[Biojava-l] problem running demos from the biojava-live dir ...

[Matthew Pocock]

Hi Sarath,

Weird. It sounds like alphabetmanager.xml can't be found within the 
biojava.jar repository. To test this out, can you add the 'resources' 
directory to the beginning of your classpath explicitly? If the program 
works then Java is having trouble finding the file within the jar file. 
Could you check that alphabetmanager.xml is in the same directory as 
AlphabetManager.class in the jar?

I've occasionaly come up against strange resource resolution problems 
(do you or don't you add a leading slash to the path-name?). Mabey it is 
one of these.

Matthew

ps I've never seen a stack-trace quite like this. What Java are you running?


sarathchandra wrote:

> hi thomas and pocock
>    I have been using biojava for quite some time
> now,But recently i installed red hat linux 7.1 and
> added biojava.jar , xerces.jar, xml.jar,bytecode.jar
> and the jakarta-regexp.jar but inspite of this when i
> try to run the demos from the biojava-live directory i
> am getting the followingstack trace for the programs
> [sarath@localhost demos]javac seq/GCCgbk.java
> [sarath@localhost demos]java  seq.GCCgbk seq/utrs.fa
>  java.lang.ExceptionInIntializerError: [exception was
> org.biojava.bio.bioerror: unable to initialize
> AlphabetManager]
> java.lang.NullpointerException
>  rethrown as org.biojava.bio.BioError:unable to
> initialize AlphabetManager
>  at
> java.lang.Throwable.FillInstanceTrace(Throwable.java:native)
> at java.lang.Throwable.<init>(Throwable.java:38)
> at java.lang.Error.<init>(Error.java:21)
> at org.biojava.utils.NestedError.<init>(Nested
> Error.java:60)
> at org.biojava.bio.bioError,<init>(BioError.java:48)
> 
>      Hope this stack trace will help you to tell me
> whats wrong with the running of programs is it because
> the file alphabetmanager.xml in manifest directory is
> missing as i found that such file exists in this
> directory.. Anyway hope to hear an early reply from
> you
> from sarath
> 
> 
> 
> =====
> TIME AND TIDE WAIT FOR NO MAN
> KNOWLEDGE IS POWER
> 
> sarath chandra J
> B.tech 3rd yr
> IIT Delhi
> 
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