Details
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Type: Bug
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Status: Being tested
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Priority: Blocker
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Resolution: Unresolved
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Affects Version/s: 2.9
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Fix Version/s: 2.9.0b1
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Component/s: jvlite, Structures
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Labels:None
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Epic Link:
Description
This looks like something is missing in the applet classpath.
Currrent build:
http://www.jalview.org/builds/develop/examples/applets.html
Click on '1gaq associated with fer1_maize' - see exception:
Java Plug-in 11.51.2.16
Using JRE version 1.8.0_51-b16 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/jprocter
----------------------------------------------------
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>
----------------------------------------------------
Sep 03, 2015 11:59:40 AM jalview.o.k <clinit>
INFO: Getting messages for lang: en_US
0
1822 script command tokens
applet context: -applet
appletDocumentBase=http://www.jalview.org/builds/develop/examples/applets.html
appletCodeBase=http://www.jalview.org/builds/develop/examples/
(C) 2009 Jmol Development
Jmol Version: 12.2.4 2011-10-11 21:29
java.vendor: Oracle Corporation
java.version: 1.8.0_51
os.name: Mac OS X
memory: 30.0/161.0
processors available: 4
useCommandThread: false
appletId:panel0_jmol_jalview.appletgui.I@27bb05f3
Exception in thread "Thread-40" java.lang.NoSuchMethodError: org.jmol.api.JmolAppConsoleInterface.start(Lorg/jmol/viewer/Viewer;)V
at jalview.appletgui.I.f(Unknown Source)
at jalview.f.a.a.a(Unknown Source)
at jalview.appletgui.F.<init>(Unknown Source)
at jalview.appletgui.AlignFrame.newStructureView(Unknown Source)
at jalview.bin.m.a(Unknown Source)
at jalview.bin.m.run(Unknown Source)
from debug link:
http://www.jalview.org/builds/develop/examples/debug/applets.html
Sep 03, 2015 12:09:57 PM jalview.util.MessageManager <clinit>
INFO: Getting messages for lang: en_US
1822 script command tokens
applet context: -applet
appletDocumentBase=http://www.jalview.org/builds/develop/examples/debug/applets.html
appletCodeBase=http://www.jalview.org/builds/develop/examples/debug/
(C) 2009 Jmol Development
Jmol Version: 12.2.4 2011-10-11 21:29
java.vendor: Oracle Corporation
java.version: 1.8.0_51
os.name: Mac OS X
memory: 48.2/152.6
processors available: 4
useCommandThread: false
appletId:panel6_jmol_jalview.appletgui.AppletJmolBinding@1ea57342
Exception in thread "Thread-84" java.lang.NoSuchMethodError: org.jmol.api.JmolAppConsoleInterface.start(Lorg/jmol/viewer/Viewer;)V
at jalview.appletgui.AppletJmolBinding.createJmolConsole(AppletJmolBinding.java:169)
at jalview.ext.jmol.JalviewJmolBinding.allocateViewer(JalviewJmolBinding.java:1380)
at jalview.appletgui.AppletJmol.<init>(AppletJmol.java:270)
at jalview.appletgui.AlignFrame.newStructureView(AlignFrame.java:4090)
at jalview.bin.JalviewLite$LoadingThread.loadPdbFiles(JalviewLite.java:2123)
at jalview.bin.JalviewLite$LoadingThread.startLoading(JalviewLite.java:1864)
at jalview.bin.JalviewLite$LoadingThread.run(JalviewLite.java:1835)
Currrent build:
http://www.jalview.org/builds/develop/examples/applets.html
Click on '1gaq associated with fer1_maize' - see exception:
Java Plug-in 11.51.2.16
Using JRE version 1.8.0_51-b16 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/jprocter
----------------------------------------------------
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>
----------------------------------------------------
Sep 03, 2015 11:59:40 AM jalview.o.k <clinit>
INFO: Getting messages for lang: en_US
0
1822 script command tokens
applet context: -applet
appletDocumentBase=http://www.jalview.org/builds/develop/examples/applets.html
appletCodeBase=http://www.jalview.org/builds/develop/examples/
(C) 2009 Jmol Development
Jmol Version: 12.2.4 2011-10-11 21:29
java.vendor: Oracle Corporation
java.version: 1.8.0_51
os.name: Mac OS X
memory: 30.0/161.0
processors available: 4
useCommandThread: false
appletId:panel0_jmol_jalview.appletgui.I@27bb05f3
Exception in thread "Thread-40" java.lang.NoSuchMethodError: org.jmol.api.JmolAppConsoleInterface.start(Lorg/jmol/viewer/Viewer;)V
at jalview.appletgui.I.f(Unknown Source)
at jalview.f.a.a.a(Unknown Source)
at jalview.appletgui.F.<init>(Unknown Source)
at jalview.appletgui.AlignFrame.newStructureView(Unknown Source)
at jalview.bin.m.a(Unknown Source)
at jalview.bin.m.run(Unknown Source)
from debug link:
http://www.jalview.org/builds/develop/examples/debug/applets.html
Sep 03, 2015 12:09:57 PM jalview.util.MessageManager <clinit>
INFO: Getting messages for lang: en_US
1822 script command tokens
applet context: -applet
appletDocumentBase=http://www.jalview.org/builds/develop/examples/debug/applets.html
appletCodeBase=http://www.jalview.org/builds/develop/examples/debug/
(C) 2009 Jmol Development
Jmol Version: 12.2.4 2011-10-11 21:29
java.vendor: Oracle Corporation
java.version: 1.8.0_51
os.name: Mac OS X
memory: 48.2/152.6
processors available: 4
useCommandThread: false
appletId:panel6_jmol_jalview.appletgui.AppletJmolBinding@1ea57342
Exception in thread "Thread-84" java.lang.NoSuchMethodError: org.jmol.api.JmolAppConsoleInterface.start(Lorg/jmol/viewer/Viewer;)V
at jalview.appletgui.AppletJmolBinding.createJmolConsole(AppletJmolBinding.java:169)
at jalview.ext.jmol.JalviewJmolBinding.allocateViewer(JalviewJmolBinding.java:1380)
at jalview.appletgui.AppletJmol.<init>(AppletJmol.java:270)
at jalview.appletgui.AlignFrame.newStructureView(AlignFrame.java:4090)
at jalview.bin.JalviewLite$LoadingThread.loadPdbFiles(JalviewLite.java:2123)
at jalview.bin.JalviewLite$LoadingThread.startLoading(JalviewLite.java:1864)
at jalview.bin.JalviewLite$LoadingThread.run(JalviewLite.java:1835)