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

[Minh Duc, Cao]

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