diff --git a/src/share/demo/applets/MoleculeViewer/Matrix3D.java b/src/share/demo/applets/MoleculeViewer/Matrix3D.java index bc5939d54bd8bb9574cfcd5c1b0c71710ad6edca..0dda042c3c9a6faeadc7d2d7f27f99112432d2ff 100644 --- a/src/share/demo/applets/MoleculeViewer/Matrix3D.java +++ b/src/share/demo/applets/MoleculeViewer/Matrix3D.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 1995, 2006, Oracle and/or its affiliates. All rights reserved. + * Copyright (c) 1995, 2011, 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 @@ -29,22 +29,23 @@ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -/* - */ /** A fairly conventional 3D matrix object that can transform sets of - 3D points and perform a variety of manipulations on the transform */ +3D points and perform a variety of manipulations on the transform */ class Matrix3D { + float xx, xy, xz, xo; float yx, yy, yz, yo; float zx, zy, zz, zo; static final double pi = 3.14159265; + /** Create a new unit matrix */ - Matrix3D () { + Matrix3D() { xx = 1.0f; yy = 1.0f; zz = 1.0f; } + /** Scale by f in all dimensions */ void scale(float f) { xx *= f; @@ -60,6 +61,7 @@ class Matrix3D { zz *= f; zo *= f; } + /** Scale along each axis independently */ void scale(float xf, float yf, float zf) { xx *= xf; @@ -75,12 +77,14 @@ class Matrix3D { zz *= zf; zo *= zf; } + /** Translate the origin */ void translate(float x, float y, float z) { xo += x; yo += y; zo += z; } + /** rotate theta degrees about the y axis */ void yrot(double theta) { theta *= (pi / 180); @@ -106,6 +110,7 @@ class Matrix3D { zy = Nzy; zz = Nzz; } + /** rotate theta degrees about the x axis */ void xrot(double theta) { theta *= (pi / 180); @@ -131,6 +136,7 @@ class Matrix3D { zy = Nzy; zz = Nzz; } + /** rotate theta degrees about the z axis */ void zrot(double theta) { theta *= (pi / 180); @@ -156,6 +162,7 @@ class Matrix3D { xy = Nxy; xz = Nxz; } + /** Multiply this matrix by a second: M = M*R */ void mult(Matrix3D rhs) { float lxx = xx * rhs.xx + yx * rhs.xy + zx * rhs.xz; @@ -204,10 +211,11 @@ class Matrix3D { zy = 0; zz = 1; } + /** Transform nvert points from v into tv. v contains the input - coordinates in floating point. Three successive entries in - the array constitute a point. tv ends up holding the transformed - points as integers; three successive entries per point */ + coordinates in floating point. Three successive entries in + the array constitute a point. tv ends up holding the transformed + points as integers; three successive entries per point */ void transform(float v[], int tv[], int nvert) { float lxx = xx, lxy = xy, lxz = xz, lxo = xo; float lyx = yx, lyy = yy, lyz = yz, lyo = yo; @@ -216,11 +224,13 @@ class Matrix3D { float x = v[i]; float y = v[i + 1]; float z = v[i + 2]; - tv[i ] = (int) (x * lxx + y * lxy + z * lxz + lxo); + tv[i] = (int) (x * lxx + y * lxy + z * lxz + lxo); tv[i + 1] = (int) (x * lyx + y * lyy + z * lyz + lyo); tv[i + 2] = (int) (x * lzx + y * lzy + z * lzz + lzo); } } + + @Override public String toString() { return ("[" + xo + "," + xx + "," + xy + "," + xz + ";" + yo + "," + yx + "," + yy + "," + yz + ";" diff --git a/src/share/demo/applets/MoleculeViewer/XYZApp.java b/src/share/demo/applets/MoleculeViewer/XYZApp.java index 719e6f55ef551bc3a9cdb8aa22afcddd832099ec..78717bef21f07580c134d50bf4020e9e88c4d29c 100644 --- a/src/share/demo/applets/MoleculeViewer/XYZApp.java +++ b/src/share/demo/applets/MoleculeViewer/XYZApp.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 1995, 2006, Oracle and/or its affiliates. All rights reserved. + * Copyright (c) 1995, 2011, 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 @@ -29,37 +29,43 @@ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ -/* - */ - -/* - * A set of classes to parse, represent and display Chemical compounds in - * .xyz format (see http://chem.leeds.ac.uk/Project/MIME.html) - */ import java.applet.Applet; import java.awt.Image; -import java.awt.Event; import java.awt.Graphics; import java.awt.Dimension; -import java.io.*; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; import java.net.URL; -import java.util.Hashtable; import java.awt.image.IndexColorModel; -import java.awt.image.ColorModel; import java.awt.image.MemoryImageSource; -import java.awt.event.*; +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 */ -class XYZChemModel { +final class XYZChemModel { + float vert[]; Atom atoms[]; int tvert[]; int ZsortMap[]; int nvert, maxvert; - - static Hashtable atomTable = new Hashtable(); + static final Map atomTable = new HashMap(); static Atom defaultAtom; + static { atomTable.put("c", new Atom(0, 0, 0)); atomTable.put("h", new Atom(210, 210, 210)); @@ -70,77 +76,72 @@ class XYZChemModel { 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 () { + 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) { + } - /** Create a Cehmical 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('#'); - int slot = 0; - - 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()); + 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 (i >= maxvert) { if (vert == null) { maxvert = 100; vert = new float[maxvert * 3]; @@ -154,8 +155,11 @@ scan: System.arraycopy(atoms, 0, na, 0, atoms.length); atoms = na; } - Atom a = (Atom) atomTable.get(name.toLowerCase()); - if (a == null) a = defaultAtom; + } + Atom a = atomTable.get(name.toLowerCase()); + if (a == null) { + a = defaultAtom; + } atoms[i] = a; i *= 3; vert[i] = x; @@ -166,29 +170,32 @@ scan: /** Transform all the points in this model */ void transform() { - if (transformed || nvert <= 0) + if (transformed || nvert <= 0) { return; - if (tvert == null || tvert.length < nvert * 3) + } + 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 */ + 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) + 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;) + for (int i = nvert; --i >= 0;) { zs[i] = i * 3; + } } /* @@ -209,24 +216,26 @@ scan: flipped = true; } } - if (!flipped) + if (!flipped) { break; + } } - int lg = 0; int lim = nvert; - Atom ls[] = atoms; - if (lim <= 0 || nvert <= 0) + 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) + if (grey < 0) { grey = 0; - if (grey > 15) + } + 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); + 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)); } @@ -234,47 +243,55 @@ scan: /** Find the bounding box of this model */ void findBB() { - if (nvert <= 0) + 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; + 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; + 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; + 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; + 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; + 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 */ -public class XYZApp - extends Applet - implements Runnable, MouseListener, MouseMotionListener { +@SuppressWarnings("serial") +public class XYZApp extends Applet implements Runnable, MouseListener, + MouseMotionListener { + XYZChemModel md; boolean painted = true; float xfac; int prevx, prevy; - float xtheta, ytheta; float scalefudge = 1; Matrix3D amat = new Matrix3D(), tmat = new Matrix3D(); String mdname = null; @@ -283,7 +300,6 @@ public class XYZApp Graphics backGC; Dimension backSize; - private synchronized void newBackBuffer() { backBuffer = createImage(getSize().width, getSize().height); if (backGC != null) { @@ -293,164 +309,190 @@ public class XYZApp backSize = getSize(); } + @Override public void init() { mdname = getParameter("model"); try { scalefudge = Float.valueOf(getParameter("scale")).floatValue(); - } catch(Exception e) { - }; + } catch (Exception ignored) { + } amat.yrot(20); amat.xrot(20); - if (mdname == null) + if (mdname == null) { mdname = "model.obj"; + } resize(getSize().width <= 20 ? 400 : getSize().width, - getSize().height <= 20 ? 400 : getSize().height); + 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 = new URL(getDocumentBase(), mdname).openStream(); - XYZChemModel m = new XYZChemModel (is); + 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) + if (yw > xw) { xw = yw; - if (zw > xw) + } + 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) { - e.printStackTrace(); + } catch (Exception e) { + Logger.getLogger(XYZApp.class.getName()).log(Level.SEVERE, null, e); md = null; message = e.toString(); } try { - if (is != null) + if (is != null) { is.close(); - } catch(Exception e) { + } + } catch (Exception ignored) { } repaint(); } + + @Override public void start() { - if (md == null && message == null) + if (md == null && message == null) { new Thread(this).start(); + } } + + @Override public void stop() { } - /* event handling */ - public void mouseClicked(MouseEvent e) { - } - public void mousePressed(MouseEvent e) { - prevx = e.getX(); - prevy = e.getY(); - e.consume(); - } - public void mouseReleased(MouseEvent e) { - } - public void mouseEntered(MouseEvent e) { - } - public void mouseExited(MouseEvent e) { - } - 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(); + /* event handling */ + + @Override + public void mouseClicked(MouseEvent e) { } - prevx = x; - prevy = y; - e.consume(); - } - public void mouseMoved(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) + 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.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())) + if (!backSize.equals(getSize())) { newBackBuffer(); + } backGC.setColor(getBackground()); - backGC.fillRect(0,0,getSize().width,getSize().height); + backGC.fillRect(0, 0, getSize().width, getSize().height); md.paint(backGC); g.drawImage(backBuffer, 0, 0, this); - } - else + } 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(); } - private synchronized void waitPainted() - { - while (!painted) - { - try - { - wait(); - } - catch (InterruptedException e) {} - } - painted = false; + @Override + public String getAppletInfo() { + return "Title: XYZApp \nAuthor: James Gosling \nAn applet to put" + + " a Chemical model into a page."; } - public String getAppletInfo() { - return "Title: XYZApp \nAuthor: James Gosling \nAn applet to put a Chemical model into a page."; - } - - 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; - } + @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 final static int R = 40; @@ -459,7 +501,6 @@ class Atom { private final static int bgGrey = 192; private final static int nBalls = 16; private static int maxr; - private int Rl; private int Gl; private int Bl; @@ -475,24 +516,29 @@ class Atom { int x = X + hx; int y = Y - R + hy; int r = (int) (Math.sqrt(x * x + y * y) + 0.5); - if (r > mr) + 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 final int blend(int fg, int bg, float fgfactor) { + + 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]; @@ -502,7 +548,7 @@ class Atom { byte blue[] = new byte[256]; blue[0] = (byte) bgGrey; for (int r = 0; r < nBalls; r++) { - float b = (float) (r+1) / nBalls; + 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); @@ -510,11 +556,12 @@ class Atom { blue[i] = (byte) blend(blend(Bl, 255, d), bgGrey, b); } IndexColorModel model = new IndexColorModel(8, maxr + 1, - red, green, blue, 0); + red, green, blue, 0); balls[r] = applet.createImage( - new MemoryImageSource(R*2, R*2, model, data, 0, R*2)); + 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) { diff --git a/src/share/demo/applets/MoleculeViewer/example1.html b/src/share/demo/applets/MoleculeViewer/example1.html index f8b708136c396e60f28f007d81f2c9287f252bbf..de2e84b09431d4d8086372bec08e3fc79af14a82 100644 --- a/src/share/demo/applets/MoleculeViewer/example1.html +++ b/src/share/demo/applets/MoleculeViewer/example1.html @@ -6,7 +6,7 @@

MoleculeViewer (example 1)

- + alt="Your browser understands the <APPLET> tag but isn't running the applet, for some reason." Your browser is completely ignoring the <APPLET> tag! diff --git a/src/share/demo/applets/MoleculeViewer/example2.html b/src/share/demo/applets/MoleculeViewer/example2.html index 5570180908815af48391cb3130b095f7318cbb27..bb8f93a0b3184076953fd56b9ff3772300d86b94 100644 --- a/src/share/demo/applets/MoleculeViewer/example2.html +++ b/src/share/demo/applets/MoleculeViewer/example2.html @@ -6,7 +6,7 @@

MoleculeViewer (example 2)

- + alt="Your browser understands the <APPLET> tag but isn't running the applet, for some reason." Your browser is completely ignoring the <APPLET> tag! diff --git a/src/share/demo/applets/MoleculeViewer/example3.html b/src/share/demo/applets/MoleculeViewer/example3.html index 2542706f1bf2adf81d8de9e0f7c8b33e9258ced7..952bc8d5cbd977775c04560b55ff570a36eec28a 100644 --- a/src/share/demo/applets/MoleculeViewer/example3.html +++ b/src/share/demo/applets/MoleculeViewer/example3.html @@ -6,25 +6,25 @@

MoleculeViewer (example 3)

- + alt="Your browser understands the <APPLET> tag but isn't running the applet, for some reason." Your browser is completely ignoring the <APPLET> tag!

- + alt="Your browser understands the <APPLET> tag but isn't running the applet, for some reason." Your browser is completely ignoring the <APPLET> tag!

- + alt="Your browser understands the <APPLET> tag but isn't running the applet, for some reason." Your browser is completely ignoring the <APPLET> tag!

- + alt="Your browser understands the <APPLET> tag but isn't running the applet, for some reason." Your browser is completely ignoring the <APPLET> tag!