Revision: 20785
http://sourceforge.net/p/jmol/code/20785
Author: hansonr
Date: 2015-09-22 02:52:54 +0000 (Tue, 22 Sep 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.09.21b"
bug fix: for (key in hash){...} fails upon functional iteration (deepCopy)
-- code was reusing the FOR variable when it should have been caching it in
the context stack
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/dssx/DSSR1.java
trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java
trunk/Jmol/src/org/jmol/script/ContextToken.java
trunk/Jmol/src/org/jmol/script/ScriptContext.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/dssx/DSSR1.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-21 14:32:59 UTC (rev
20784)
+++ trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-22 02:52:54 UTC (rev
20785)
@@ -171,7 +171,7 @@
// smap.put("res_long", removeUnitAtom((String) smap.get("atom1_id"))
// + "," + removeUnitAtom((String) smap.get("atom2_id")));
// }
-// }
+// }
if (map.containsKey("counts"))
s += "_M.dssr.counts = " + map.get("counts").toString() + "\n";
@@ -360,7 +360,7 @@
}
unit2 = (String) map.get("atom2_id");
bs.clearAll();
- a2 = ms.getSequenceBits(unit1, bsAtoms, bs).nextSetBit(0);
+ a2 = ms.getSequenceBits(unit2, bsAtoms, bs).nextSetBit(0);
if (a2 < 0) {
Logger.error("Atom " + unit2 + " was not found");
continue;
Modified: trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java 2015-09-21 14:32:59 UTC
(rev 20784)
+++ trunk/Jmol/src/org/jmol/popup/JmolGenericPopup.java 2015-09-22 02:52:54 UTC
(rev 20785)
@@ -671,7 +671,8 @@
menuEnable(htMenus.get("PDBnucleicMenu"), (nItems > 0));
@SuppressWarnings("unchecked")
Map<String, Object> dssr = (nItems > 0 && modelIndex >= 0 ? (Map<String,
Object>) vwr.ms.getInfo(modelIndex, "dssr") : null);
- setSecStrucMenu(htMenus.get("aaStructureMenu"), dssr);
+ if (dssr != null)
+ setSecStrucMenu(htMenus.get("aaStructureMenu"), dssr);
nItems = augmentGroup3List(menu2, "c>", false);
menuEnable(menu2, nItems > 0);
menuEnable(htMenus.get("PDBcarboMenu"), (nItems > 0));
Modified: trunk/Jmol/src/org/jmol/script/ContextToken.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ContextToken.java 2015-09-21 14:32:59 UTC
(rev 20784)
+++ trunk/Jmol/src/org/jmol/script/ContextToken.java 2015-09-22 02:52:54 UTC
(rev 20785)
@@ -28,7 +28,7 @@
class ContextToken extends T {
Map<String, SV> contextVariables;
- SV[] loopVars;
+ SV[] forVars;
static ContextToken newContext(boolean isOpen) {
ContextToken ct = (isOpen ? newCmd(T.push, "{") : newCmd(T.pop, "}"));
ct.intValue = 0;
Modified: trunk/Jmol/src/org/jmol/script/ScriptContext.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptContext.java 2015-09-21 14:32:59 UTC
(rev 20784)
+++ trunk/Jmol/src/org/jmol/script/ScriptContext.java 2015-09-22 02:52:54 UTC
(rev 20785)
@@ -55,6 +55,7 @@
public boolean isJSThread;
boolean isStateScript;
boolean isTryCatch;
+ SV[] forVars;
int iToken;
int lineEnd = Integer.MAX_VALUE;
public int[][] lineIndices;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-09-21 14:32:59 UTC
(rev 20784)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-09-22 02:52:54 UTC
(rev 20785)
@@ -3406,7 +3406,7 @@
private boolean cmdFor(int tok, boolean isForCheck) throws ScriptException {
ContextToken cmdToken = (ContextToken) theToken;
int pt = st[0].intValue;
- SV[] loopVars = cmdToken.loopVars;
+ SV[] forVars = cmdToken.forVars;
pt = st[0].intValue;
int[] pts = new int[2];
Object bsOrList = null;
@@ -3417,15 +3417,15 @@
boolean isMinusMinus = false;
int j = 0;
String key = null;
- if (isForCheck && loopVars != null) {
+ if (isForCheck && forVars != null) {
// for xx IN [...] or for xx FROM [...]
tok = T.in;
// i in x, already initialized
- forVar = loopVars[0];
- forVal = loopVars[1];
- bsOrList = loopVars[1].value;
+ forVar = forVars[0];
+ forVal = forVars[1];
+ bsOrList = forVars[1].value;
// nth time through
j = ++forVal.intValue;
if (forVal.tok == T.integer) {
@@ -3518,8 +3518,11 @@
break;
}
}
- if (!isForCheck)
- pushContext(cmdToken, "FOR");
+ if (!isForCheck) {
+ pushContext(cmdToken, "FOR");
+ thisContext.forVars = forVars;
+ forVars = null;
+ }
if (key == null) {
if (isForCheck) {
j = (bsOrList == null ? pts[1] + 1 : 2);
@@ -3554,10 +3557,10 @@
j = -1;
}
}
- if (loopVars == null)
- loopVars = cmdToken.loopVars = new SV[2];
- loopVars[0] = forVar;
- loopVars[1] = forVal;
+ if (forVars == null)
+ forVars = cmdToken.forVars = new SV[2];
+ forVars[0] = forVar;
+ forVars[1] = forVal;
} else {
if (T.tokAttr(tokAt(j), T.misc)
|| (forVal = getContextVariableAsVariable(key)) != null) {
@@ -3581,8 +3584,10 @@
}
}
pt++;
- if (!isOK)
+ if (!isOK) {
+ cmdToken.forVars = thisContext.forVars;
popContext(true, false);
+ }
isForCheck = false;
if (!isOK && !chk)
pc = Math.abs(pt) - 1;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-21 14:32:59 UTC
(rev 20784)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-22 02:52:54 UTC
(rev 20785)
@@ -61,8 +61,13 @@
TODO: ketene messes up orbitals for O;
-Jmol.___JmolVersion="14.3.16_2015.09.21"
+Jmol.___JmolVersion="14.3.16_2015.09.21b"
+bug fix: for (key in hash){...} fails upon functional iteration (deepCopy)
+ -- code was reusing the FOR variable when it should have been caching it in
the context stack
+
+JmolVersion="14.3.16_2015.09.21"
+
new feature: Raster3D triangle-only file reader (for DSSR cartoon-block
representation)
-- see http://skuld.bmsc.washington.edu/raster3d/html/render.html
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