File	Doc	Category	Size	Date	Package
XYZApp.java	API Doc	Sun JDK 1.5.0 Example	14468	Sat Jan 08 15:09:03 GMT 2005	None

XYZChemModel

• java.lang.Object

Fields Summary
float[]	vert
Atom[]	atoms
int[]	tvert
int[]	ZsortMap
int	nvert
int	maxvert
static Hashtable	atomTable
static Atom	defaultAtom
boolean	transformed
Matrix3D	mat
float	xmin
float	xmax
float	ymin
float	ymax
float	zmin
float	zmax

Constructors Summary
XYZChemModel() mat = new Matrix3D(); mat.xrot(20); mat.yrot(30);
XYZChemModel(InputStream is) Create a Cehmical model by parsing an input stream this(); StreamTokenizer st = new StreamTokenizer(new BufferedReader(new InputStreamReader(is))); 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());

Methods Summary
int	addVert(java.lang.String name, float x, float y, float z) Add a vertex to this model 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 = (Atom) 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++;
void	findBB() Find the bounding box of this model 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;
void	paint(java.awt.Graphics g) 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 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 lg = 0; int lim = nvert; Atom ls[] = atoms; 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)); }
void	transform() Transform all the points in this model if (transformed || nvert <= 0) return; if (tvert == null || tvert.length < nvert * 3) tvert = new int[nvert * 3]; mat.transform(vert, tvert, nvert); transformed = true;