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[Jmol-commits] SF.net SVN: jmol: [7206] trunk/Jmol
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From: <ha...@us...> - 2007-03-23 10:44:24
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Revision: 7206
http://svn.sourceforge.net/jmol/?rev=7206&view=rev
Author: hansonr
Date: 2007-03-23 03:44:22 -0700 (Fri, 23 Mar 2007)
Log Message:
-----------
11.1.27
fixes two state bugs:
1) dots/geosurface not being saved properly in state
2) animation parameters not being saved properly in state
Modified Paths:
--------------
trunk/Jmol/build.xml
trunk/Jmol/src/org/jmol/viewer/Dots.java
trunk/Jmol/src/org/jmol/viewer/EnvelopeCalculation.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
trunk/Jmol/src/org/jmol/viewer/Mmset.java
trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
Modified: trunk/Jmol/build.xml
===================================================================
--- trunk/Jmol/build.xml 2007-03-23 07:28:46 UTC (rev 7205)
+++ trunk/Jmol/build.xml 2007-03-23 10:44:22 UTC (rev 7206)
@@ -14,7 +14,7 @@
<property name="deprecation" value="off" />
<property name="optimization" value="off" />
- <property name="version" value="11.1.26" />
+ <property name="version" value="11.1.27" />
<property name="tests.source.dir" value="source-tests" />
<property name="lib.dir" value="jars" />
Modified: trunk/Jmol/src/org/jmol/viewer/Dots.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Dots.java 2007-03-23 07:28:46 UTC (rev 7205)
+++ trunk/Jmol/src/org/jmol/viewer/Dots.java 2007-03-23 10:44:22 UTC (rev 7206)
@@ -78,41 +78,47 @@
initialize();
return;
}
-
+
if ("translucency" == propertyName) {
- return; // no translucent dots
+ return; // no translucent dots
}
if ("ignore" == propertyName) {
- ec.setIgnore((BitSet)value);
+ ec.setIgnore((BitSet) value);
return;
}
if ("select" == propertyName) {
- bsSelected = (BitSet)value;
+ bsSelected = (BitSet) value;
return;
}
// next four are for serialization
if ("radius" == propertyName) {
- thisRadius = ((Float)value).floatValue();
+ thisRadius = ((Float) value).floatValue();
return;
}
if ("colorRGB" == propertyName) {
- thisArgb = ((Integer)value).intValue();
+ thisArgb = ((Integer) value).intValue();
return;
}
if ("atom" == propertyName) {
- thisAtom = ((Integer)value).intValue();
+ thisAtom = ((Integer) value).intValue();
atoms[thisAtom].setShapeVisibility(myVisibilityFlag, true);
ec.dotsConvexMax = Math.max(thisAtom + 1, ec.dotsConvexMax);
- return;
+ return;
}
if ("dots" == propertyName) {
isActive = true;
- ec.setFromBits(thisAtom, (BitSet)value);
- if (mads == null)
+ ec.setFromBits(thisAtom, (BitSet) value);
+ atoms[thisAtom].setShapeVisibility(myVisibilityFlag, true);
+ if (mads == null) {
mads = new short[atomCount];
+ for (int i = 0; i < atomCount; i++)
+ if (atoms[i].isShapeVisible(myVisibilityFlag))
+ mads[i] = (short) (ec.getAppropriateRadius(atoms[i]) * 1000);
+ ec.setMads(mads);
+ }
mads[thisAtom] = (short) (thisRadius * 1000f);
if (colixes == null) {
colixes = new short[atomCount];
@@ -121,7 +127,7 @@
colixes[thisAtom] = Graphics3D.getColix(thisArgb);
//all done!
return;
- }
+ }
super.setProperty(propertyName, value, bs);
}
@@ -204,8 +210,8 @@
atoms[i].setShapeVisibility(myVisibilityFlag, bsOn.get(i));
}
if (newSet) {
+ mads = null;
ec.newSet();
- mads = null;
lastSolventRadius = addRadius;
}
// always delete old surfaces for selected atoms
@@ -255,19 +261,24 @@
int atomCount = viewer.getAtomCount();
String type = (isSurface ? "geoSurface " : "dots ");
for (int i = 0; i < atomCount; i++) {
- if (ec.dotsConvexMaps[i] == null)
+ if (ec.dotsConvexMaps[i] == null
+ || !atoms[i].isShapeVisible(myVisibilityFlag))
continue;
if (!isSurface && bsColixSet != null && bsColixSet.get(i))
- setStateInfo(temp, i, getColorCommand(type, paletteIDs[i], colixes[i]));
+ setStateInfo(temp, i, getColorCommand(type, paletteIDs[i], colixes[i]));
BitSet bs = new BitSet();
int[] map = ec.dotsConvexMaps[i];
int iDot = map.length << 5;
+ int n = 0;
while (--iDot >= 0)
- if (EnvelopeCalculation.getBit(map, iDot))
+ if (EnvelopeCalculation.getBit(map, iDot)) {
+ n++;
bs.set(iDot);
- appendCmd(s, type + i + " radius "
- + ec.getAppropriateRadius(atoms[i]) + " "
- + StateManager.escape(bs));
+ }
+ if (n > 0) {
+ appendCmd(s, type + i + " radius " + ec.getAppropriateRadius(atoms[i])
+ + " " + StateManager.escape(bs));
+ }
}
s.append(getShapeCommands(temp, null, atomCount));
return s.toString();
Modified: trunk/Jmol/src/org/jmol/viewer/EnvelopeCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/EnvelopeCalculation.java 2007-03-23 07:28:46 UTC (rev 7205)
+++ trunk/Jmol/src/org/jmol/viewer/EnvelopeCalculation.java 2007-03-23 10:44:22 UTC (rev 7206)
@@ -185,6 +185,10 @@
boolean isCalcOnly;
+ void setMads(short[] mads) {
+ this.mads = mads;
+ }
+
void setFromBits(int index, BitSet bs) {
setAllBits(geodesicMap, geodesicCount);
for (int iDot = geodesicCount; --iDot >= 0;)
@@ -199,7 +203,7 @@
System.arraycopy(geodesicMap, 0, map, 0, count);
}
dotsConvexMaps[index] = map;
-
+ dotsConvexMax = Math.max(dotsConvexMax, index);
}
void setIgnore(BitSet value) {
@@ -223,6 +227,7 @@
dotsConvexMax = 0;
dotsConvexMaps = null;
radiusP = diameterP = 0;
+ mads = null;
}
void calculate(float addRadius, float setRadius, float scale,
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-23 07:28:46 UTC (rev 7205)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-23 10:44:22 UTC (rev 7206)
@@ -4906,10 +4906,10 @@
float startDelay = 1, endDelay = 1;
if (statementLength > 5)
badArgumentCount();
- int animationMode = 0;
+ int animationMode = RepaintManager.ANIMATION_ONCE;
switch (getToken(2).tok) {
case Token.loop:
- ++animationMode;
+ animationMode = RepaintManager.ANIMATION_LOOP;
break;
case Token.identifier:
String cmd = parameterAsString(2);
@@ -4918,7 +4918,7 @@
break;
}
if (cmd.equalsIgnoreCase("palindrome")) {
- animationMode = 2;
+ animationMode = RepaintManager.ANIMATION_PALINDROME;
break;
}
invalidArgument();
Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2007-03-23 07:28:46 UTC (rev 7205)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2007-03-23 10:44:22 UTC (rev 7206)
@@ -34,13 +34,19 @@
// for now, just update this by hand
// perhaps use ant filter later ... but mth doesn't like it :-(
public final static String copyright = "(C) 2007 Jmol Development";
- public final static String version = "11.1.26";
+ public final static String version = "11.1.27";
/*
*
*
*
*
+ 11.1.27
+ fixes two state bugs:
+ 1) dots/geosurface not being saved properly in state
+ 2) animation parameters not being saved properly in state
+
+
11.1.26
fixes two nasty bugs relating to isosurfaces and JVXL files.
-- JVXL files created from molecular orbitals will show up with no color
Modified: trunk/Jmol/src/org/jmol/viewer/Mmset.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Mmset.java 2007-03-23 07:28:46 UTC (rev 7205)
+++ trunk/Jmol/src/org/jmol/viewer/Mmset.java 2007-03-23 10:44:22 UTC (rev 7206)
@@ -327,6 +327,7 @@
if (models[0].modelNumber < 1000000) {
for (int i = 0; i < baseModelCount; i++) {
models[i].modelNumber = 1000000 + i + 1;
+ models[i].modelNumberDotted = "1." + (i + 1);
models[i].modelTag = "" + models[i].modelNumber;
}
}
@@ -336,6 +337,7 @@
modelnumber += 1000000;
for (int i = baseModelCount; i < modelCount; i++) {
models[i].modelNumber += modelnumber;
+ models[i].modelNumberDotted = (modelnumber / 1000000) + "." + (modelnumber % 1000000);
models[i].modelTag = "" + models[i].modelNumber;
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2007-03-23 07:28:46 UTC (rev 7205)
+++ trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2007-03-23 10:44:22 UTC (rev 7206)
@@ -163,12 +163,11 @@
int firstModelIndex;
int lastModelIndex;
int frameStep;
- int modelCount;
+
void initializePointers(int frameStep) {
firstModelIndex = 0;
- modelCount = (frameStep == 0 ? 0 : viewer.getModelCount());
- lastModelIndex = modelCount - 1;
- this.frameStep = frameStep;
+ lastModelIndex = (frameStep == 0 ? 0 : viewer.getModelCount()) - 1;
+ this.frameStep = frameStep;
}
void clear() {
@@ -195,7 +194,7 @@
info.put("displayModelNumber", new Integer(currentModelIndex >=0 ? viewer.getModelNumberDotted(currentModelIndex) : "0"));
info.put("displayModelName", (currentModelIndex >=0 ? viewer.getModelName(currentModelIndex) : ""));
info.put("animationFps", new Integer(animationFps));
- info.put("animationReplayMode", new Integer(animationReplayMode));
+ info.put("animationReplayMode", getAnimationModeName());
info.put("firstFrameDelay", new Float(firstFrameDelay));
info.put("lastFrameDelay", new Float(lastFrameDelay));
info.put("animationOn", new Boolean(animationOn));
@@ -204,26 +203,32 @@
}
String getState() {
+ int modelCount = viewer.getModelCount();
if (modelCount < 2)
return "";
- StringBuffer commands = new StringBuffer("# frame state;\n# modelCount ").
- append(modelCount).append(";\n# first ").
- append(viewer.getModelNumberDotted(0)).append(";\n# last ").
- append(viewer.getModelNumberDotted(modelCount - 1)).append(";\n");
+ StringBuffer commands = new StringBuffer("# frame state;\n# modelCount ")
+ .append(modelCount).append(";\n# first ").append(
+ viewer.getModelNumberDotted(0)).append(";\n# last ").append(
+ viewer.getModelNumberDotted(modelCount - 1)).append(";\n");
if (backgroundModelIndex >= 0)
- commands.append("background model ").append(backgroundModelIndex).append(";\n");
- if (true || currentModelIndex >= 0) {
- commands.append("frame RANGE " + viewer.getModelNumberDotted(firstModelIndex)
- + " " + viewer.getModelNumberDotted(lastModelIndex) + ";\n");
- commands.append("animation DIRECTION "
- + (animationDirection == 1 ? "+1" : "-1") + ";\n");
- commands.append("animation " + (animationOn ? "ON" : "OFF") + ";\n");
- if (animationOn && animationPaused)
- commands.append("animation PAUSE;\n");
- commands.append("frame " + viewer.getModelNumberDotted(currentModelIndex) + ";\n");
- } else {
- commands.append("frame ALL;\n");
- }
+ commands.append("background model ").append(backgroundModelIndex).append(
+ ";\n");
+ commands.append(
+ "frame RANGE " + viewer.getModelNumberDotted(firstModelIndex) + " "
+ + viewer.getModelNumberDotted(lastModelIndex)).append(";\n");
+ commands.append(
+ "animation DIRECTION " + (animationDirection == 1 ? "+1" : "-1"))
+ .append(";\n");
+ commands.append("animation MODE " + getAnimationModeName()).append(" ")
+ .append(firstFrameDelay).append(" ").append(lastFrameDelay).append(
+ ";\n");
+ commands.append("frame " + viewer.getModelNumberDotted(currentModelIndex)
+ + ";\n");
+ commands.append(
+ "animation " + (!animationOn ? "OFF" : currentDirection == 1 ? "PLAY"
+ : "PLAYREV")).append(";\n");
+ if (animationOn && animationPaused)
+ commands.append("animation PAUSE;\n");
commands.append("\n");
return commands.toString();
}
@@ -246,6 +251,11 @@
// 0 = once
// 1 = loop
// 2 = palindrome
+
+ final static int ANIMATION_ONCE = 0;
+ final static int ANIMATION_LOOP = 1;
+ final static int ANIMATION_PALINDROME = 2;
+
int animationReplayMode = 0;
float firstFrameDelay, lastFrameDelay;
int firstFrameDelayMs, lastFrameDelayMs;
@@ -256,14 +266,14 @@
firstFrameDelayMs = (int)(this.firstFrameDelay * 1000);
this.lastFrameDelay = lastFrameDelay > 0 ? lastFrameDelay : 0;
lastFrameDelayMs = (int)(this.lastFrameDelay * 1000);
- if (animationReplayMode >= 0 && animationReplayMode <= 2)
+ if (animationReplayMode >= ANIMATION_ONCE && animationReplayMode <= ANIMATION_PALINDROME)
this.animationReplayMode = animationReplayMode;
else
Logger.error("invalid animationReplayMode:" + animationReplayMode);
}
void setAnimationRange(int framePointer, int framePointer2) {
- modelCount = viewer.getModelCount();
+ int modelCount = viewer.getModelCount();
if (framePointer < 0) framePointer = 0;
if (framePointer2 < 0) framePointer2 = modelCount;
if (framePointer >= modelCount) framePointer = modelCount - 1;
@@ -311,7 +321,7 @@
void resumeAnimation() {
if(currentModelIndex < 0)
setAnimationRange(firstModelIndex, lastModelIndex);
- if (modelCount <= 1) {
+ if (viewer.getModelCount() <= 1) {
animationOn = false;
return;
}
@@ -346,39 +356,49 @@
int modelIndexNext = currentModelIndex + frameStep;
boolean isDone = (modelIndexNext > firstModelIndex && modelIndexNext > lastModelIndex
|| modelIndexNext < firstModelIndex && modelIndexNext < lastModelIndex);
-
-
/*
Logger.debug("setAnimationRelative: " +
" firstModelIndex=" + firstModelIndex +
" displayModelIndex=" + displayModelIndex +
" lastModelIndex=" + lastModelIndex +
" currentDirection=" + currentDirection +
+ " animationDirection=" + animationDirection +
" direction=" + direction +
" isDone="+isDone +
" modelIndexNext=" + modelIndexNext +
- " modelCount=" + modelCount +
+ " modelCount=" + viewer.getModelCount() +
" animationReplayMode=" + animationReplayMode +
" animationDirection=" + animationDirection);
*/
if (isDone) {
switch (animationReplayMode) {
- case 0: //once through
+ case ANIMATION_ONCE:
return false;
- case 1: //repeat
+ case ANIMATION_LOOP:
modelIndexNext = (animationDirection > 0 ? firstModelIndex : lastModelIndex);
break;
- case 2: //palindrome
+ case ANIMATION_PALINDROME:
currentDirection = -currentDirection;
modelIndexNext -= 2 * frameStep;
}
}
//Logger.debug("next="+modelIndexNext+" dir="+currentDirection+" isDone="+isDone);
- if (modelIndexNext < 0 || modelIndexNext >= modelCount)
+ if (modelIndexNext < 0 || modelIndexNext >= viewer.getModelCount())
return false;
setCurrentModelIndex(modelIndexNext);
return true;
}
+
+ String getAnimationModeName() {
+ switch (animationReplayMode) {
+ case ANIMATION_LOOP:
+ return "LOOP";
+ case ANIMATION_PALINDROME:
+ return "PALINDROME";
+ default:
+ return "ONCE";
+ }
+ }
class AnimationThread extends Thread implements Runnable {
final int framePointer;
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