[Biojava-dev] Problem with read RichFormat file from an applet

[Richard Holland]

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Hello.

This is the root of your problem:

Caused by: java.security.AccessControlException: access denied (
java.lang.RuntimePermission createClassLoader)
     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
 GeneratedClassLoader.java:29)
     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)

The applet runtime environment is not allowing BioJava to create a
custom class loader. It's not to do with disk access at all unfortunately.

I don't know of a solution myself as I've not done much work with applets.

Does anyone else on this list have any suggestions?

cheers,
Richard


Minh Duc, Cao wrote:
> Hi,
> 
> I used IOTools.readFastaDNA(in,null) to read Fasta file and, for a stand
> alone application, it works perfectly. However, when the code is called from
> an applet, the following exception is thrown
> 
> Exception in thread "Thread-8" java.lang.ExceptionInInitializerError
>     at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
>     at org.biojava.bio.seq.SimpleFeatureHolder.<init>(
> SimpleFeatureHolder.java:54)
>     at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(
> RichFeature.java:167)
>     at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java
> :61)
>     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> SimpleRichSequenceBuilder.java:100)
>     at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(
> SimpleRichSequenceBuilder.java:81)
>     at
> org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder
> (SimpleRichSequenceBuilderFactory.java:68)
>     at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(
> RichStreamReader.java:109)
>     at org.biojavax.bio.seq.io.RichStreamReader.nextSequence(
> RichStreamReader.java:92)
>     at dnaPlatform.function.ReadFormatFileFunction.guessFormat(
> ReadFormatFileFunction.java:134)
>     at dnaPlatform.gui.RunFunction.run(MainPanel.java:929)
> Caused by: java.security.AccessControlException: access denied (
> java.lang.RuntimePermission createClassLoader)
>     at java.security.AccessControlContext.checkPermission(Unknown Source)
>     at java.security.AccessController.checkPermission(Unknown Source)
>     at java.lang.SecurityManager.checkPermission(Unknown Source)
>     at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
>     at java.lang.ClassLoader.<init>(Unknown Source)
>     at org.biojava.utils.bytecode.GeneratedClassLoader.<init>(
> GeneratedClassLoader.java:29)
>     at org.biojava.utils.walker.WalkerFactory.<init>(WalkerFactory.java:68)
>     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> :51)
>     at org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java
> :58)
>     at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(
> FeatureFilter.java:1270)
>     ... 11 more
> 
> It is noted that the applet is signed and can read files from client
> harddisk if other method is used.
> 
> Do anyone have an idea how can I go about to fix this problem?
> 
> Thank you very much
> 
> Minh
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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