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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel Dots.java,NONE,1.1 DotsRenderer.java,NONE,1.1 AtomRenderer.java,1.6,1.7 AtomShape.java,1.8,1.9
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From: Michael T H. <mic...@us...> - 2003-08-26 14:32:33
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1:/tmp/cvs-serv28935/src/org/openscience/jmol/viewer/datamodel
Modified Files:
AtomRenderer.java AtomShape.java
Added Files:
Dots.java DotsRenderer.java
Log Message:
colors are correct for dots + checkin new classes
--- NEW FILE: Dots.java ---
/* $RCSfile: Dots.java,v $
* $Author: michaelthoward $
* $Date: 2003/08/26 14:32:29 $
* $Revision: 1.1 $
*
* Copyright (C) 2003 The Jmol Development Team
*
* Contact: jmo...@li...
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA.
*/
package org.openscience.jmol.viewer.datamodel;
public class Dots {
AtomShape atom;
Dots (AtomShape atom) {
this.atom = atom;
}
}
--- NEW FILE: DotsRenderer.java ---
/* $RCSfile: DotsRenderer.java,v $
* $Author: michaelthoward $
* $Date: 2003/08/26 14:32:29 $
* $Revision: 1.1 $
*
* Copyright (C) 2003 The Jmol Development Team
*
* Contact: jmo...@li...
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA.
*/
package org.openscience.jmol.viewer.datamodel;
import org.openscience.jmol.viewer.JmolViewer;
import org.openscience.jmol.viewer.g3d.Graphics3D;
import org.openscience.jmol.viewer.g3d.Colix;
import java.awt.Rectangle;
import java.util.Hashtable;
import javax.vecmath.Vector3d;
import javax.vecmath.Point3i;
public class DotsRenderer {
JmolViewer viewer;
Graphics3D g3d;
boolean perspectiveDepth;
short colixDots;
public DotsRenderer(JmolViewer viewer) {
this.viewer = viewer;
this.icosohedron = new Icosohedron();
icosohedron.quadruple();
icosohedron.quadruple();
icosohedron.quadruple();
}
public void setGraphicsContext(Graphics3D g3d, Rectangle rectClip) {
this.g3d = g3d;
perspectiveDepth = viewer.getPerspectiveDepth();
colixDots = viewer.getColixDots();
}
Icosohedron icosohedron;
void transform() {
icosohedron.transform();
}
public void render(AtomShape atomShape) {
if (atomShape.dots == null)
return;
render(colixDots == 0 ? atomShape.colixAtom : colixDots,
atomShape.getVanderwaalsRadius(),
atomShape.x, atomShape.y, atomShape.z);
}
void render(short colix, double vdwRadius, int x, int y, int z) {
icosohedron.calcScreenPoints(vdwRadius, x, y, z);
short[] faceIndices = icosohedron.faceIndices;
g3d.plotPoints(colix,
icosohedron.vertices.length,
icosohedron.screenCoordinates);
}
final static double halfRoot5 = 0.5 * Math.sqrt(5);
final static double oneFifth = 2 * Math.PI / 5;
final static double oneTenth = oneFifth / 2;
final static short[] faceIndicesInitial = {
0, 1, 2,
0, 2, 3,
0, 3, 4,
0, 4, 5,
0, 5, 1,
1, 6, 2,
2, 7, 3,
3, 8, 4,
4, 9, 5,
5, 10, 1,
6, 1, 10,
7, 2, 6,
8, 3, 7,
9, 4, 8,
10, 5, 9,
11, 6, 10,
11, 7, 6,
11, 8, 7,
11, 9, 8,
11, 10, 9,
};
class Icosohedron {
Vector3d[] vertices;
Vector3d[] verticesTransformed;
int[] screenCoordinates;
short[] faceIndices;
Icosohedron() {
vertices = new Vector3d[12];
vertices[0] = new Vector3d(0, 0, halfRoot5);
for (int i = 0; i < 5; ++i) {
vertices[i+1] = new Vector3d(Math.cos(i * oneFifth),
Math.sin(i * oneFifth),
0.5);
vertices[i+6] = new Vector3d(Math.cos(i * oneFifth + oneTenth),
Math.sin(i * oneFifth + oneTenth),
-0.5);
}
vertices[11] = new Vector3d(0, 0, -halfRoot5);
for (int i = 12; --i >= 0; )
vertices[i].normalize();
faceIndices = faceIndicesInitial;
verticesTransformed = new Vector3d[12];
for (int i = 12; --i >= 0; )
verticesTransformed[i] = new Vector3d();
screenCoordinates = new int[3 * 12];
}
void transform() {
for (int i = vertices.length; --i >= 0; )
viewer.transformVector(vertices[i], verticesTransformed[i]);
}
void calcScreenPoints(double radius, int x, int y, int z) {
double scaledRadius = viewer.scaleToPerspective(z, radius);
for (int i = vertices.length, icoordinates = screenCoordinates.length;
--i >= 0; ) {
Vector3d vertex = verticesTransformed[i];
screenCoordinates[--icoordinates] = z
+ (int)((scaledRadius*vertex.z) + (vertex.z < 0 ? -0.5 : 0.5));
screenCoordinates[--icoordinates] = y
+ (int)((scaledRadius*vertex.y) + (vertex.y < 0 ? -0.5 : 0.5));
screenCoordinates[--icoordinates] = x
+ (int)((scaledRadius*vertex.x) + (vertex.x < 0 ? -0.5 : 0.5));
}
}
short iVertexNew;
Hashtable htVertex;
void quadruple() {
htVertex = new Hashtable();
int nVerticesOld = vertices.length;
short[] faceIndicesOld = faceIndices;
int nFaceIndicesOld = faceIndicesOld.length;
int nEdgesOld = nVerticesOld + nFaceIndicesOld/3 - 2;
int nVerticesNew = nVerticesOld + nEdgesOld;
Vector3d[] verticesNew = new Vector3d[nVerticesNew];
System.arraycopy(vertices, 0, verticesNew, 0, nVerticesOld);
vertices = verticesNew;
verticesTransformed = new Vector3d[nVerticesNew];
for (int i = nVerticesNew; --i >= 0; )
verticesTransformed[i] = new Vector3d();
screenCoordinates = new int[3 * nVerticesNew];
short[] faceIndicesNew = new short[4 * nFaceIndicesOld];
faceIndices = faceIndicesNew;
iVertexNew = (short)nVerticesOld;
int iFaceNew = 0;
for (int i = 0; i < nFaceIndicesOld; ) {
short iA = faceIndicesOld[i++];
short iB = faceIndicesOld[i++];
short iC = faceIndicesOld[i++];
short iAB = getVertex(iA, iB);
short iBC = getVertex(iB, iC);
short iCA = getVertex(iC, iA);
faceIndicesNew[iFaceNew++] = iA;
faceIndicesNew[iFaceNew++] = iAB;
faceIndicesNew[iFaceNew++] = iCA;
faceIndicesNew[iFaceNew++] = iB;
faceIndicesNew[iFaceNew++] = iBC;
faceIndicesNew[iFaceNew++] = iAB;
faceIndicesNew[iFaceNew++] = iC;
faceIndicesNew[iFaceNew++] = iCA;
faceIndicesNew[iFaceNew++] = iBC;
faceIndicesNew[iFaceNew++] = iCA;
faceIndicesNew[iFaceNew++] = iAB;
faceIndicesNew[iFaceNew++] = iBC;
}
if (iFaceNew != faceIndicesNew.length) {
System.out.println("que?");
throw new NullPointerException();
}
if (iVertexNew != nVerticesNew) {
System.out.println("huh? " + " iVertexNew=" + iVertexNew +
"nVerticesNew=" + nVerticesNew);
throw new NullPointerException();
}
htVertex = null;
}
private short getVertex(short i1, short i2) {
if (i1 > i2) {
short t = i1;
i1 = i2;
i2 = t;
}
Integer hashKey = new Integer((i1 << 16) + i2);
Short iv = (Short)htVertex.get(hashKey);
if (iv != null)
return iv.shortValue();
Vector3d vertexNew = new Vector3d(vertices[i1]);
vertexNew.add(vertices[i2]);
vertexNew.scale(0.5);
vertexNew.normalize();
htVertex.put(hashKey, new Short(iVertexNew));
vertices[iVertexNew] = vertexNew;
return iVertexNew++;
}
}
}
Index: AtomRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/AtomRenderer.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- AtomRenderer.java 26 Aug 2003 13:52:26 -0000 1.6
+++ AtomRenderer.java 26 Aug 2003 14:32:29 -0000 1.7
@@ -79,8 +79,6 @@
y - radius >= maxY)
return;
colix = atomShape.colixAtom;
- if (atomShape.marDots > 0)
- renderDots(atomShape.colixDots, atomShape.diameterDots);
renderAtom();
// if (atomShape.strLabel != null)
// viewer.labelRenderer.render(atomShape);
Index: AtomShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/AtomShape.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- AtomShape.java 22 Aug 2003 11:52:25 -0000 1.8
+++ AtomShape.java 26 Aug 2003 14:32:29 -0000 1.9
@@ -47,9 +47,7 @@
short marAtom;
short colixAtom;
short diameter;
- short marDots = 0;
- short colixDots;
- short diameterDots = 0;
+ Dots dots;
BondShape[] bonds;
String strLabel;
@@ -67,8 +65,6 @@
if (pdbRecord != null)
pprop = new ProteinProp(pdbRecord);
}
- this.colixDots = 0;
- this.marDots = 0;
setStyleMarAtom(viewer.getStyleAtom(), viewer.getMarAtom());
this.point3d = viewer.getPoint3d(clientAtom);
this.strLabel = viewer.getLabelAtom(this, atomIndex);
@@ -220,13 +216,11 @@
this.marAtom = marAtom;
}
- public void setColixMarDots(short colixDots, short marDots) {
- if (this.styleAtom == JmolViewer.DELETED) return;
- this.colixDots = colixDots;
- if (marDots < 0)
- marDots = (short)((-10 * marDots) *
- frame.viewer.getVanderwaalsRadius(atomicNumber, clientAtom));
- this.marDots = marDots;
+ public void setDotsOn(boolean dotsOn) {
+ if (! dotsOn)
+ dots = null;
+ else if (dots == null)
+ dots = new Dots(this);
}
public int getRasMolRadius() {
@@ -264,8 +258,6 @@
y = screen.y;
z = screen.z;
diameter = viewer.scaleToScreen(z, marAtom * 2);
- if (marDots > 0)
- diameterDots = viewer.scaleToScreen(z, marDots * 2);
}
public int getAtomicNumber() {
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