J. Duke | 319a3b9 | 2007-12-01 00:00:00 +0000 | [diff] [blame^] | 1 | /* |
| 2 | * Copyright 1995-2006 Sun Microsystems, Inc. All Rights Reserved. |
| 3 | * |
| 4 | * Redistribution and use in source and binary forms, with or without |
| 5 | * modification, are permitted provided that the following conditions |
| 6 | * are met: |
| 7 | * |
| 8 | * - Redistributions of source code must retain the above copyright |
| 9 | * notice, this list of conditions and the following disclaimer. |
| 10 | * |
| 11 | * - Redistributions in binary form must reproduce the above copyright |
| 12 | * notice, this list of conditions and the following disclaimer in the |
| 13 | * documentation and/or other materials provided with the distribution. |
| 14 | * |
| 15 | * - Neither the name of Sun Microsystems nor the names of its |
| 16 | * contributors may be used to endorse or promote products derived |
| 17 | * from this software without specific prior written permission. |
| 18 | * |
| 19 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS |
| 20 | * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, |
| 21 | * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR |
| 22 | * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR |
| 23 | * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, |
| 24 | * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, |
| 25 | * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR |
| 26 | * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF |
| 27 | * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING |
| 28 | * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS |
| 29 | * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| 30 | */ |
| 31 | |
| 32 | /* |
| 33 | */ |
| 34 | |
| 35 | /* |
| 36 | * A set of classes to parse, represent and display Chemical compounds in |
| 37 | * .xyz format (see http://chem.leeds.ac.uk/Project/MIME.html) |
| 38 | */ |
| 39 | |
| 40 | import java.applet.Applet; |
| 41 | import java.awt.Image; |
| 42 | import java.awt.Event; |
| 43 | import java.awt.Graphics; |
| 44 | import java.awt.Dimension; |
| 45 | import java.io.*; |
| 46 | import java.net.URL; |
| 47 | import java.util.Hashtable; |
| 48 | import java.awt.image.IndexColorModel; |
| 49 | import java.awt.image.ColorModel; |
| 50 | import java.awt.image.MemoryImageSource; |
| 51 | import java.awt.event.*; |
| 52 | |
| 53 | /** The representation of a Chemical .xyz model */ |
| 54 | class XYZChemModel { |
| 55 | float vert[]; |
| 56 | Atom atoms[]; |
| 57 | int tvert[]; |
| 58 | int ZsortMap[]; |
| 59 | int nvert, maxvert; |
| 60 | |
| 61 | static Hashtable atomTable = new Hashtable(); |
| 62 | static Atom defaultAtom; |
| 63 | static { |
| 64 | atomTable.put("c", new Atom(0, 0, 0)); |
| 65 | atomTable.put("h", new Atom(210, 210, 210)); |
| 66 | atomTable.put("n", new Atom(0, 0, 255)); |
| 67 | atomTable.put("o", new Atom(255, 0, 0)); |
| 68 | atomTable.put("p", new Atom(255, 0, 255)); |
| 69 | atomTable.put("s", new Atom(255, 255, 0)); |
| 70 | atomTable.put("hn", new Atom(150, 255, 150)); /* !!*/ |
| 71 | defaultAtom = new Atom(255, 100, 200); |
| 72 | } |
| 73 | |
| 74 | boolean transformed; |
| 75 | Matrix3D mat; |
| 76 | |
| 77 | float xmin, xmax, ymin, ymax, zmin, zmax; |
| 78 | |
| 79 | |
| 80 | XYZChemModel () { |
| 81 | mat = new Matrix3D(); |
| 82 | mat.xrot(20); |
| 83 | mat.yrot(30); |
| 84 | } |
| 85 | |
| 86 | |
| 87 | /** Create a Cehmical model by parsing an input stream */ |
| 88 | XYZChemModel (InputStream is) throws Exception |
| 89 | { |
| 90 | this(); |
| 91 | StreamTokenizer st = new StreamTokenizer( |
| 92 | new BufferedReader(new InputStreamReader(is, "UTF-8"))); |
| 93 | st.eolIsSignificant(true); |
| 94 | st.commentChar('#'); |
| 95 | int slot = 0; |
| 96 | |
| 97 | try |
| 98 | { |
| 99 | scan: |
| 100 | while (true) |
| 101 | { |
| 102 | switch ( st.nextToken() ) |
| 103 | { |
| 104 | case StreamTokenizer.TT_EOF: |
| 105 | break scan; |
| 106 | default: |
| 107 | break; |
| 108 | case StreamTokenizer.TT_WORD: |
| 109 | String name = st.sval; |
| 110 | double x = 0, y = 0, z = 0; |
| 111 | if (st.nextToken() == StreamTokenizer.TT_NUMBER) |
| 112 | { |
| 113 | x = st.nval; |
| 114 | if (st.nextToken() == StreamTokenizer.TT_NUMBER) |
| 115 | { |
| 116 | y = st.nval; |
| 117 | if (st.nextToken() == StreamTokenizer.TT_NUMBER) |
| 118 | z = st.nval; |
| 119 | } |
| 120 | } |
| 121 | addVert(name, (float) x, (float) y, (float) z); |
| 122 | while( st.ttype != StreamTokenizer.TT_EOL && |
| 123 | st.ttype != StreamTokenizer.TT_EOF ) |
| 124 | st.nextToken(); |
| 125 | |
| 126 | } // end Switch |
| 127 | |
| 128 | } // end while |
| 129 | |
| 130 | is.close(); |
| 131 | |
| 132 | } // end Try |
| 133 | catch( IOException e) {} |
| 134 | |
| 135 | if (st.ttype != StreamTokenizer.TT_EOF) |
| 136 | throw new Exception(st.toString()); |
| 137 | |
| 138 | } // end XYZChemModel() |
| 139 | |
| 140 | /** Add a vertex to this model */ |
| 141 | int addVert(String name, float x, float y, float z) { |
| 142 | int i = nvert; |
| 143 | if (i >= maxvert) |
| 144 | if (vert == null) { |
| 145 | maxvert = 100; |
| 146 | vert = new float[maxvert * 3]; |
| 147 | atoms = new Atom[maxvert]; |
| 148 | } else { |
| 149 | maxvert *= 2; |
| 150 | float nv[] = new float[maxvert * 3]; |
| 151 | System.arraycopy(vert, 0, nv, 0, vert.length); |
| 152 | vert = nv; |
| 153 | Atom na[] = new Atom[maxvert]; |
| 154 | System.arraycopy(atoms, 0, na, 0, atoms.length); |
| 155 | atoms = na; |
| 156 | } |
| 157 | Atom a = (Atom) atomTable.get(name.toLowerCase()); |
| 158 | if (a == null) a = defaultAtom; |
| 159 | atoms[i] = a; |
| 160 | i *= 3; |
| 161 | vert[i] = x; |
| 162 | vert[i + 1] = y; |
| 163 | vert[i + 2] = z; |
| 164 | return nvert++; |
| 165 | } |
| 166 | |
| 167 | /** Transform all the points in this model */ |
| 168 | void transform() { |
| 169 | if (transformed || nvert <= 0) |
| 170 | return; |
| 171 | if (tvert == null || tvert.length < nvert * 3) |
| 172 | tvert = new int[nvert * 3]; |
| 173 | mat.transform(vert, tvert, nvert); |
| 174 | transformed = true; |
| 175 | } |
| 176 | |
| 177 | |
| 178 | /** Paint this model to a graphics context. It uses the matrix associated |
| 179 | with this model to map from model space to screen space. |
| 180 | The next version of the browser should have double buffering, |
| 181 | which will make this *much* nicer */ |
| 182 | void paint(Graphics g) { |
| 183 | if (vert == null || nvert <= 0) |
| 184 | return; |
| 185 | transform(); |
| 186 | int v[] = tvert; |
| 187 | int zs[] = ZsortMap; |
| 188 | if (zs == null) { |
| 189 | ZsortMap = zs = new int[nvert]; |
| 190 | for (int i = nvert; --i >= 0;) |
| 191 | zs[i] = i * 3; |
| 192 | } |
| 193 | |
| 194 | /* |
| 195 | * I use a bubble sort since from one iteration to the next, the sort |
| 196 | * order is pretty stable, so I just use what I had last time as a |
| 197 | * "guess" of the sorted order. With luck, this reduces O(N log N) |
| 198 | * to O(N) |
| 199 | */ |
| 200 | |
| 201 | for (int i = nvert - 1; --i >= 0;) { |
| 202 | boolean flipped = false; |
| 203 | for (int j = 0; j <= i; j++) { |
| 204 | int a = zs[j]; |
| 205 | int b = zs[j + 1]; |
| 206 | if (v[a + 2] > v[b + 2]) { |
| 207 | zs[j + 1] = a; |
| 208 | zs[j] = b; |
| 209 | flipped = true; |
| 210 | } |
| 211 | } |
| 212 | if (!flipped) |
| 213 | break; |
| 214 | } |
| 215 | |
| 216 | int lg = 0; |
| 217 | int lim = nvert; |
| 218 | Atom ls[] = atoms; |
| 219 | if (lim <= 0 || nvert <= 0) |
| 220 | return; |
| 221 | for (int i = 0; i < lim; i++) { |
| 222 | int j = zs[i]; |
| 223 | int grey = v[j + 2]; |
| 224 | if (grey < 0) |
| 225 | grey = 0; |
| 226 | if (grey > 15) |
| 227 | grey = 15; |
| 228 | // g.drawString(names[i], v[j], v[j+1]); |
| 229 | atoms[j/3].paint(g, v[j], v[j + 1], grey); |
| 230 | // g.drawImage(iBall, v[j] - (iBall.width >> 1), v[j + 1] - |
| 231 | // (iBall.height >> 1)); |
| 232 | } |
| 233 | } |
| 234 | |
| 235 | /** Find the bounding box of this model */ |
| 236 | void findBB() { |
| 237 | if (nvert <= 0) |
| 238 | return; |
| 239 | float v[] = vert; |
| 240 | float xmin = v[0], xmax = xmin; |
| 241 | float ymin = v[1], ymax = ymin; |
| 242 | float zmin = v[2], zmax = zmin; |
| 243 | for (int i = nvert * 3; (i -= 3) > 0;) { |
| 244 | float x = v[i]; |
| 245 | if (x < xmin) |
| 246 | xmin = x; |
| 247 | if (x > xmax) |
| 248 | xmax = x; |
| 249 | float y = v[i + 1]; |
| 250 | if (y < ymin) |
| 251 | ymin = y; |
| 252 | if (y > ymax) |
| 253 | ymax = y; |
| 254 | float z = v[i + 2]; |
| 255 | if (z < zmin) |
| 256 | zmin = z; |
| 257 | if (z > zmax) |
| 258 | zmax = z; |
| 259 | } |
| 260 | this.xmax = xmax; |
| 261 | this.xmin = xmin; |
| 262 | this.ymax = ymax; |
| 263 | this.ymin = ymin; |
| 264 | this.zmax = zmax; |
| 265 | this.zmin = zmin; |
| 266 | } |
| 267 | } |
| 268 | |
| 269 | /** An applet to put a Chemical model into a page */ |
| 270 | public class XYZApp |
| 271 | extends Applet |
| 272 | implements Runnable, MouseListener, MouseMotionListener { |
| 273 | XYZChemModel md; |
| 274 | boolean painted = true; |
| 275 | float xfac; |
| 276 | int prevx, prevy; |
| 277 | float xtheta, ytheta; |
| 278 | float scalefudge = 1; |
| 279 | Matrix3D amat = new Matrix3D(), tmat = new Matrix3D(); |
| 280 | String mdname = null; |
| 281 | String message = null; |
| 282 | Image backBuffer; |
| 283 | Graphics backGC; |
| 284 | Dimension backSize; |
| 285 | |
| 286 | |
| 287 | private synchronized void newBackBuffer() { |
| 288 | backBuffer = createImage(getSize().width, getSize().height); |
| 289 | if (backGC != null) { |
| 290 | backGC.dispose(); |
| 291 | } |
| 292 | backGC = backBuffer.getGraphics(); |
| 293 | backSize = getSize(); |
| 294 | } |
| 295 | |
| 296 | public void init() { |
| 297 | mdname = getParameter("model"); |
| 298 | try { |
| 299 | scalefudge = Float.valueOf(getParameter("scale")).floatValue(); |
| 300 | } catch(Exception e) { |
| 301 | }; |
| 302 | amat.yrot(20); |
| 303 | amat.xrot(20); |
| 304 | if (mdname == null) |
| 305 | mdname = "model.obj"; |
| 306 | resize(getSize().width <= 20 ? 400 : getSize().width, |
| 307 | getSize().height <= 20 ? 400 : getSize().height); |
| 308 | newBackBuffer(); |
| 309 | addMouseListener(this); |
| 310 | addMouseMotionListener(this); |
| 311 | } |
| 312 | |
| 313 | public void destroy() { |
| 314 | removeMouseListener(this); |
| 315 | removeMouseMotionListener(this); |
| 316 | } |
| 317 | |
| 318 | public void run() { |
| 319 | InputStream is = null; |
| 320 | try { |
| 321 | Thread.currentThread().setPriority(Thread.MIN_PRIORITY); |
| 322 | is = new URL(getDocumentBase(), mdname).openStream(); |
| 323 | XYZChemModel m = new XYZChemModel (is); |
| 324 | Atom.setApplet(this); |
| 325 | md = m; |
| 326 | m.findBB(); |
| 327 | float xw = m.xmax - m.xmin; |
| 328 | float yw = m.ymax - m.ymin; |
| 329 | float zw = m.zmax - m.zmin; |
| 330 | if (yw > xw) |
| 331 | xw = yw; |
| 332 | if (zw > xw) |
| 333 | xw = zw; |
| 334 | float f1 = getSize().width / xw; |
| 335 | float f2 = getSize().height / xw; |
| 336 | xfac = 0.7f * (f1 < f2 ? f1 : f2) * scalefudge; |
| 337 | } catch(Exception e) { |
| 338 | e.printStackTrace(); |
| 339 | md = null; |
| 340 | message = e.toString(); |
| 341 | } |
| 342 | try { |
| 343 | if (is != null) |
| 344 | is.close(); |
| 345 | } catch(Exception e) { |
| 346 | } |
| 347 | repaint(); |
| 348 | } |
| 349 | public void start() { |
| 350 | if (md == null && message == null) |
| 351 | new Thread(this).start(); |
| 352 | } |
| 353 | public void stop() { |
| 354 | } |
| 355 | /* event handling */ |
| 356 | public void mouseClicked(MouseEvent e) { |
| 357 | } |
| 358 | public void mousePressed(MouseEvent e) { |
| 359 | prevx = e.getX(); |
| 360 | prevy = e.getY(); |
| 361 | e.consume(); |
| 362 | } |
| 363 | public void mouseReleased(MouseEvent e) { |
| 364 | } |
| 365 | public void mouseEntered(MouseEvent e) { |
| 366 | } |
| 367 | public void mouseExited(MouseEvent e) { |
| 368 | } |
| 369 | public void mouseDragged(MouseEvent e) { |
| 370 | int x = e.getX(); |
| 371 | int y = e.getY(); |
| 372 | tmat.unit(); |
| 373 | float xtheta = (prevy - y) * (360.0f / getSize().width); |
| 374 | float ytheta = (x - prevx) * (360.0f / getSize().height); |
| 375 | tmat.xrot(xtheta); |
| 376 | tmat.yrot(ytheta); |
| 377 | amat.mult(tmat); |
| 378 | if (painted) { |
| 379 | painted = false; |
| 380 | repaint(); |
| 381 | } |
| 382 | prevx = x; |
| 383 | prevy = y; |
| 384 | e.consume(); |
| 385 | } |
| 386 | public void mouseMoved(MouseEvent e) { |
| 387 | } |
| 388 | |
| 389 | public void update(Graphics g) { |
| 390 | if (backBuffer == null) |
| 391 | g.clearRect(0, 0, getSize().width, getSize().height); |
| 392 | paint(g); |
| 393 | } |
| 394 | |
| 395 | public void paint(Graphics g) { |
| 396 | if (md != null) { |
| 397 | md.mat.unit(); |
| 398 | md.mat.translate(-(md.xmin + md.xmax) / 2, |
| 399 | -(md.ymin + md.ymax) / 2, |
| 400 | -(md.zmin + md.zmax) / 2); |
| 401 | md.mat.mult(amat); |
| 402 | // md.mat.scale(xfac, -xfac, 8 * xfac / getSize().width); |
| 403 | md.mat.scale(xfac, -xfac, 16 * xfac / getSize().width); |
| 404 | md.mat.translate(getSize().width / 2, getSize().height / 2, 8); |
| 405 | md.transformed = false; |
| 406 | if (backBuffer != null) { |
| 407 | if (!backSize.equals(getSize())) |
| 408 | newBackBuffer(); |
| 409 | backGC.setColor(getBackground()); |
| 410 | backGC.fillRect(0,0,getSize().width,getSize().height); |
| 411 | md.paint(backGC); |
| 412 | g.drawImage(backBuffer, 0, 0, this); |
| 413 | } |
| 414 | else |
| 415 | md.paint(g); |
| 416 | setPainted(); |
| 417 | } else if (message != null) { |
| 418 | g.drawString("Error in model:", 3, 20); |
| 419 | g.drawString(message, 10, 40); |
| 420 | } |
| 421 | } |
| 422 | private synchronized void setPainted() { |
| 423 | painted = true; |
| 424 | notifyAll(); |
| 425 | } |
| 426 | |
| 427 | private synchronized void waitPainted() |
| 428 | { |
| 429 | while (!painted) |
| 430 | { |
| 431 | try |
| 432 | { |
| 433 | wait(); |
| 434 | } |
| 435 | catch (InterruptedException e) {} |
| 436 | } |
| 437 | painted = false; |
| 438 | } |
| 439 | |
| 440 | public String getAppletInfo() { |
| 441 | return "Title: XYZApp \nAuthor: James Gosling \nAn applet to put a Chemical model into a page."; |
| 442 | } |
| 443 | |
| 444 | public String[][] getParameterInfo() { |
| 445 | String[][] info = { |
| 446 | {"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."}, |
| 447 | {"scale", "float", "Scale factor. Default is 1 (i.e. no scale)."} |
| 448 | }; |
| 449 | return info; |
| 450 | } |
| 451 | } // end class XYZApp |
| 452 | |
| 453 | class Atom { |
| 454 | private static Applet applet; |
| 455 | private static byte[] data; |
| 456 | private final static int R = 40; |
| 457 | private final static int hx = 15; |
| 458 | private final static int hy = 15; |
| 459 | private final static int bgGrey = 192; |
| 460 | private final static int nBalls = 16; |
| 461 | private static int maxr; |
| 462 | |
| 463 | private int Rl; |
| 464 | private int Gl; |
| 465 | private int Bl; |
| 466 | private Image balls[]; |
| 467 | |
| 468 | static { |
| 469 | data = new byte[R * 2 * R * 2]; |
| 470 | int mr = 0; |
| 471 | for (int Y = 2 * R; --Y >= 0;) { |
| 472 | int x0 = (int) (Math.sqrt(R * R - (Y - R) * (Y - R)) + 0.5); |
| 473 | int p = Y * (R * 2) + R - x0; |
| 474 | for (int X = -x0; X < x0; X++) { |
| 475 | int x = X + hx; |
| 476 | int y = Y - R + hy; |
| 477 | int r = (int) (Math.sqrt(x * x + y * y) + 0.5); |
| 478 | if (r > mr) |
| 479 | mr = r; |
| 480 | data[p++] = r <= 0 ? 1 : (byte) r; |
| 481 | } |
| 482 | } |
| 483 | maxr = mr; |
| 484 | } |
| 485 | static void setApplet(Applet app) { |
| 486 | applet = app; |
| 487 | } |
| 488 | Atom(int Rl, int Gl, int Bl) { |
| 489 | this.Rl = Rl; |
| 490 | this.Gl = Gl; |
| 491 | this.Bl = Bl; |
| 492 | } |
| 493 | private final int blend(int fg, int bg, float fgfactor) { |
| 494 | return (int) (bg + (fg - bg) * fgfactor); |
| 495 | } |
| 496 | private void Setup() { |
| 497 | balls = new Image[nBalls]; |
| 498 | byte red[] = new byte[256]; |
| 499 | red[0] = (byte) bgGrey; |
| 500 | byte green[] = new byte[256]; |
| 501 | green[0] = (byte) bgGrey; |
| 502 | byte blue[] = new byte[256]; |
| 503 | blue[0] = (byte) bgGrey; |
| 504 | for (int r = 0; r < nBalls; r++) { |
| 505 | float b = (float) (r+1) / nBalls; |
| 506 | for (int i = maxr; i >= 1; --i) { |
| 507 | float d = (float) i / maxr; |
| 508 | red[i] = (byte) blend(blend(Rl, 255, d), bgGrey, b); |
| 509 | green[i] = (byte) blend(blend(Gl, 255, d), bgGrey, b); |
| 510 | blue[i] = (byte) blend(blend(Bl, 255, d), bgGrey, b); |
| 511 | } |
| 512 | IndexColorModel model = new IndexColorModel(8, maxr + 1, |
| 513 | red, green, blue, 0); |
| 514 | balls[r] = applet.createImage( |
| 515 | new MemoryImageSource(R*2, R*2, model, data, 0, R*2)); |
| 516 | } |
| 517 | } |
| 518 | void paint(Graphics gc, int x, int y, int r) { |
| 519 | Image ba[] = balls; |
| 520 | if (ba == null) { |
| 521 | Setup(); |
| 522 | ba = balls; |
| 523 | } |
| 524 | Image i = ba[r]; |
| 525 | int size = 10 + r; |
| 526 | gc.drawImage(i, x - (size >> 1), y - (size >> 1), size, size, applet); |
| 527 | } |
| 528 | } |