (i < validVertexCount) {
for (int j = 0; j < 4; j++) {
vtxIndexArr[j] = i;
getVertexData(i++, pnts[j]);
}
if (intersectCone(pnts, pickCone, sdist, iPnt)) {
if (flags == 0) {
return true;
}
if (sdist[0] < minDist) {
minDist = sdist[0];
x = iPnt.x;
y = iPnt.y;
z = iPnt.z;
if ((flags & PickInfo.CLOSEST_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
if ((flags & PickInfo.ALL_GEOM_INFO) != 0) {
storeInterestData(pickInfo, flags, geom, geomIndex, vtxIndexArr, iPnt, sdist[0]);
}
}
}
break;
case PickShape.PICKPOINT:
// Should not happen since API already check for this
throw new IllegalArgumentException(J3dI18N.getString("QuadArrayRetained0"));
default:
throw new RuntimeException("PickShape not supported for intersection ");
}
if (minDist < Double.MAX_VALUE) {
iPnt.x = x;
iPnt.y = y;
iPnt.z = z;
return true;
}
return false;
}
public Annotations(View view, Context context, Volume vol) {
super(view, context, vol);
viewPtAttr = (CoordAttr) context.getAttr("Vol Ref Pt");
perspectiveAttr = (ToggleAttr) context.getAttr("Perspective");
boxAttr[PLUS_X] = (ToggleAttr) context.getAttr("Plus X Box");
boxAttr[PLUS_Y] = (ToggleAttr) context.getAttr("Plus Y Box");
boxAttr[PLUS_Z] = (ToggleAttr) context.getAttr("Plus Z Box");
boxAttr[MINUS_X] = (ToggleAttr) context.getAttr("Minus X Box");
boxAttr[MINUS_Y] = (ToggleAttr) context.getAttr("Minus Y Box");
boxAttr[MINUS_Z] = (ToggleAttr) context.getAttr("Minus Z Box");
imageAttr[PLUS_X] = (StringAttr) context.getAttr("Plus X Image");
imageAttr[PLUS_Y] = (StringAttr) context.getAttr("Plus Y Image");
imageAttr[PLUS_Z] = (StringAttr) context.getAttr("Plus Z Image");
imageAttr[MINUS_X] = (StringAttr) context.getAttr("Minus X Image");
imageAttr[MINUS_Y] = (StringAttr) context.getAttr("Minus Y Image");
imageAttr[MINUS_Z] = (StringAttr) context.getAttr("Minus Z Image");
volume = vol;
frontRoot = new BranchGroup();
frontRoot.setCapability(BranchGroup.ALLOW_DETACH);
frontRoot.setCapability(Node.ALLOW_LOCAL_TO_VWORLD_READ);
backRoot = new BranchGroup();
backRoot.setCapability(BranchGroup.ALLOW_DETACH);
backRoot.setCapability(Node.ALLOW_LOCAL_TO_VWORLD_READ);
int stripLength[] = new int[1];
stripLength[0] = 5;
ColoringAttributes ca = new ColoringAttributes(1.0f, 0.0f, 0.0f, ColoringAttributes.SHADE_FLAT);
Appearance boxAppearance = new Appearance();
boxAppearance.setColoringAttributes(ca);
TexCoord2f[] texCoords = new TexCoord2f[4];
texCoords[0] = new TexCoord2f(0.0f, 0.0f);
texCoords[1] = new TexCoord2f(1.0f, 0.0f);
texCoords[2] = new TexCoord2f(1.0f, 1.0f);
texCoords[3] = new TexCoord2f(0.0f, 1.0f);
TransparencyAttributes ta = new TransparencyAttributes(TransparencyAttributes.BLENDED, 0.0f);
TextureAttributes texAttr = new TextureAttributes();
texAttr.setTextureMode(TextureAttributes.MODULATE);
PolygonAttributes pa = new PolygonAttributes();
pa.setCullFace(PolygonAttributes.CULL_NONE);
RenderingAttributes ra = new RenderingAttributes();
ra.setDepthBufferEnable(false);
for (int i = 0; i < 6; i++) {
faceGroup[i] = new SharedGroup();
frontAnnotations.addChild(new Link(faceGroup[i]));
backAnnotations.addChild(new Link(faceGroup[i]));
boxLine[i] = new LineStripArray(5, GeometryArray.COORDINATES, stripLength);
boxLine[i].setCoordinates(0, volume.facePoints[i], 0, 4);
boxLine[i].setCoordinate(4, volume.facePoints[i][0]);
boxLine[i].setCapability(GeometryArray.ALLOW_COORDINATE_WRITE);
Shape3D box = new Shape3D(boxLine[i], boxAppearance);
boxSwitch[i] = new Switch();
boxSwitch[i].setCapability(Switch.ALLOW_SWITCH_WRITE);
boxSwitch[i].addChild(box);
if (boxAttr[i].getValue() == true) {
boxSwitch[i].setWhichChild(Switch.CHILD_ALL);
} else {
boxSwitch[i].setWhichChild(Switch.CHILD_NONE);
}
faceGroup[i].addChild(boxSwitch[i]);
imageQuad[i] =
new QuadArray(4, GeometryArray.COORDINATES | GeometryArray.TEXTURE_COORDINATE_2);
imageQuad[i].setCapability(GeometryArray.ALLOW_COORDINATE_WRITE);
imageQuad[i].setCoordinates(0, volume.facePoints[i], 0, 4);
imageQuad[i].setTextureCoordinates(0, 0, texCoords, 0, 4);
imageAppearance[i] = new Appearance();
imageAppearance[i].setTransparencyAttributes(ta);
imageAppearance[i].setPolygonAttributes(pa);
imageAppearance[i].setRenderingAttributes(ra);
imageAppearance[i].setTextureAttributes(texAttr);
imageAppearance[i].setCapability(Appearance.ALLOW_TEXTURE_WRITE);
imageSwitch[i] = new Switch();
imageSwitch[i].setCapability(Switch.ALLOW_SWITCH_WRITE);
imageFile[i] = imageAttr[i].getValue();
if (imageFile[i].length() > 0) {
try {
URL imageURL = new URL(context.getCodeBase().toString() + imageFile[i]);
imageTexture[i] = new TextureLoader(imageURL, null).getTexture();
} catch (Exception e) {
System.err.println("Error " + e + " loading image:" + imageFile[i] + ".");
}
}
imageAppearance[i].setTexture(imageTexture[i]);
if (imageTexture[i] != null) {
imageSwitch[i].setWhichChild(Switch.CHILD_ALL);
} else {
imageSwitch[i].setWhichChild(Switch.CHILD_NONE);
}
Shape3D imageShape = new Shape3D(imageQuad[i], imageAppearance[i]);
imageSwitch[i].addChild(imageShape);
faceGroup[i].addChild(imageSwitch[i]);
}
frontAnnotations.setCapability(Switch.ALLOW_SWITCH_WRITE);
backAnnotations.setCapability(Switch.ALLOW_SWITCH_WRITE);
faceNormal[PLUS_X] = new Vector3d(1.0, 0.0, 0.0);
faceCenter[PLUS_X] = new Point3d(volume.maxCoord.x, 0.0, 0.0);
faceNormal[PLUS_Y] = new Vector3d(0.0, 1.0, 0.0);
faceCenter[PLUS_Y] = new Point3d(0.0, volume.maxCoord.y, 0.0);
faceNormal[PLUS_Z] = new Vector3d(0.0, 0.0, 1.0);
faceCenter[PLUS_Z] = new Point3d(0.0, 0.0, volume.maxCoord.z);
faceNormal[MINUS_X] = new Vector3d(-1.0, 0.0, 0.0);
faceCenter[MINUS_X] = new Point3d(volume.minCoord.x, 0.0, 0.0);
faceNormal[MINUS_Y] = new Vector3d(0.0, -1.0, 0.0);
faceCenter[MINUS_Y] = new Point3d(0.0, volume.minCoord.y, 0.0);
faceNormal[MINUS_Z] = new Vector3d(0.0, 0.0, -1.0);
faceCenter[MINUS_Z] = new Point3d(0.0, 0.0, volume.minCoord.z);
volCenter.x = (volume.maxCoord.x + volume.minCoord.x) / 2;
volCenter.y = (volume.maxCoord.y + volume.minCoord.y) / 2;
volCenter.z = (volume.maxCoord.z + volume.minCoord.z) / 2;
frontRoot.addChild(frontAnnotations);
backRoot.addChild(backAnnotations);
}
