/usr/share/doc/openjdk-11-jre-headless/demo/applets/MoleculeViewer/XYZApp.java is in openjdk-11-demo 10.0.1+10-3ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 | /*
* Copyright (c) 1995, 2013, Oracle and/or its affiliates. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* - Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* - Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* - Neither the name of Oracle nor the names of its
* contributors may be used to endorse or promote products derived
* from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
* IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
* THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
* PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/*
* This source code is provided to illustrate the usage of a given feature
* or technique and has been deliberately simplified. Additional steps
* required for a production-quality application, such as security checks,
* input validation and proper error handling, might not be present in
* this sample code.
*/
import java.applet.Applet;
import java.awt.Image;
import java.awt.Graphics;
import java.awt.Dimension;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.net.URL;
import java.awt.image.IndexColorModel;
import java.awt.image.MemoryImageSource;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StreamTokenizer;
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
/*
* A set of classes to parse, represent and display Chemical compounds in
* .xyz format (see http://chem.leeds.ac.uk/Project/MIME.html)
*/
/** The representation of a Chemical .xyz model */
final class XYZChemModel {
float vert[];
Atom atoms[];
int tvert[];
int ZsortMap[];
int nvert, maxvert;
static final Map<String, Atom> atomTable = new HashMap<String, Atom>();
static Atom defaultAtom;
static {
atomTable.put("c", new Atom(0, 0, 0));
atomTable.put("h", new Atom(210, 210, 210));
atomTable.put("n", new Atom(0, 0, 255));
atomTable.put("o", new Atom(255, 0, 0));
atomTable.put("p", new Atom(255, 0, 255));
atomTable.put("s", new Atom(255, 255, 0));
atomTable.put("hn", new Atom(150, 255, 150)); /* !!*/
defaultAtom = new Atom(255, 100, 200);
}
boolean transformed;
Matrix3D mat;
float xmin, xmax, ymin, ymax, zmin, zmax;
XYZChemModel() {
mat = new Matrix3D();
mat.xrot(20);
mat.yrot(30);
}
/** Create a Chemical model by parsing an input stream */
XYZChemModel(InputStream is) throws Exception {
this();
StreamTokenizer st = new StreamTokenizer(
new BufferedReader(new InputStreamReader(is, "UTF-8")));
st.eolIsSignificant(true);
st.commentChar('#');
try {
scan:
while (true) {
switch (st.nextToken()) {
case StreamTokenizer.TT_EOF:
break scan;
default:
break;
case StreamTokenizer.TT_WORD:
String name = st.sval;
double x = 0,
y = 0,
z = 0;
if (st.nextToken() == StreamTokenizer.TT_NUMBER) {
x = st.nval;
if (st.nextToken() == StreamTokenizer.TT_NUMBER) {
y = st.nval;
if (st.nextToken() == StreamTokenizer.TT_NUMBER) {
z = st.nval;
}
}
}
addVert(name, (float) x, (float) y, (float) z);
while (st.ttype != StreamTokenizer.TT_EOL
&& st.ttype != StreamTokenizer.TT_EOF) {
st.nextToken();
}
} // end Switch
} // end while
is.close();
} // end Try
catch (IOException e) {
}
if (st.ttype != StreamTokenizer.TT_EOF) {
throw new Exception(st.toString());
}
} // end XYZChemModel()
/** Add a vertex to this model */
int addVert(String name, float x, float y, float z) {
int i = nvert;
if (i >= maxvert) {
if (vert == null) {
maxvert = 100;
vert = new float[maxvert * 3];
atoms = new Atom[maxvert];
} else {
maxvert *= 2;
float nv[] = new float[maxvert * 3];
System.arraycopy(vert, 0, nv, 0, vert.length);
vert = nv;
Atom na[] = new Atom[maxvert];
System.arraycopy(atoms, 0, na, 0, atoms.length);
atoms = na;
}
}
Atom a = atomTable.get(name.toLowerCase());
if (a == null) {
a = defaultAtom;
}
atoms[i] = a;
i *= 3;
vert[i] = x;
vert[i + 1] = y;
vert[i + 2] = z;
return nvert++;
}
/** Transform all the points in this model */
void transform() {
if (transformed || nvert <= 0) {
return;
}
if (tvert == null || tvert.length < nvert * 3) {
tvert = new int[nvert * 3];
}
mat.transform(vert, tvert, nvert);
transformed = true;
}
/** Paint this model to a graphics context. It uses the matrix associated
with this model to map from model space to screen space.
The next version of the browser should have double buffering,
which will make this *much* nicer */
void paint(Graphics g) {
if (vert == null || nvert <= 0) {
return;
}
transform();
int v[] = tvert;
int zs[] = ZsortMap;
if (zs == null) {
ZsortMap = zs = new int[nvert];
for (int i = nvert; --i >= 0;) {
zs[i] = i * 3;
}
}
/*
* I use a bubble sort since from one iteration to the next, the sort
* order is pretty stable, so I just use what I had last time as a
* "guess" of the sorted order. With luck, this reduces O(N log N)
* to O(N)
*/
for (int i = nvert - 1; --i >= 0;) {
boolean flipped = false;
for (int j = 0; j <= i; j++) {
int a = zs[j];
int b = zs[j + 1];
if (v[a + 2] > v[b + 2]) {
zs[j + 1] = a;
zs[j] = b;
flipped = true;
}
}
if (!flipped) {
break;
}
}
int lim = nvert;
if (lim <= 0 || nvert <= 0) {
return;
}
for (int i = 0; i < lim; i++) {
int j = zs[i];
int grey = v[j + 2];
if (grey < 0) {
grey = 0;
}
if (grey > 15) {
grey = 15;
}
// g.drawString(names[i], v[j], v[j+1]);
atoms[j / 3].paint(g, v[j], v[j + 1], grey);
// g.drawImage(iBall, v[j] - (iBall.width >> 1), v[j + 1] -
// (iBall.height >> 1));
}
}
/** Find the bounding box of this model */
void findBB() {
if (nvert <= 0) {
return;
}
float v[] = vert;
float _xmin = v[0], _xmax = _xmin;
float _ymin = v[1], _ymax = _ymin;
float _zmin = v[2], _zmax = _zmin;
for (int i = nvert * 3; (i -= 3) > 0;) {
float x = v[i];
if (x < _xmin) {
_xmin = x;
}
if (x > _xmax) {
_xmax = x;
}
float y = v[i + 1];
if (y < _ymin) {
_ymin = y;
}
if (y > _ymax) {
_ymax = y;
}
float z = v[i + 2];
if (z < _zmin) {
_zmin = z;
}
if (z > _zmax) {
_zmax = z;
}
}
this.xmax = _xmax;
this.xmin = _xmin;
this.ymax = _ymax;
this.ymin = _ymin;
this.zmax = _zmax;
this.zmin = _zmin;
}
}
/** An applet to put a Chemical model into a page */
@SuppressWarnings("serial")
public class XYZApp extends Applet implements Runnable, MouseListener,
MouseMotionListener {
XYZChemModel md;
boolean painted = true;
float xfac;
int prevx, prevy;
float scalefudge = 1;
Matrix3D amat = new Matrix3D(), tmat = new Matrix3D();
String mdname = null;
String message = null;
Image backBuffer;
Graphics backGC;
Dimension backSize;
private synchronized void newBackBuffer() {
backBuffer = createImage(getSize().width, getSize().height);
if (backGC != null) {
backGC.dispose();
}
backGC = backBuffer.getGraphics();
backSize = getSize();
}
@Override
public void init() {
mdname = getParameter("model");
try {
scalefudge = Float.valueOf(getParameter("scale")).floatValue();
} catch (Exception ignored) {
}
amat.yrot(20);
amat.xrot(20);
if (mdname == null) {
mdname = "model.obj";
}
resize(getSize().width <= 20 ? 400 : getSize().width,
getSize().height <= 20 ? 400 : getSize().height);
newBackBuffer();
addMouseListener(this);
addMouseMotionListener(this);
}
@Override
public void destroy() {
removeMouseListener(this);
removeMouseMotionListener(this);
}
@Override
public void run() {
InputStream is = null;
try {
Thread.currentThread().setPriority(Thread.MIN_PRIORITY);
is = getClass().getResourceAsStream(mdname);
XYZChemModel m = new XYZChemModel(is);
Atom.setApplet(this);
md = m;
m.findBB();
float xw = m.xmax - m.xmin;
float yw = m.ymax - m.ymin;
float zw = m.zmax - m.zmin;
if (yw > xw) {
xw = yw;
}
if (zw > xw) {
xw = zw;
}
float f1 = getSize().width / xw;
float f2 = getSize().height / xw;
xfac = 0.7f * (f1 < f2 ? f1 : f2) * scalefudge;
} catch (Exception e) {
Logger.getLogger(XYZApp.class.getName()).log(Level.SEVERE, null, e);
md = null;
message = e.toString();
}
try {
if (is != null) {
is.close();
}
} catch (Exception ignored) {
}
repaint();
}
@Override
public void start() {
if (md == null && message == null) {
new Thread(this).start();
}
}
@Override
public void stop() {
}
/* event handling */
@Override
public void mouseClicked(MouseEvent e) {
}
@Override
public void mousePressed(MouseEvent e) {
prevx = e.getX();
prevy = e.getY();
e.consume();
}
@Override
public void mouseReleased(MouseEvent e) {
}
@Override
public void mouseEntered(MouseEvent e) {
}
@Override
public void mouseExited(MouseEvent e) {
}
@Override
public void mouseDragged(MouseEvent e) {
int x = e.getX();
int y = e.getY();
tmat.unit();
float xtheta = (prevy - y) * (360.0f / getSize().width);
float ytheta = (x - prevx) * (360.0f / getSize().height);
tmat.xrot(xtheta);
tmat.yrot(ytheta);
amat.mult(tmat);
if (painted) {
painted = false;
repaint();
}
prevx = x;
prevy = y;
e.consume();
}
@Override
public void mouseMoved(MouseEvent e) {
}
@Override
public void update(Graphics g) {
if (backBuffer == null) {
g.clearRect(0, 0, getSize().width, getSize().height);
}
paint(g);
}
@Override
public void paint(Graphics g) {
if (md != null) {
md.mat.unit();
md.mat.translate(-(md.xmin + md.xmax) / 2,
-(md.ymin + md.ymax) / 2,
-(md.zmin + md.zmax) / 2);
md.mat.mult(amat);
// md.mat.scale(xfac, -xfac, 8 * xfac / getSize().width);
md.mat.scale(xfac, -xfac, 16 * xfac / getSize().width);
md.mat.translate(getSize().width / 2, getSize().height / 2, 8);
md.transformed = false;
if (backBuffer != null) {
if (!backSize.equals(getSize())) {
newBackBuffer();
}
backGC.setColor(getBackground());
backGC.fillRect(0, 0, getSize().width, getSize().height);
md.paint(backGC);
g.drawImage(backBuffer, 0, 0, this);
} else {
md.paint(g);
}
setPainted();
} else if (message != null) {
g.drawString("Error in model:", 3, 20);
g.drawString(message, 10, 40);
}
}
private synchronized void setPainted() {
painted = true;
notifyAll();
}
@Override
public String getAppletInfo() {
return "Title: XYZApp \nAuthor: James Gosling \nAn applet to put"
+ " a Chemical model into a page.";
}
@Override
public String[][] getParameterInfo() {
String[][] info = {
{ "model", "path string", "The path to the model to be displayed"
+ " in .xyz format "
+ "(see http://chem.leeds.ac.uk/Project/MIME.html)."
+ " Default is model.obj." },
{ "scale", "float", "Scale factor. Default is 1 (i.e. no scale)." }
};
return info;
}
} // end class XYZApp
class Atom {
private static Applet applet;
private static byte[] data;
private static final int R = 40;
private static final int hx = 15;
private static final int hy = 15;
private static final int bgGrey = 192;
private static final int nBalls = 16;
private static int maxr;
private int Rl;
private int Gl;
private int Bl;
private Image balls[];
static {
data = new byte[R * 2 * R * 2];
int mr = 0;
for (int Y = 2 * R; --Y >= 0;) {
int x0 = (int) (Math.sqrt(R * R - (Y - R) * (Y - R)) + 0.5);
int p = Y * (R * 2) + R - x0;
for (int X = -x0; X < x0; X++) {
int x = X + hx;
int y = Y - R + hy;
int r = (int) (Math.sqrt(x * x + y * y) + 0.5);
if (r > mr) {
mr = r;
}
data[p++] = r <= 0 ? 1 : (byte) r;
}
}
maxr = mr;
}
static void setApplet(Applet app) {
applet = app;
}
Atom(int Rl, int Gl, int Bl) {
this.Rl = Rl;
this.Gl = Gl;
this.Bl = Bl;
}
private int blend(int fg, int bg, float fgfactor) {
return (int) (bg + (fg - bg) * fgfactor);
}
private void Setup() {
balls = new Image[nBalls];
byte red[] = new byte[256];
red[0] = (byte) bgGrey;
byte green[] = new byte[256];
green[0] = (byte) bgGrey;
byte blue[] = new byte[256];
blue[0] = (byte) bgGrey;
for (int r = 0; r < nBalls; r++) {
float b = (float) (r + 1) / nBalls;
for (int i = maxr; i >= 1; --i) {
float d = (float) i / maxr;
red[i] = (byte) blend(blend(Rl, 255, d), bgGrey, b);
green[i] = (byte) blend(blend(Gl, 255, d), bgGrey, b);
blue[i] = (byte) blend(blend(Bl, 255, d), bgGrey, b);
}
IndexColorModel model = new IndexColorModel(8, maxr + 1,
red, green, blue, 0);
balls[r] = applet.createImage(
new MemoryImageSource(R * 2, R * 2, model, data, 0, R * 2));
}
}
void paint(Graphics gc, int x, int y, int r) {
Image ba[] = balls;
if (ba == null) {
Setup();
ba = balls;
}
Image i = ba[r];
int size = 10 + r;
gc.drawImage(i, x - (size >> 1), y - (size >> 1), size, size, applet);
}
}
|