Menu
▾
▴
[Jmol-commits] CVS: Jmol/src/org/openscience/jmol Atom.java,1.62,1.63 ChemFrame.java,1.108,1.109 CrystalFrame.java,1.15,1.16 DisplayControl.java,1.111,1.112 ModelManager.java,1.20,1.21 RepaintManager.java,1.16,1.17
|
From: Michael T H. <mic...@us...> - 2003-08-01 01:13:26
|
Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol
In directory sc8-pr-cvs1:/tmp/cvs-serv29740/src/org/openscience/jmol
Modified Files:
Atom.java ChemFrame.java CrystalFrame.java DisplayControl.java
ModelManager.java RepaintManager.java
Log Message:
initial work on a JmolFrame ... to split out the rendering engine
Index: Atom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/Atom.java,v
retrieving revision 1.62
retrieving revision 1.63
diff -u -r1.62 -r1.63
--- Atom.java 23 Jul 2003 11:58:55 -0000 1.62
+++ Atom.java 1 Aug 2003 01:13:15 -0000 1.63
@@ -27,6 +27,7 @@
import org.openscience.jmol.Bspt;
import org.openscience.jmol.DisplayControl;
import org.openscience.jmol.render.AtomShape;
+import org.openscience.jmol.render.JmolAtom;
import java.util.Vector;
import java.util.Enumeration;
import javax.vecmath.Point3d;
@@ -36,7 +37,8 @@
* Stores and manipulations information and properties of
* atoms.
*/
-public class Atom extends org.openscience.cdk.Atom implements Bspt.Tuple {
+public class Atom extends org.openscience.cdk.Atom
+ implements Bspt.Tuple, JmolAtom {
/**
* Creates an atom with the given type.
@@ -202,6 +204,7 @@
/**
* Sets the atom's vector.
*/
+
public void setVector(Point3d vector) {
if (vector == null) {
@@ -274,6 +277,10 @@
bondedAtoms = null;
bondOrders = null;
getAtomShape().clearBonds();
+ }
+
+ public int getBondOrder(int i) {
+ return (bondOrders==null || bondOrders.length <= i) ? 1 : bondOrders[i] + 1;
}
public int getBondOrder(Atom atom2) {
Index: ChemFrame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/ChemFrame.java,v
retrieving revision 1.108
retrieving revision 1.109
diff -u -r1.108 -r1.109
--- ChemFrame.java 23 Jul 2003 11:58:55 -0000 1.108
+++ ChemFrame.java 1 Aug 2003 01:13:15 -0000 1.109
@@ -27,6 +27,8 @@
import org.openscience.jmol.Bspt;
import org.openscience.jmol.Atom;
import org.openscience.jmol.render.AtomShape;
+import org.openscience.jmol.render.VectorShape;
+import org.openscience.jmol.render.JmolFrame;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.geometry.BondTools;
import java.beans.PropertyChangeSupport;
@@ -50,6 +52,7 @@
// This stuff can vary for each frame in the dynamics:
DisplayControl control;
+ JmolFrame jmframe;
private String info; // The title or info string for this frame.
private Vector properties = new Vector();
@@ -175,8 +178,7 @@
jmolAtom.setAtomNumber(this.getAtomCount());
super.addAtom(jmolAtom);
}
-
-
+
public int addAtom(Atom type, double x, double y, double z) {
return addAtom(type, x, y, z, null);
}
@@ -233,31 +235,62 @@
}
public double getGeometricRadius() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getGeometricRadius();
+ }
findBounds();
return radiusBoundingBox;
}
public Point3d getBoundingBoxCenter() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getBoundingBoxCenter();
+ }
findBounds();
return centerBoundingBox;
}
public Point3d getBoundingBoxCorner() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getBoundingBoxCorner();
+ }
findBounds();
return cornerBoundingBox;
}
public Point3d getRotationCenter() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getRotationCenter();
+ }
findBounds();
return centerRotation;
}
public double getRotationRadius() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getRotationRadius();
+ }
findBounds();
return radiusRotation;
}
public void setRotationCenter(Point3d newCenterOfRotation) {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ jmframe.setRotationCenter(newCenterOfRotation);
+ return;
+ }
if (newCenterOfRotation != null) {
centerRotation = newCenterOfRotation;
radiusRotation = calcRadius(centerRotation);
@@ -268,16 +301,31 @@
}
public double getMinAtomVectorMagnitude() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getMinAtomVectorMagnitude();
+ }
findBounds();
return minAtomVectorMagnitude;
}
public double getMaxAtomVectorMagnitude() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getMaxAtomVectorMagnitude();
+ }
findBounds();
return maxAtomVectorMagnitude;
}
public double getAtomVectorRange() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe.getAtomVectorRange();
+ }
findBounds();
return maxAtomVectorMagnitude - minAtomVectorMagnitude;
}
@@ -374,6 +422,12 @@
* Clears the bounds cache for this model.
*/
private void clearBounds() {
+ if (control.getUseJmolFrame()) {
+ if (jmframe == null)
+ buildJmolFrame();
+ jmframe.clearBounds();
+ return;
+ }
centerBoundingBox = centerRotation = null;
radiusBoundingBox = radiusRotation =
minAtomVectorMagnitude = maxAtomVectorMagnitude = atomVectorRange = 0f;
@@ -409,9 +463,9 @@
}
void calcBoundingBox() {
- /**
- * Note that this method is overridden by CrystalFrame
- */
+ //
+ // Note that this method is overridden by CrystalFrame
+ //
// bounding box is defined as the center of the cartesian coordinates
// as stored in the file
// Note that this is not really the geometric center of the molecule
@@ -441,9 +495,9 @@
}
double calcRadius(Point3d center) {
- /**
- * Note that this method is overridden by CrystalFrame
- */
+ //
+ // Note that this method is overridden by CrystalFrame
+ //
// Now that we have defined the center, find the radius to the outermost
// atom, including the radius of the atom itself. Note that this is
// currently the vdw radius as scaled by the vdw display radius as set
@@ -605,6 +659,14 @@
return vibrations.elements();
}
+ public void addAtomVector(int atomIndex, double[] vector) {
+ Atom atom = getJmolAtomAt(atomIndex);
+ Point3d vector3d = new Point3d(vector);
+ atom.setVector(vector3d);
+
+ jmframe.addVectorShape(new VectorShape(atom.getPoint3D(), vector3d));
+ }
+
private void setAtomArraySize(int newArraySize) {
Atom[] nat = new Atom[newArraySize];
int countToMove = atoms.length;
@@ -662,6 +724,27 @@
}
}
+ private void buildJmolFrame() {
+ jmframe = new JmolFrame(control);
+ for (int i = getAtomCount(); --i >= 0; ) {
+ Atom jmolAtom = getJmolAtomAt(i);
+ AtomShape atomShape =
+ new AtomShape(jmolAtom, jmolAtom.isHydrogen(), control);
+ jmframe.addAtomShape(atomShape);
+ Atom[] bondedAtoms = jmolAtom.getBondedAtoms();
+ if (bondedAtoms != null)
+ for (int j = bondedAtoms.length; --j >= 0; ) {
+ jmframe.bondAtomShapes(atomShape, bondedAtoms[j], jmolAtom.getBondOrder(j));
+ }
+ }
+ }
+
+ public JmolFrame getJmolFrame() {
+ if (jmframe == null)
+ buildJmolFrame();
+ return jmframe;
+ }
+
public JmolAtomIterator getAtomIterator() {
return new ChemFrameIterator();
}
@@ -760,5 +843,6 @@
return ibond;
}
}
+
}
Index: CrystalFrame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/CrystalFrame.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- CrystalFrame.java 25 Jul 2003 10:43:04 -0000 1.15
+++ CrystalFrame.java 1 Aug 2003 01:13:15 -0000 1.16
@@ -65,6 +65,7 @@
return this.boxEdges;
}
+ /*
void calcBoundingBox() {
Vector boxEdges;
@@ -97,7 +98,9 @@
cornerBoundingBox = new Point3d(maxX, maxY, maxZ);
cornerBoundingBox.sub(centerBoundingBox);
}
+ */
+ /*
// arrowhead size isn't included because it is currently in screen
// coordinates .. oh well.
public double calcRadius(Point3d center) {
@@ -112,4 +115,5 @@
}
return radius;
}
+ */
}
Index: DisplayControl.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/DisplayControl.java,v
retrieving revision 1.111
retrieving revision 1.112
diff -u -r1.111 -r1.112
--- DisplayControl.java 26 Jul 2003 12:40:05 -0000 1.111
+++ DisplayControl.java 1 Aug 2003 01:13:15 -0000 1.112
@@ -28,10 +28,13 @@
import org.openscience.jmol.render.BondRenderer;
import org.openscience.jmol.render.LabelRenderer;
import org.openscience.jmol.render.ChemFrameRenderer;
+import org.openscience.jmol.render.JmolFrame;
import org.openscience.jmol.render.MeasureRenderer;
import org.openscience.jmol.render.Axes;
import org.openscience.jmol.render.BoundingBox;
+import org.openscience.jmol.render.AtomShape;
import org.openscience.jmol.render.BondShape;
+import org.openscience.jmol.render.JmolAtom;
import org.openscience.jmol.script.Eval;
import org.openscience.jmol.g25d.Graphics25D;
import org.openscience.jmol.g25d.Colix;
@@ -544,6 +547,10 @@
return colorManager.colorVector;
}
+ public short getColixVector() {
+ return colorManager.colixVector;
+ }
+
public void setColorBackground(Color bg) {
colorManager.setColorBackground(bg);
refresh();
@@ -562,6 +569,10 @@
return colorManager.getColorFromString(colorName);
}
+ public short getColixAtom(JmolAtom atom) {
+ return colorManager.getColixAtom((Atom)atom);
+ }
+
public short getColixAtom(Atom atom) {
return colorManager.getColixAtom(atom);
}
@@ -653,24 +664,26 @@
return selectionManager.isSelected(atomIndex);
}
- public boolean hasSelectionHalo(Atom atom) {
+ public boolean hasSelectionHalo(int atomIndex) {
return
selectionHaloEnabled &&
!repaintManager.fastRendering &&
- selectionManager.isSelected(atom.getAtomNumber());
+ selectionManager.isSelected(atomIndex);
}
- public boolean hasSelectionHalo(Atom atom, int iatom) {
+ public boolean hasBondSelectionHalo(AtomShape atomShape, int bondIndex) {
if (!selectionHaloEnabled || repaintManager.fastRendering)
return false;
- boolean isAtomSelected = isSelected(atom.getAtomNumber());
+ int atomIndex =
+ useJmolFrame ? atomShape.getAtomIndex() : atomShape.atom.getAtomNumber();
+ boolean isAtomSelected = isSelected(atomIndex);
if (bondSelectionModeOr && isAtomSelected)
return true;
if (!bondSelectionModeOr && !isAtomSelected)
return false;
- Atom atomOther = atom.getBondedAtom(iatom);
+ int atomIndexOther = atomShape.getBondedAtomIndex(bondIndex);
boolean isOtherSelected =
- selectionManager.isSelected(atomOther.getAtomNumber());
+ selectionManager.isSelected(atomIndexOther);
return isOtherSelected;
}
@@ -825,6 +838,10 @@
return modelManager.haveFile();
}
+ public JmolFrame getJmolFrame() {
+ return modelManager.chemframe.getJmolFrame();
+ }
+
public ChemFrame getFrame() {
return modelManager.chemframe;
}
@@ -1303,6 +1320,8 @@
return getOversampleAlwaysEnabled();
if (key.equals("oversampleStopped"))
return getOversampleStoppedEnabled();
+ if (key.equals("useJmolFrame"))
+ return getUseJmolFrame();
System.out.println("control.getBooleanProperty(" +
key + ") - unrecognized");
return false;
@@ -1333,6 +1352,8 @@
{ setOversampleAlwaysEnabled(value); return; }
if (key.equals("oversampleStopped"))
{ setOversampleStoppedEnabled(value); return; }
+ if (key.equals("useJmolFrame"))
+ { setUseJmolFrame(value); return; }
System.out.println("control.setBooleanProperty(" +
key + "," + value + ") - unrecognized");
}
@@ -1372,6 +1393,19 @@
}
/****************************************************************
+ * JmolFrame
+ ****************************************************************/
+
+ public boolean useJmolFrame = false;
+ public void setUseJmolFrame(boolean value) {
+ setStructuralChange();
+ useJmolFrame = value;
+ }
+ public boolean getUseJmolFrame() {
+ return useJmolFrame;
+ }
+
+ /****************************************************************
* delegated to StyleManager
****************************************************************/
@@ -1588,6 +1622,10 @@
public byte getStyleLabel() {
return labelManager.styleLabel;
+ }
+
+ public String getLabelAtom(JmolAtom atom) {
+ return labelManager.getLabelAtom(labelManager.styleLabel, (Atom)atom);
}
public String getLabelAtom(Atom atom) {
Index: ModelManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/ModelManager.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- ModelManager.java 2 Jun 2003 13:35:05 -0000 1.20
+++ ModelManager.java 1 Aug 2003 01:13:15 -0000 1.21
@@ -24,7 +24,7 @@
*/
package org.openscience.jmol;
-import org.openscience.jmol.Atom;
+import org.openscience.jmol.render.JmolFrame;
import java.util.BitSet;
import java.util.Vector;
@@ -202,10 +202,14 @@
}
public int findNearestAtomIndex(int x, int y) {
+ if (control.getUseJmolFrame())
+ return control.getJmolFrame().findNearestAtomIndex(x, y);
return chemframe.findNearestAtomIndex(x, y);
}
public BitSet findAtomsInRectangle(Rectangle rectRubber) {
+ if (control.getUseJmolFrame())
+ return control.getJmolFrame().findAtomsInRectangle(rectRubber);
return chemframe.findAtomsInRectangle(rectRubber);
/*
return chemframe.findAtomsInRegion(rectRubber.x,
Index: RepaintManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/RepaintManager.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- RepaintManager.java 26 Jul 2003 12:40:05 -0000 1.16
+++ RepaintManager.java 1 Aug 2003 01:13:15 -0000 1.17
@@ -159,12 +159,18 @@
rectClip.width, rectClip.height);
if (control.getFrame() != null) {
control.setGraphicsContext(g25d, rectClip);
- control.frameRenderer.paint(g25d, control);
- // FIXME -- measurements rendered incorrectly
- // this is in the wrong spot because the display of measurements
- // needs to take z-order into account
- if (control.getShowMeasurements())
- control.measureRenderer.paint(g25d, rectClip, control);
+
+ if (control.getUseJmolFrame()) {
+ control.getJmolFrame().render(g25d, control);
+ } else {
+ control.frameRenderer.paint(g25d, control);
+ // FIXME -- measurements rendered incorrectly
+ // this is in the wrong spot because the display of measurements
+ // needs to take z-order into account
+ if (control.getShowMeasurements())
+ control.measureRenderer.render(g25d, control);
+ }
+
Rectangle band = control.getRubberBandSelection();
if (band != null)
g25d.drawRect(control.getColixRubberband(),
|