Revision: 20878
http://sourceforge.net/p/jmol/code/20878
Author: hansonr
Date: 2015-12-01 18:17:20 +0000 (Tue, 01 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.12.01"
bug fix: JSON generation from arrays broken in HTML5 version due to browser
changes in Array.toString().
bug fix: DCD reader broken.
bug fix: getProperty("JSON", "variableInfo", "x") will fail if x is an array
-- was problem with JSV_predict2 failing to properly map atoms between Jmol
and JSME
Modified Paths:
--------------
branches/v14_4/Jmol/src/javajs/util/PT.java
branches/v14_4/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/javajs/util/PT.java
trunk/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/javajs/util/PT.java
===================================================================
--- branches/v14_4/Jmol/src/javajs/util/PT.java 2015-12-01 12:58:59 UTC (rev
20877)
+++ branches/v14_4/Jmol/src/javajs/util/PT.java 2015-12-01 18:17:20 UTC (rev
20878)
@@ -873,8 +873,9 @@
/**
* @j2sNative
*
- * var s = x.toString(); return (s.startsWith("[object") &&
- * s.endsWith("Array]") ? null : s);
+ * var s = x.constructor.toString();
+ * var pt = s.indexOf("Array(");
+ * return (pt <= 0 || pt >= s.indexOf("{") ? x.toString() : null);
*
*/
{
Modified:
branches/v14_4/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
2015-12-01 12:58:59 UTC (rev 20877)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
2015-12-01 18:17:20 UTC (rev 20878)
@@ -117,9 +117,8 @@
// read DCD header
- int n = binaryDoc.readInt();
- binaryDoc.setStream(vwr.getJzt(), null, n != 0x54);
- n = binaryDoc.readInt(); // "CORD"
+ binaryDoc.setStream(vwr.getJzt(), null, binaryDoc.readInt() == 0x54);
+ binaryDoc.readInt(); // "CORD"
nModels = binaryDoc.readInt();
/* int nPriv = */ binaryDoc.readInt();
/* int nSaveC = */ binaryDoc.readInt();
@@ -133,23 +132,22 @@
/* int delta4 = */ binaryDoc.readInt();
binaryDoc.readByteArray(bytes, 0, 36);
/* int nTitle = */ binaryDoc.readInt();
- n = binaryDoc.readInt(); // TRAILER
+ binaryDoc.readInt(); // TRAILER
// read titles
- n = binaryDoc.readInt(); // HEADER
- n = binaryDoc.readInt();
+ binaryDoc.readInt(); // HEADER
SB sb = new SB();
- for (int i = 0; i < n; i++)
+ for (int i = 0, n = binaryDoc.readInt(); i < n; i++)
sb.append(binaryDoc.readString(80).trim()).appendC('\n');
- n = binaryDoc.readInt(); // TRAILER
+ binaryDoc.readInt(); // TRAILER
Logger.info("BinaryDcdReadaer:\n" + sb);
// read number of atoms and free-atom list
- n = binaryDoc.readInt(); // HEADER
+ binaryDoc.readInt(); // HEADER
nAtoms = binaryDoc.readInt();
- n = binaryDoc.readInt(); // TRAILER
+ binaryDoc.readInt(); // TRAILER
nFree = nAtoms - nFixed;
if (nFixed != 0) {
// read list of free atoms
@@ -157,7 +155,7 @@
bsFree = BS.newN(nFree);
for (int i = 0; i < nFree; i++)
bsFree.set(binaryDoc.readInt() - 1);
- n = binaryDoc.readInt() / 4; // TRAILER
+ binaryDoc.readInt(); // TRAILER
Logger.info("free: " + bsFree.cardinality() + " " + Escape.eBS(bsFree));
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-01
12:58:59 UTC (rev 20877)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-01
18:17:20 UTC (rev 20878)
@@ -8,8 +8,10 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.11.30"
+Jmol.___JmolVersion="14.4.0_2015.12.01"
+bug fix: JSON generation from arrays broken in HTML5 version due to browser
changes in Array.toString().
+bug fix: DCD reader broken.
bug fix: getProperty("JSON", "variableInfo", "x") will fail if x is an array
-- was problem with JSV_predict2 failing to properly map atoms between Jmol
and JSME
bug fix: {atomset}.sxyz gives incorrect screen coordinate when antialiased
Modified: trunk/Jmol/src/javajs/util/PT.java
===================================================================
--- trunk/Jmol/src/javajs/util/PT.java 2015-12-01 12:58:59 UTC (rev 20877)
+++ trunk/Jmol/src/javajs/util/PT.java 2015-12-01 18:17:20 UTC (rev 20878)
@@ -873,8 +873,9 @@
/**
* @j2sNative
*
- * var s = x.toString(); return (s.startsWith("[object") &&
- * s.endsWith("Array]") ? null : s);
+ * var s = x.constructor.toString();
+ * var pt = s.indexOf("Array(");
+ * return (pt <= 0 || pt >= s.indexOf("{") ? x.toString() : null);
*
*/
{
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
2015-12-01 12:58:59 UTC (rev 20877)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/BinaryDcdReader.java
2015-12-01 18:17:20 UTC (rev 20878)
@@ -117,9 +117,8 @@
// read DCD header
- int n = binaryDoc.readInt();
- binaryDoc.setStream(vwr.getJzt(), null, n != 0x54);
- n = binaryDoc.readInt(); // "CORD"
+ binaryDoc.setStream(vwr.getJzt(), null, binaryDoc.readInt() == 0x54);
+ binaryDoc.readInt(); // "CORD"
nModels = binaryDoc.readInt();
/* int nPriv = */ binaryDoc.readInt();
/* int nSaveC = */ binaryDoc.readInt();
@@ -133,23 +132,22 @@
/* int delta4 = */ binaryDoc.readInt();
binaryDoc.readByteArray(bytes, 0, 36);
/* int nTitle = */ binaryDoc.readInt();
- n = binaryDoc.readInt(); // TRAILER
+ binaryDoc.readInt(); // TRAILER
// read titles
- n = binaryDoc.readInt(); // HEADER
- n = binaryDoc.readInt();
+ binaryDoc.readInt(); // HEADER
SB sb = new SB();
- for (int i = 0; i < n; i++)
+ for (int i = 0, n = binaryDoc.readInt(); i < n; i++)
sb.append(binaryDoc.readString(80).trim()).appendC('\n');
- n = binaryDoc.readInt(); // TRAILER
+ binaryDoc.readInt(); // TRAILER
Logger.info("BinaryDcdReadaer:\n" + sb);
// read number of atoms and free-atom list
- n = binaryDoc.readInt(); // HEADER
+ binaryDoc.readInt(); // HEADER
nAtoms = binaryDoc.readInt();
- n = binaryDoc.readInt(); // TRAILER
+ binaryDoc.readInt(); // TRAILER
nFree = nAtoms - nFixed;
if (nFixed != 0) {
// read list of free atoms
@@ -157,7 +155,7 @@
bsFree = BS.newN(nFree);
for (int i = 0; i < nFree; i++)
bsFree.set(binaryDoc.readInt() - 1);
- n = binaryDoc.readInt() / 4; // TRAILER
+ binaryDoc.readInt(); // TRAILER
Logger.info("free: " + bsFree.cardinality() + " " + Escape.eBS(bsFree));
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-01 12:58:59 UTC
(rev 20877)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-01 18:17:20 UTC
(rev 20878)
@@ -62,8 +62,10 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.11.30"
+Jmol.___JmolVersion="14.5.0_2015.12.01"
+bug fix: JSON generation from arrays broken in HTML5 version due to browser
changes in Array.toString().
+bug fix: DCD reader broken.
bug fix: getProperty("JSON", "variableInfo", "x") will fail if x is an array
-- was problem with JSV_predict2 failing to properly map atoms between Jmol
and JSME
bug fix: {atomset}.sxyz gives incorrect screen coordinate when antialiased
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