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[Jmol-commits] SF.net SVN: jmol: [5550] trunk/Jmol/src/org/jmol/viewer
|
From: <ha...@us...> - 2006-09-14 21:06:19
|
Revision: 5550
http://svn.sourceforge.net/jmol/?rev=5550&view=rev
Author: hansonr
Date: 2006-09-14 14:06:04 -0700 (Thu, 14 Sep 2006)
Log Message:
-----------
halos added -- Halos.java, HalosRenderer.java
reorganization of Viewer to bring all the global settings together.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Atom.java
trunk/Jmol/src/org/jmol/viewer/Balls.java
trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Frame.java
trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
trunk/Jmol/src/org/jmol/viewer/ModelManager.java
trunk/Jmol/src/org/jmol/viewer/Token.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/viewer/Halos.java
trunk/Jmol/src/org/jmol/viewer/HalosRenderer.java
Modified: trunk/Jmol/src/org/jmol/viewer/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/Atom.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -294,6 +294,8 @@
}
short convertEncodedMad(int size) {
+ if (size == 0)
+ return 0;
if (size == -1000) { // temperature
int diameter = getBfactor100() * 10 * 2;
if (diameter > 4000)
Modified: trunk/Jmol/src/org/jmol/viewer/Balls.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Balls.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/Balls.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -66,14 +66,33 @@
void setModelClickability() {
Atom[] atoms = frame.atoms;
- int haloVisibilityFlag = Viewer.getShapeVisibilityFlag(JmolConstants.SHAPE_HALO);
for (int i = frame.atomCount; --i >= 0; ) {
Atom atom = atoms[i];
atom.clickabilityFlags = 0;
if((atom.shapeVisibilityFlags & myVisibilityFlag) != 0)
atom.clickabilityFlags |= myVisibilityFlag;
- if((atom.shapeVisibilityFlags & haloVisibilityFlag) != 0)
- atom.clickabilityFlags |= haloVisibilityFlag;
}
}
+
+ void setVisibilityFlags(BitSet bs) {
+ Atom[] atoms = frame.atoms;
+ int displayModelIndex = viewer.getDisplayModelIndex();
+ boolean isOneFrame = (displayModelIndex >= 0);
+ boolean showHydrogens = viewer.getShowHydrogens();
+ for (int i = frame.atomCount; --i >= 0; ) {
+ Atom atom = atoms[i];
+ atom.shapeVisibilityFlags &= (
+ ~JmolConstants.ATOM_IN_MODEL
+ & ~myVisibilityFlag);
+ if (atom.madAtom == JmolConstants.MAR_DELETED
+ || ! showHydrogens && atom.elementNumber == 1)
+ continue;
+ if (! isOneFrame && bs.get(atom.modelIndex)
+ || atom.modelIndex == displayModelIndex) {
+ atom.shapeVisibilityFlags |= JmolConstants.ATOM_IN_MODEL;
+ if (atom.madAtom != 0)
+ atom.shapeVisibilityFlags |= myVisibilityFlag;
+ }
+ }
+ }
}
Modified: trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -28,13 +28,10 @@
class BallsRenderer extends ShapeRenderer {
int minX, maxX, minY, maxY, minZ, maxZ;
- short colixSelection;
int ballVisibilityFlag;
- int haloVisibilityFlag;
void initRenderer() {
ballVisibilityFlag = Viewer.getShapeVisibilityFlag(JmolConstants.SHAPE_BALLS);
- haloVisibilityFlag = Viewer.getShapeVisibilityFlag(JmolConstants.SHAPE_HALO);
}
boolean labelsGroup;
@@ -49,7 +46,6 @@
maxZ = g3d.getDepth();
}
labelsGroup = viewer.getLabelsGroupFlag() && !viewer.getLabelsFrontFlag();
- colixSelection = viewer.getColixSelection();
Atom[] atoms = frame.atoms;
if (labelsGroup)
for (int i = frame.groupCount; --i >= 0;)
@@ -77,8 +73,6 @@
}
if ((atom.shapeVisibilityFlags & ballVisibilityFlag) != 0)
renderBall(atom);
- if ((atom.shapeVisibilityFlags & haloVisibilityFlag) != 0)
- renderHalo(atom);
}
}
@@ -87,18 +81,4 @@
atom.screenX, atom.screenY, atom.screenZ);
}
- void renderHalo(Atom atom) {
- int diameter = atom.screenDiameter;
- if (diameter == 0)
- diameter = viewer.scaleToScreen(atom.screenZ, 500);
- int halowidth = (diameter / 4);
- if (halowidth < 4)
- halowidth = 4;
- if (halowidth > 10)
- halowidth = 10;
- int haloDiameter = diameter + 2 * halowidth;
- if (haloDiameter > 0)
- g3d.fillScreenedCircleCentered(colixSelection, haloDiameter,
- atom.screenX, atom.screenY, atom.screenZ);
- }
}
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -490,6 +490,9 @@
case Token.star:
star();
break;
+ case Token.halo:
+ halo();
+ break;
case Token.cpk:
spacefill();
break;
@@ -1858,7 +1861,8 @@
argb);
return;
}
- if (str.equalsIgnoreCase("selectionHalo")) {
+ if (str.equalsIgnoreCase("selectionHalo")
+ || str.equalsIgnoreCase("selectionHalos")) {
viewer.setSelectionArgb(argb);
return;
}
@@ -2656,7 +2660,7 @@
}
void star() throws ScriptException {
- short mad = 0;
+ short mad = 0; // means back to selection business
int tok = Token.on;
if (statementLength > 1) {
tok = statement[1].tok;
@@ -2704,6 +2708,57 @@
viewer.setShapeSize(JmolConstants.SHAPE_STARS, mad);
}
+ void halo() throws ScriptException {
+ short mad = 0;
+ int tok = Token.on;
+ if (statementLength > 1) {
+ tok = statement[1].tok;
+ if (!((statementLength == 2) || (statementLength == 3
+ && tok == Token.integer && statement[2].tok == Token.percent))) {
+ badArgumentCount();
+ }
+ }
+ switch (tok) {
+ case Token.on:
+ mad = -20; // on goes to 25%
+ break;
+ case Token.vanderwaals:
+ mad = -100; // cpk with no args goes to 100%
+ break;
+ case Token.off:
+ break;
+ case Token.integer:
+ int radiusRasMol = statement[1].intValue;
+ if (statementLength == 2) {
+ if (radiusRasMol >= 750 || radiusRasMol < -100)
+ numberOutOfRange(-100, 749);
+ mad = (short) radiusRasMol;
+ if (radiusRasMol > 0)
+ mad *= 4 * 2;
+ } else {
+ if (radiusRasMol < 0 || radiusRasMol > 100)
+ numberOutOfRange(0, 100);
+ mad = (short) -radiusRasMol; // use a negative number to specify %vdw
+ }
+ break;
+ case Token.decimal:
+ float angstroms = floatParameter(1);
+ if (angstroms < 0 || angstroms > 3)
+ numberOutOfRange(0f, 3f);
+ mad = (short) (angstroms * 1000 * 2);
+ break;
+ case Token.temperature:
+ mad = -1000;
+ break;
+ case Token.ionic:
+ mad = -1001;
+ break;
+ default:
+ booleanOrNumberExpected();
+ }
+ viewer.setShapeSize(JmolConstants.SHAPE_HALOS, mad);
+ }
+
/// aka cpk
void spacefill() throws ScriptException {
short mad = 0;
Modified: trunk/Jmol/src/org/jmol/viewer/Frame.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/Frame.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -1010,7 +1010,7 @@
}
void increaseRotationRadius(float increaseInAngstroms) {
- if (viewer.isWindowCentered())
+ if (isWindowCentered())
rotationRadius += increaseInAngstroms;
}
@@ -1023,7 +1023,7 @@
boolean andRadius) {
if (newCenterOfRotation != null) {
rotationCenter = newCenterOfRotation;
- if (andRadius && viewer.isWindowCentered())
+ if (andRadius && isWindowCentered())
rotationRadius = calcRotationRadius(rotationCenter);
} else {
rotationCenter = rotationCenterDefault;
@@ -1032,6 +1032,16 @@
return rotationCenter;
}
+ boolean windowCenteredFlag = true;
+
+ boolean isWindowCentered() {
+ return windowCenteredFlag;
+ }
+
+ void setWindowCentered(boolean TF) {
+ windowCenteredFlag = TF;
+ }
+
Point3f setRotationCenterAndRadiusXYZ(String relativeTo, Point3f pt) {
Point3f pointT = new Point3f(pt);
if (relativeTo == "average")
@@ -2862,4 +2872,17 @@
}
return hAtoms;
}
+
+ boolean selectionHaloEnabled = false;
+
+ public void setSelectionHaloEnabled(boolean selectionHaloEnabled) {
+ if (this.selectionHaloEnabled != selectionHaloEnabled) {
+ this.selectionHaloEnabled = selectionHaloEnabled;
+ }
+ }
+
+ boolean getSelectionHaloEnabled() {
+ return selectionHaloEnabled;
+ }
+
}
Added: trunk/Jmol/src/org/jmol/viewer/Halos.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Halos.java (rev 0)
+++ trunk/Jmol/src/org/jmol/viewer/Halos.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -0,0 +1,89 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2006-08-22 03:13:40 -0500 (Tue, 22 Aug 2006) $
+ * $Revision: 5412 $
+
+ *
+ * Copyright (C) 2002-2005 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 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.jmol.viewer;
+
+import java.util.BitSet;
+
+import org.jmol.g3d.Graphics3D;
+
+class Halos extends Shape {
+
+ short[] mads;
+ short[] colixes;
+
+ void setSize(int size, BitSet bsSelected) {
+ Atom[] atoms = frame.atoms;
+ for (int i = frame.atomCount; --i >= 0;)
+ if (bsSelected.get(i)) {
+ if (mads == null)
+ mads = new short[frame.atomCount];
+ Atom atom = atoms[i];
+ mads[i] = atom.convertEncodedMad(size);
+ }
+ }
+
+ void setProperty(String propertyName, Object value, BitSet bs) {
+ int atomCount = frame.atomCount;
+ Atom[] atoms = frame.atoms;
+ if ("color" == propertyName) {
+ short colix = Graphics3D.getColix(value);
+ for (int i = atomCount; --i >= 0;)
+ if (bs.get(i)) {
+ if (colixes == null)
+ colixes = new short[atomCount];
+ colixes[i] = ((colix != Graphics3D.UNRECOGNIZED) ? colix : viewer
+ .getColixAtomPalette(atoms[i], (String) value));
+ }
+ return;
+ }
+ if ("translucency" == propertyName) {
+ return;
+ }
+ }
+
+ void setVisibilityFlags() {
+ BitSet bsSelected = (viewer.getSelectionHaloEnabled() ? viewer
+ .getSelectionSet() : null);
+ for (int i = frame.atomCount; --i >= 0;) {
+ Atom atom = frame.atoms[i];
+ if ((atom.shapeVisibilityFlags & JmolConstants.ATOM_IN_MODEL) == 0)
+ continue;
+ boolean isVisible = bsSelected != null && bsSelected.get(i)
+ || (mads != null && mads[i] != 0);
+ atom.setShapeVisibility(myVisibilityFlag, isVisible);
+ }
+ }
+
+ void setModelClickability() {
+ if (mads == null)
+ return;
+ for (int i = frame.atomCount; --i >= 0;) {
+ Atom atom = frame.atoms[i];
+ if ((atom.shapeVisibilityFlags & myVisibilityFlag) != 0)
+ atom.clickabilityFlags |= myVisibilityFlag;
+ }
+ }
+}
Added: trunk/Jmol/src/org/jmol/viewer/HalosRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/HalosRenderer.java (rev 0)
+++ trunk/Jmol/src/org/jmol/viewer/HalosRenderer.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -0,0 +1,80 @@
+/* $RCSfile$
+ * $Author: migueljmol $
+ * $Date: 2006-03-25 09:27:43 -0600 (Sat, 25 Mar 2006) $
+ * $Revision: 4696 $
+
+ *
+ * Copyright (C) 2003-2005 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.jmol.viewer;
+
+import org.jmol.g3d.Graphics3D;
+import java.util.BitSet;
+
+class HalosRenderer extends ShapeRenderer {
+
+ void render() {
+ Halos halos = (Halos) shape;
+ boolean selectDisplayTrue = viewer.getSelectionHaloEnabled();
+ if (halos.mads == null && !selectDisplayTrue)
+ return;
+ Atom[] atoms = frame.atoms;
+ BitSet bsSelected = (selectDisplayTrue ? viewer.getSelectionSet() : null);
+ for (int i = frame.atomCount; --i >= 0;) {
+ Atom atom = atoms[i];
+ if ((atom.shapeVisibilityFlags & JmolConstants.ATOM_IN_MODEL) == 0)
+ continue;
+ short mad = (halos.mads == null ? 0 : halos.mads[i]);
+ short colix = (halos.colixes == null ? 0 : halos.colixes[i]);
+ if (selectDisplayTrue && bsSelected.get(i)) {
+ if (mad == 0)
+ mad = -1; // unsized
+ if (colix == 0)
+ colix = viewer.getColixSelection();
+ }
+ if (mad == 0)
+ continue;
+ render1(atom, mad, colix);
+ }
+ }
+
+ void render1(Atom atom, short mad, short colix) {
+ int z = atom.screenZ;
+ int diameter = mad;
+ if (diameter < 0) { //unsized selection
+ diameter = atom.screenDiameter;
+ if (diameter == 0)
+ diameter = viewer.scaleToScreen(z, 500);
+ } else {
+ diameter = viewer.scaleToScreen(z, mad);
+ }
+ int halowidth = (diameter / 4);
+ if (halowidth < 4)
+ halowidth = 4;
+ if (halowidth > 10)
+ halowidth = 10;
+ int haloDiameter = diameter + 2 * halowidth;
+ if (haloDiameter <= 0)
+ return;
+ colix = Graphics3D.inheritColix(colix, atom.colixAtom);
+ g3d.fillScreenedCircleCentered(colix, haloDiameter, atom.screenX,
+ atom.screenY, atom.screenZ);
+ }
+}
Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -2200,26 +2200,26 @@
public final static int SHAPE_RIBBONS = 13;
public final static int SHAPE_ROCKETS = 14;
public final static int SHAPE_STARS = 15;
+ public final static int SHAPE_HALOS = 16;
- public final static int SHAPE_MIN_SELECTION_INDEPENDENT = 16;
- public final static int SHAPE_AXES = 16;
- public final static int SHAPE_BBCAGE = 17;
- public final static int SHAPE_UCCAGE = 18;
- public final static int SHAPE_FRANK = 19;
- public final static int SHAPE_ECHO = 20;
- public final static int SHAPE_HOVER = 21;
- public final static int SHAPE_POLYHEDRA = 22;
- public final static int SHAPE_MIN_NAMED_OBJECT = 23;
- public final static int SHAPE_DIPOLES = 23;
- public final static int SHAPE_MIN_MESH_COLLECTION = 24;
- public final static int SHAPE_PMESH = 24;
- public final static int SHAPE_MO = 25;
- public final static int SHAPE_ISOSURFACE = 26;
- public final static int SHAPE_LCAOCARTOON = 27;
- public final static int SHAPE_DRAW = 28;
+ public final static int SHAPE_MIN_SELECTION_INDEPENDENT = 17;
+ public final static int SHAPE_AXES = 17;
+ public final static int SHAPE_BBCAGE = 18;
+ public final static int SHAPE_UCCAGE = 19;
+ public final static int SHAPE_FRANK = 20;
+ public final static int SHAPE_ECHO = 21;
+ public final static int SHAPE_HOVER = 22;
+ public final static int SHAPE_POLYHEDRA = 23;
+ public final static int SHAPE_MIN_NAMED_OBJECT = 24;
+ public final static int SHAPE_DIPOLES = 24;
+ public final static int SHAPE_MIN_MESH_COLLECTION = 25;
+ public final static int SHAPE_PMESH = 25;
+ public final static int SHAPE_MO = 26;
+ public final static int SHAPE_ISOSURFACE = 27;
+ public final static int SHAPE_LCAOCARTOON = 28;
+ public final static int SHAPE_DRAW = 29;
public final static int SHAPE_MAX = SHAPE_DRAW + 1;
//handled in Balls.java: (It's ok that this is SHAPE_MAX)
- public final static int SHAPE_HALO = SHAPE_MAX;
//see Jmol 10.2 for programming information --- pruned from 11.0
//Bob Hanson 7/17/06
@@ -2233,7 +2233,7 @@
"Balls", "Sticks", "Hsticks", "Sssticks",
"Labels", "Vectors", "Measures", "Dots",
"Backbone", "Trace", "Cartoon", "Strands",
- "MeshRibbon", "Ribbons", "Rockets", "Stars",
+ "MeshRibbon", "Ribbons", "Rockets", "Stars", "Halos",
"Axes", "Bbcage", "Uccage",
"Frank", "Echo", "Hover",
"Polyhedra", "Dipoles",
@@ -2252,7 +2252,7 @@
Token.atom, Token.bonds, Token.hbond, Token.ssbond,
Token.label, Token.vector, Token.monitor, Token.dots,
Token.backbone, Token.trace, Token.cartoon, Token.strands,
- Token.meshRibbon, Token.ribbon, Token.rocket, Token.star,
+ Token.meshRibbon, Token.ribbon, Token.rocket, Token.star, Token.halo,
Token.axes, Token.boundbox, Token.unitcell,
Token.frank, Token.echo, Token.hover,
Token.polyhedra, Token.dipole,
Modified: trunk/Jmol/src/org/jmol/viewer/ModelManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/ModelManager.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -365,7 +365,9 @@
void setNewRotationCenter(Point3f center, boolean doScale) {
// once we have the center, we need to optionally move it to
// the proper XY position and possibly scale
- if (viewer.isWindowCentered()) {
+ if (frame == null)
+ return;
+ if (frame.isWindowCentered()) {
viewer.translateToXPercent(0);
viewer.translateToYPercent(0);///CenterTo(0, 0);
frame.setRotationCenterAndRadiusXYZ(center, true);
@@ -376,6 +378,18 @@
}
}
+ boolean isWindowCentered() {
+ if (frame == null)
+ return false;
+ return frame.isWindowCentered();
+ }
+
+ void setWindowCentered(boolean TF) {
+ if (frame == null)
+ return;
+ frame.setWindowCentered(TF);
+ }
+
Point3f setRotationCenterAndRadiusXYZ(Point3f center, boolean andRadius) {
if (frame == null)
return null;
@@ -1373,12 +1387,6 @@
void setModelVisibility() {
if (frame == null)
return;
- Atom[] atoms = frame.atoms;
- int displayModelIndex = viewer.getDisplayModelIndex();
- boolean isOneFrame = (displayModelIndex >= 0);
- boolean showHydrogens = viewer.getShowHydrogens();
- int ballVisibilityFlag = Viewer.getShapeVisibilityFlag(JmolConstants.SHAPE_BALLS);
- int haloVisibilityFlag = Viewer.getShapeVisibilityFlag(JmolConstants.SHAPE_HALO);
//named objects must be set individually
//in the future, we might include here a BITSET of models rather than just a modelIndex
@@ -1390,25 +1398,9 @@
Polyhedra p = (Polyhedra) frame.shapes[JmolConstants.SHAPE_POLYHEDRA];
if (p != null)
p.setVisibilityFlags(bs);
-
- for (int i = frame.atomCount; --i >= 0; ) {
- Atom atom = atoms[i];
- atom.shapeVisibilityFlags &= (
- ~JmolConstants.ATOM_IN_MODEL
- & ~ballVisibilityFlag
- & ~haloVisibilityFlag);
- if (atom.madAtom == JmolConstants.MAR_DELETED
- || ! showHydrogens && atom.elementNumber == 1)
- continue;
- if (! isOneFrame && bs.get(atom.modelIndex)
- || atom.modelIndex == displayModelIndex) {
- atom.shapeVisibilityFlags |= JmolConstants.ATOM_IN_MODEL;
- if (atom.madAtom != 0)
- atom.shapeVisibilityFlags |= ballVisibilityFlag;
- if(viewer.hasSelectionHalo(atom.atomIndex))
- atom.shapeVisibilityFlags |= haloVisibilityFlag;
- }
- }
+ if (frame.shapes[JmolConstants.SHAPE_HALOS] != null)
+ frame.shapes[JmolConstants.SHAPE_HALOS].setVisibilityFlags(bs);
+ frame.shapes[JmolConstants.SHAPE_BALLS].setVisibilityFlags(bs);
}
void setModelClickability() {
@@ -1460,13 +1452,6 @@
info.put(shapeType, shapeinfo);
}
}
- if (viewer.selectionHaloEnabled) {
- Hashtable shapeinfo = new Hashtable();
- shapeinfo.put("index", new Integer(JmolConstants.SHAPE_HALO));
- shapeinfo.put("myVisibilityFlag", new Integer(Viewer
- .getShapeVisibilityFlag(JmolConstants.SHAPE_HALO)));
- info.put("halo", shapeinfo);
- }
return info;
}
@@ -1627,4 +1612,16 @@
public int getSpaceGroupIndexFromName(String spaceGroup) {
return SpaceGroup.determineSpaceGroupIndex(spaceGroup);
}
+
+ public void setSelectionHaloEnabled(boolean selectionHaloEnabled) {
+ if (frame == null)
+ return;
+ frame.setSelectionHaloEnabled(selectionHaloEnabled);
+ }
+
+ boolean getSelectionHaloEnabled() {
+ if (frame == null)
+ return false;
+ return frame.getSelectionHaloEnabled();
+ }
}
Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -173,7 +173,7 @@
final static int vibration = command | 82;
final static int vector = command | 83 | negnums;
final static int meshRibbon = command | 84;
- //final static int prueba = command | 85; //free
+ final static int halo = command | 85;
final static int rocket = command | 86;
final static int geosurface = command | 87;
final static int moveto = command | 88 | negnums;
@@ -543,7 +543,8 @@
"vectors", null,
"meshribbon", new Token(meshRibbon,onDefault1, "meshribbon"),
"meshribbons", null,
- //"prueba", new Token(prueba, onDefault1, "prueba"),
+ "halo", new Token(halo, varArgCount, "halo"),
+ "halos", null,
"rocket", new Token(rocket, onDefault1, "rocket"),
"rockets", null,
"moveto", new Token(moveto, varArgCount, "moveto"),
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-14 20:19:35 UTC (rev 5549)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2006-09-14 21:06:04 UTC (rev 5550)
@@ -74,6 +74,7 @@
public class Viewer extends JmolViewer {
+ GlobalSettings global = new GlobalSettings();
Component awtComponent;
ColorManager colorManager;
PropertyManager propertyManager;
@@ -529,8 +530,6 @@
final Rectangle rectClip = new Rectangle();
- boolean enableFullSceneAntialiasing = false;
-
public void setScreenDimension(Dimension dim) {
// There is a bug in Netscape 4.7*+MacOS 9 when comparing dimension objects
// so don't try dim1.equals(dim2)
@@ -544,7 +543,7 @@
dimScreen.height = height;
transformManager.setScreenDimension(width, height);
transformManager.scaleFitToScreen();
- g3d.setWindowSize(width, height, enableFullSceneAntialiasing);
+ g3d.setWindowSize(width, height, global.enableFullSceneAntialiasing);
}
public int getScreenWidth() {
@@ -824,15 +823,11 @@
}
void reportSelection(String msg) {
- if (selectionHaloEnabled)
+ if (modelManager.getSelectionHaloEnabled())
setTainted(true);
scriptStatus(msg);
}
- boolean hasSelectionHalo(int atomIndex) {
- return selectionHaloEnabled && selectionManager.isSelected(atomIndex);
- }
-
public void selectAll() {
selectionManager.selectAll();
refresh(0, "Viewer:selectAll()");
@@ -1002,18 +997,16 @@
return fileManager.inlineData;
}
- char inlineNewlineChar = '|';
-
public void setInlineChar(char newLine) {
- inlineNewlineChar = newLine;
+ global.inlineNewlineChar = newLine;
}
public char getInlineChar() {
- return inlineNewlineChar;
+ return global.inlineNewlineChar;
}
public void loadInline(String strModel) {
- loadInline(strModel, inlineNewlineChar);
+ loadInline(strModel, global.inlineNewlineChar);
}
public void loadInline(String strModel, char newLine) {
@@ -1029,10 +1022,7 @@
strModel = strModel.substring(i + 1);
strModel = strModel.replace(newLine, '\n');
}
- int[] A = new int[4];
- A[1] = (int) ptDefaultLattice.x;
- A[2] = (int) ptDefaultLattice.y;
- A[3] = (int) ptDefaultLattice.z;
+ int[] A = global.getDefaultLattice();
openStringInline(strModel, A);
}
@@ -1144,7 +1134,6 @@
modelManager.setClientFile(null, null, null);
selectionManager.clearSelection();
clearMeasurements();
- setWindowCentered(true);
transformManager.setFixedRotationCenter(new Point3f(0, 0, 0));
setStatusFileLoaded(0, null, null, null, null, null);
refresh(0, "Viewer:clear()");
@@ -1808,14 +1797,13 @@
return repaintManager.frameRenderer;
}
+ boolean wasInMotion = false;
int motionEventNumber;
public int getMotionEventNumber() {
return motionEventNumber;
}
- boolean wasInMotion = false;
-
void setInMotion(boolean inMotion) {
// Logger.debug("viewer.setInMotion("+inMotion+")");
if (wasInMotion ^ inMotion) {
@@ -2086,14 +2074,12 @@
eval.haltExecution();
}
- String defaultLoadScript = "";
-
void setDefaultLoadScript(String script) {
- defaultLoadScript = script;
+ global.defaultLoadScript = script;
}
String getDefaultLoadScript() {
- return defaultLoadScript;
+ return global.defaultLoadScript;
}
String getStandardLabelFormat() {
@@ -2241,34 +2227,28 @@
return Graphics3D.getColix(object);
}
- boolean rasmolHydrogenSetting = true;
-
void setRasmolHydrogenSetting(boolean b) {
- rasmolHydrogenSetting = b;
+ global.rasmolHydrogenSetting = b;
}
boolean getRasmolHydrogenSetting() {
- return rasmolHydrogenSetting;
+ return global.rasmolHydrogenSetting;
}
- boolean rasmolHeteroSetting = true;
-
void setRasmolHeteroSetting(boolean b) {
- rasmolHeteroSetting = b;
+ global.rasmolHeteroSetting = b;
}
boolean getRasmolHeteroSetting() {
- return rasmolHeteroSetting;
+ return global.rasmolHeteroSetting;
}
- boolean debugScript = false;
-
boolean getDebugScript() {
- return debugScript;
+ return global.debugScript;
}
public void setDebugScript(boolean debugScript) {
- this.debugScript = debugScript;
+ global.debugScript = debugScript;
Logger.setActiveLevel(Logger.LEVEL_DEBUG, debugScript);
}
@@ -2344,7 +2324,7 @@
}
void popupMenu(int x, int y) {
- if (disablePopupMenu)
+ if (global.disablePopupMenu)
return;
statusManager.popupMenu(x, y);
}
@@ -2605,132 +2585,108 @@
//////// flags and settings ////////
- boolean dotSurfaceFlag = true;
-
boolean getDotSurfaceFlag() {
- return dotSurfaceFlag;
+ return global.dotSurfaceFlag;
}
void setDotSurfaceFlag(boolean TF) {
- dotSurfaceFlag = TF;
+ global.dotSurfaceFlag = TF;
}
- boolean dotsSelectedOnlyFlag = false;
-
boolean getDotsSelectedOnlyFlag() {
- return dotsSelectedOnlyFlag;
+ return global.dotsSelectedOnlyFlag;
}
void setDotsSelectedOnlyFlag(boolean TF) {
- dotsSelectedOnlyFlag = TF;
+ global.dotsSelectedOnlyFlag = TF;
}
- boolean rangeSelected = false;
-
boolean isRangeSelected() {
- return rangeSelected;
+ return global.rangeSelected;
}
void setRangeSelected(boolean TF) {
- rangeSelected = TF;
+ global.rangeSelected = TF;
}
- boolean windowCenteredFlag = true;
-
boolean isWindowCentered() {
- return windowCenteredFlag;
+ return modelManager.isWindowCentered();
}
void setWindowCentered(boolean TF) {
- windowCenteredFlag = TF;
+ modelManager.setWindowCentered(TF);
}
- boolean adjustCameraFlag = true;
-
boolean isCameraAdjustable() {
- return adjustCameraFlag;
+ return global.adjustCameraFlag;
}
void setAdjustCamera(boolean TF) {
- adjustCameraFlag = TF;
+ global.adjustCameraFlag = TF;
}
- boolean allowCameraMoveFlag = true;
-
boolean allowCameraMove() {
- return allowCameraMoveFlag;
+ return global.allowCameraMoveFlag;
}
void setAllowCameraMove(boolean TF) {
- allowCameraMoveFlag = TF;
+ global.allowCameraMoveFlag = TF;
}
- float solventProbeRadius = 1.2f;
-
void setSolventProbeRadius(float radius) {
- solventProbeRadius = radius;
+ global.solventProbeRadius = radius;
}
float getSolventProbeRadius() {
- return solventProbeRadius;
+ return global.solventProbeRadius;
}
float getCurrentSolventProbeRadius() {
- return solventOn ? solventProbeRadius : 0;
+ return global.solventOn ? global.solventProbeRadius : 0;
}
- boolean solventOn = false;
-
void setSolventOn(boolean isOn) {
- solventOn = isOn;
+ global.solventOn = isOn;
}
boolean getSolventOn() {
- return solventOn;
+ return global.solventOn;
}
void setAllowStatusReporting(boolean TF) {
statusManager.setAllowStatusReporting(TF);
}
- boolean testFlag1;
-
- boolean testFlag2;
-
- boolean testFlag3;
-
- boolean testFlag4;
-
void setTestFlag1(boolean value) {
- testFlag1 = value;
+ global.testFlag1 = value;
}
boolean getTestFlag1() {
- return testFlag1;
+ return global.testFlag1;
}
void setTestFlag2(boolean value) {
- testFlag2 = value;
+ global.testFlag2 = value;
}
boolean getTestFlag2() {
- return testFlag2;
+ return global.testFlag2;
}
void setTestFlag3(boolean value) {
- testFlag3 = value;
+ global.testFlag3 = value;
}
boolean getTestFlag3() {
- return testFlag3;
+ return global.testFlag3;
}
void setTestFlag4(boolean value) {
- testFlag4 = value;
+ global.testFlag4 = value;
}
boolean getTestFlag4() {
- return testFlag4;
+ return global.testFlag4;
}
public void setPerspectiveDepth(boolean perspectiveDepth) {
@@ -2747,32 +2703,28 @@
return transformManager.axesOrientationRasmol;
}
- private int axesMode = JmolConstants.AXES_MODE_BOUNDBOX;
-
void setAxesModeMolecular(boolean TF) {
- axesMode = (TF ? JmolConstants.AXES_MODE_MOLECULAR
+ global.axesMode = (TF ? JmolConstants.AXES_MODE_MOLECULAR
: JmolConstants.AXES_MODE_BOUNDBOX);
axesAreTainted = true;
}
void setAxesModeUnitCell(boolean TF) {
- axesMode = (TF ? JmolConstants.AXES_MODE_UNITCELL
+ global.axesMode = (TF ? JmolConstants.AXES_MODE_UNITCELL
: JmolConstants.AXES_MODE_BOUNDBOX);
axesAreTainted = true;
}
int getAxesMode() {
- return axesMode;
+ return global.axesMode;
}
- private boolean displayCellParameters = true;
-
void setDisplayCellParameters(boolean displayCellParameters) {
- this.displayCellParameters = displayCellParameters;
+ global.displayCellParameters = displayCellParameters;
}
boolean getDisplayCellParameters() {
- return displayCellParameters;
+ return global.displayCellParameters;
}
public boolean getPerspectiveDepth() {
@@ -2787,68 +2739,53 @@
return transformManager.getCameraDepth();
}
- boolean selectionHaloEnabled = false;
-
public void setSelectionHaloEnabled(boolean selectionHaloEnabled) {
- if (this.selectionHaloEnabled != selectionHaloEnabled) {
- this.selectionHaloEnabled = selectionHaloEnabled;
- refresh(0, "Viewer:setSelectionHaloEnabled()");
- }
+ modelManager.setSelectionHaloEnabled(selectionHaloEnabled);
}
boolean getSelectionHaloEnabled() {
- return selectionHaloEnabled;
+ return modelManager.getSelectionHaloEnabled();
}
- private boolean bondSelectionModeOr;
-
void setBondSelectionModeOr(boolean bondSelectionModeOr) {
- this.bondSelectionModeOr = bondSelectionModeOr;
+ global.bondSelectionModeOr = bondSelectionModeOr;
refresh(0, "Viewer:setBondSelectionModeOr()");
}
boolean getBondSelectionModeOr() {
- return bondSelectionModeOr;
+ return global.bondSelectionModeOr;
}
- boolean chainCaseSensitive = false;
-
boolean getChainCaseSensitive() {
- return chainCaseSensitive;
+ return global.chainCaseSensitive;
}
void setChainCaseSensitive(boolean chainCaseSensitive) {
- this.chainCaseSensitive = chainCaseSensitive;
+ global.chainCaseSensitive = chainCaseSensitive;
}
- boolean ribbonBorder = false;
-
boolean getRibbonBorder() {
- return ribbonBorder;
+ return global.ribbonBorder;
}
void setRibbonBorder(boolean borderOn) {
- this.ribbonBorder = borderOn;
+ global.ribbonBorder = borderOn;
}
- boolean cartoonRocketFlag = false;
-
boolean getCartoonRocketFlag() {
- return cartoonRocketFlag;
+ return global.cartoonRocketFlag;
}
void setCartoonRocketFlag(boolean TF) {
- this.cartoonRocketFlag = TF;
+ global.cartoonRocketFlag = TF;
}
- boolean hideNameInPopup = false;
-
boolean getHideNameInPopup() {
- return hideNameInPopup;
+ return global.hideNameInPopup;
}
void setHideNameInPopup(boolean hideNameInPopup) {
- this.hideNameInPopup = hideNameInPopup;
+ global.hideNameInPopup = hideNameInPopup;
}
void setSsbondsBackbone(boolean ssbondsBackbone) {
@@ -2868,46 +2805,38 @@
// Graphics3D
// //////////////////////////////////////////////////////////////
- boolean greyscaleRendering;
-
void setGreyscaleRendering(boolean greyscaleRendering) {
- this.greyscaleRendering = greyscaleRendering;
+ global.greyscaleRendering = greyscaleRendering;
g3d.setGreyscaleMode(greyscaleRendering);
refresh(0, "Viewer:setGreyscaleRendering()");
}
boolean getGreyscaleRendering() {
- return greyscaleRendering;
+ return global.greyscaleRendering;
}
- boolean labelsFrontFlag;
-
void setLabelsFrontFlag(boolean labelsFrontFlag) {
- this.labelsFrontFlag = labelsFrontFlag;
+ global.labelsFrontFlag = labelsFrontFlag;
}
boolean getLabelsFrontFlag() {
- return labelsFrontFlag;
+ return global.labelsFrontFlag;
}
- boolean labelsGroupFlag;
-
void setLabelsGroupFlag(boolean labelsGroupFlag) {
- this.labelsGroupFlag = labelsGroupFlag;
+ global.labelsGroupFlag = labelsGroupFlag;
}
boolean getLabelsGroupFlag() {
- return labelsGroupFlag;
+ return global.labelsGroupFlag;
}
- boolean disablePopupMenu;
-
void setDisablePopupMenu(boolean disablePopupMenu) {
- this.disablePopupMenu = disablePopupMenu;
+ global.disablePopupMenu = disablePopupMenu;
}
boolean getDisablePopupMenu() {
- return disablePopupMenu;
+ return global.disablePopupMenu;
}
// ///////////////////////////////////////////////////////////////
@@ -3033,14 +2962,12 @@
refresh(0, "setShowMeasurements()");
}
- boolean measureAllModels = false;
-
public void setMeasureAllModels(boolean TF) {
- measureAllModels = TF;
+ global.measureAllModels = TF;
}
public boolean getMeasureAllModelsFlag() {
- return measureAllModels;
+ return global.measureAllModels;
}
public boolean getShowMeasurements() {
@@ -3245,7 +3172,6 @@
void setStereoMode(int[] twoColors) {
transformManager.setStereoMode(twoColors);
}
-
int getStereoMode() {
return transformManager.stereoMode;
@@ -3392,12 +3318,10 @@
endDegrees, false, isSpin);
}
- int pickingSpinRate = 10;
-
void setPickingSpinRate(int rate) {
if (rate < 1)
rate = 1;
- pickingSpinRate = rate;
+ global.pickingSpinRate = rate;
}
void startSpinningAxis(int atomIndex1, int atomIndex2, boolean isClockwise) {
@@ -3413,8 +3337,8 @@
setSpinOn(false);
return;
}
- transformManager.rotateAboutPointsInternal(pt1, pt2, pickingSpinRate,
- Float.MAX_VALUE, isClockwise, true);
+ transformManager.rotateAboutPointsInternal(pt1, pt2,
+ global.pickingSpinRate, Float.MAX_VALUE, isClockwise, true);
}
Point3f getDrawObjectCenter(String axisID) {
@@ -3444,14 +3368,12 @@
modelManager.getAtomIdentityInfo(atomIndex, info);
}
- Point3f ptDefaultLattice = new Point3f();
-
void setDefaultLattice(Point3f ptLattice) {
- ptDefaultLattice.set(ptLattice);
+ global.setDefaultLattice(ptLattice);
}
Point3f getDefaultLattice() {
- return ptDefaultLattice;
+ return global.ptDefaultLattice;
}
public void setAtomCoord(int atomIndex, float x, float y, float z) {
@@ -3474,15 +3396,98 @@
return modelManager.getAdditionalHydrogens(atomSet);
}
- String helpPath;
void setHelpPath(String url) {
- helpPath = url;
+ global.helpPath = url;
}
void getHelp(String what) {
- if (helpPath == null)
- helpPath = styleManager.getDefaultHelpPath();
- showUrl(helpPath + what);
+ if (global.helpPath == null)
+ global.helpPath = styleManager.getDefaultHelpPath();
+ showUrl(global.helpPath + what);
}
+ private class GlobalSettings {
+
+ /*
+ * Mostly these are just saved and restored directly from Viewer.
+ * They are collected here for reference and to ensure that no
+ * methods are written that bypass viewer's get/set methods.
+ *
+ * Because these are not Frame variables, they should persist past
+ * a new file loading. There is some question in my mind whether all
+ * should be in this category.
+ *
+ */
+ //file loading
+
+ char inlineNewlineChar = '|';
+ String defaultLoadScript = "";
+ Point3f ptDefaultLattice = new Point3f();
+
+ void setDefaultLattice(Point3f ptLattice) {
+ ptDefaultLattice.set(ptLattice);
+ }
+ int[] getDefaultLattice() {
+ int[] A = new int[4];
+ A[1] = (int) ptDefaultLattice.x;
+ A[2] = (int) ptDefaultLattice.y;
+ A[3] = (int) ptDefaultLattice.z;
+ return A;
+ }
+
+ //centering and perspective
+
+ boolean allowCameraMoveFlag = true;
+ boolean adjustCameraFlag = true;
+
+ //solvent
+
+ boolean solventOn;
+ float solventProbeRadius = 1.2f;
+
+ //measurements
+
+ boolean measureAllModels;
+
+ //rendering
+
+ boolean enableFullSceneAntialiasing;
+ boolean greyscaleRendering;
+ boolean labelsGroupFlag;
+ boolean labelsFrontFlag;
+ boolean dotsSelectedOnlyFlag;
+ boolean dotSurfaceFlag = true;
+ boolean displayCellParameters = true;
+ int axesMode = JmolConstants.AXES_MODE_BOUNDBOX;
+
+ //atoms and bonds
+
+ boolean bondSelectionModeOr;
+
+ //secondary structure + Rasmol
+
+ boolean rasmolHydrogenSetting = true;
+ boolean rasmolHeteroSetting = true;
+ boolean cartoonRocketFlag;
+ boolean ribbonBorder;
+ boolean chainCaseSensitive;
+ boolean rangeSelected;
+
+ //misc
+
+ int pickingSpinRate = 10;
+ boolean hideNameInPopup;
+ boolean disablePopupMenu;
+ String helpPath;
+
+ //testing
+
+ boolean debugScript;
+ boolean testFlag1;
+ boolean testFlag2;
+ boolean testFlag3;
+ boolean testFlag4;
+ }
+
+
}
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