Revision: 20885
http://sourceforge.net/p/jmol/code/20885
Author: hansonr
Date: 2015-12-10 21:45:39 +0000 (Thu, 10 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.12.10"
bug fix: set selectAllModels should restrict action of display/hide as well
bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
select {visible}
bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not execute
model *
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-08
16:01:40 UTC (rev 20884)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-10
21:45:39 UTC (rev 20885)
@@ -7,22 +7,15 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
+Jmol.___JmolVersion="14.4.0_2015.12.10"
-Jmol.___JmolVersion="14.4.0_2015.12.07"
-
+bug fix: set selectAllModels should restrict action of display/hide as well
bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
-
-JmolVersion="14.4.0_2015.12.05"
-
bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
select {visible}
bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not execute
model *
-JmolVersion="14.4.0_2015.12.03"
-
-bug fix: model 0 issued when more than one PDB file is open does not execute
model *
-
JmolVersion="14.4.0_2015.12.02"
bug fix: PDB reader broken for filter "biomolecule n"
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
2015-12-08 16:01:40 UTC (rev 20884)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
2015-12-10 21:45:39 UTC (rev 20885)
@@ -48,7 +48,7 @@
private final BS bsSelection = new BS();
final BS bsFixed = new BS();
- public BS bsSubset; // set in Eval and only pointed to here
+ public BS bsSubset;
public BS bsDeleted;
public Boolean noneSelected;
@@ -62,10 +62,8 @@
// }
void processDeletedModelAtoms(BS bsAtoms) {
- if (bsDeleted != null)
- BSUtil.deleteBits(bsDeleted, bsAtoms);
- if (bsSubset != null)
- BSUtil.deleteBits(bsSubset, bsAtoms);
+ BSUtil.deleteBits(bsDeleted, bsAtoms);
+ BSUtil.deleteBits(bsSubset, bsAtoms);
BSUtil.deleteBits(bsFixed, bsAtoms);
BSUtil.deleteBits(bsHidden, bsAtoms);
BS bs = BSUtil.copy(bsSelection);
@@ -84,13 +82,14 @@
void clear() {
clearSelection(true);
+ setSelectionSubset(null);
hide(null, null, 0, true);
- setSelectionSubset(null);
bsDeleted = null;
setMotionFixedAtoms(null);
}
void display(ModelSet modelSet, BS bs, int addRemove, boolean isQuiet) {
+ BS bsNotSubset = (bsSubset == null ? null :
BSUtil.andNot(BSUtil.copy(bsHidden), bsSubset));
switch (addRemove) {
default:
BS bsAll = modelSet.getModelAtomBitSetIncludingDeleted(-1, false);
@@ -105,6 +104,10 @@
bsHidden.or(bs);
break;
}
+ if (bsNotSubset != null) {
+ bsHidden.and(bsSubset);
+ bsHidden.or(bsNotSubset);
+ }
BSUtil.andNot(bsHidden, bsDeleted);
modelSet.setBsHidden(bsHidden);
if (!isQuiet)
@@ -112,7 +115,10 @@
}
void hide(ModelSet modelSet, BS bs, int addRemove, boolean isQuiet) {
+ BS bsNotSubset = (bsSubset == null ? null :
BSUtil.andNot(BSUtil.copy(bsHidden), bsSubset));
setBitSet(bsHidden, bs, addRemove);
+ if (bsNotSubset != null)
+ bsHidden.or(bsNotSubset);
if (modelSet != null)
modelSet.setBsHidden(bsHidden);
if (!isQuiet)
@@ -219,12 +225,6 @@
}
public void setSelectionSubset(BS bs) {
-
- // for informational purposes only
- // the real copy is in Eval so that eval operations
- // can all use it directly, and so that all these
- // operations still work properly on the full set of atoms
-
bsSubset = bs;
}
@@ -252,13 +252,13 @@
return 0;
empty = TRUE;
BS bs;
- if (bsSubset != null) {
+ if (bsSubset == null) {
+ bs = bsSelection;
+ } else {
bsTemp.clearAll();
bsTemp.or(bsSubset);
bsTemp.and(bsSelection);
bs = bsTemp;
- } else {
- bs = bsSelection;
}
int count = bs.cardinality();
if (count > 0)
Modified:
branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
===================================================================
---
branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-12-08 16:01:40 UTC (rev 20884)
+++
branches/v14_4/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-12-10 21:45:39 UTC (rev 20885)
@@ -30,7 +30,6 @@
import java.awt.Dimension;
import java.awt.EventQueue;
import java.awt.Font;
-import java.awt.Rectangle;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
@@ -531,7 +530,7 @@
str = str.substring(1);
if (vwr.checkHalt(str, isInterrupt))
strErrorMessage = (isScriptExecuting ? "script execution halted with "
- + strCommand : "no script was executing");
+ + strCommand : "no script was executing - use exitJmol to exit
Jmol");
//the problem is that scriptCheck is synchronized, so these might get
backed up.
if (strErrorMessage.length() > 0) {
console.outputError(strErrorMessage);
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