Dear Bob,
When I try to run FirstGlance with Jmol 14.3.7_2014.09.17 (the version
with visible vs. restrict FIXED, HOORAY!) in Java applet mode, it
crashes. JSmol mode works fine. The Java console transcript is below.
That transcript is from local files but the same error appears at the
end when it is run from a server:
_http://bioinformatics.org/firstglance/fgij2.2x/fg.htm?mol=1d66&JAVA_
The identical version of FirstGlance works correctly in Java applet mode
from local files: Jmol 14.0.17_2014.06.11, Jmol 14.2.4_2014.08.03
I can try a different version of Jmol if it will help. Let me know if I
can help with diagnosis.
Eric
--------------------
Java Console Transcript:
Java Plug-in 10.67.2.01
Using JRE version 1.7.0_67-b01 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/emartz
----------------------------------------------------
c: clear console window
f: finalize objects on finalization queue
g: garbage collect
h: display this help message
l: dump classloader list
m: print memory usage
o: trigger logging
q: hide console
r: reload policy configuration
s: dump system and deployment properties
t: dump thread list
v: dump thread stack
x: clear classloader cache
0-5: set trace level to <n>
----------------------------------------------------
CacheEntry[file:/Users/emartz/DOSFiles/D-disk/ERICS1WS/jmol/fgij/jsmol/java/JmolAppletSigned.jar]:
updateAvailable=false,lastModified=Thu Sep 18 00:06:32 EDT
2014,length=3296821
appletwrapper isSigned = true
ClassPreloader - org.jmol.viewer.JC
ClassPreloader - org.jmol.g3d.Graphics3D
ClassPreloader - org.jmol.modelset.Atom
ClassPreloader - org.jmol.util.Escape
ClassPreloader - org.jmol.adapter.smarter.SmarterJmolAdapter
Jmol JavaScript applet jmolApplet0__51636695269706__ initializing
Jmol getValue debug null
Jmol getValue logLevel null
Jmol getValue signed null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue useCommandThread null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue multiTouchSparshUI-simulated null
Jmol getValue multiTouchSparshUI null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue noScripting null
Jmol getValue MaximumSize null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue JmolAppletProxy null
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
Jmol getValue documentLocation [line deleted -- messes up email]
Jmol getValue StatusForm null
Jmol getValue StatusText null
Jmol getValue StatusTextarea null
AppletRegistry.checkIn(jmolApplet0__51636695269706__)
vwrOptions:
{ "applet":true,"documentBase":"
DELETED A BLOCK HERE THAT MESSES UP MY EMAIL SYSTEM
(C) 2012 Jmol Development
Jmol Version: 14.3.7_2014.09.17 2014-09-17 23:50
java.vendor: Java: Oracle Corporation
java.version: Java 1.7.0_67
os.name: Mac OS X
Access: ALL
memory: 26.3/81.8
processors available: 2
useCommandThread: true
appletId:jmolApplet0 (signed)
Jmol getValue emulate null
defaults = "Jmol"
Jmol getValue boxbgcolor #ffd0d0
Jmol getValue bgcolor null
backgroundColor = "#ffd0d0"
Jmol getValue ANIMFRAMECallback null
Jmol getValue APPLETREADYCallback Jmol._readyCallback
APPLETREADYCallback = "Jmol._readyCallback"
Jmol getValue ATOMMOVEDCallback null
Jmol getValue CLICKCallback null
Jmol getValue DRAGDROPCallback null
Jmol getValue ECHOCallback null
Jmol getValue ERRORCallback null
Jmol getValue EVALCallback null
Jmol getValue HOVERCallback null
Jmol getValue LOADSTRUCTCallback jmolLoadStructCallback
LOADSTRUCTCallback = "jmolLoadStructCallback"
Jmol getValue MEASURECallback null
Jmol getValue MESSAGECallback jmolMessageCallback
MESSAGECallback = "jmolMessageCallback"
Jmol getValue MINIMIZATIONCallback null
Jmol getValue PICKCallback jmolPickCallback
PICKCallback = "jmolPickCallback"
Jmol getValue RESIZECallback null
Jmol getValue SCRIPTCallback null
Jmol getValue SYNCCallback null
Jmol getValue STRUCTUREMODIFIEDCallback null
Jmol getValue doTranslate null
language=en_US
Jmol getValue doTranslate null
Note -- Presence of message callback disables disable translation; to
enable message translation use jmolSetTranslation(true) prior to
jmolApplet()
Note -- language translation disabled
Jmol getValue popupMenu null
Jmol getValue script background "#ffd0d0"
Jmol getValue loadInline null
Jmol getValue load null
script 1 started
Script completed
Jmol script terminated
Jmol applet jmolApplet0__51636695269706__ ready
CommandWatcher Exception! script processing ERROR:
java.lang.IndexOutOfBoundsException: Index: 5, Size: 5
java.util.ArrayList.rangeCheck(ArrayList.java:635)
java.util.ArrayList.set(ArrayList.java:426)
org.jmol.script.ScriptManager.runScriptNow(Unknown Source)
org.jmol.script.CommandWatcherThread.run(Unknown Source)
---------------
END OF MESSAGE
------------------------------------------------------------------------------
Slashdot TV. Video for Nerds. Stuff that Matters.
http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
