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

[sarathchandra]

hi pocock
  I have tried to check the existence of the file
alphabetmanager.xml in the directory tools nested
inside resources i think this file  should be
somewhere like this
resources/../../tools/alphabetmanager.xml but the file
alphabetmanager.xml isnt present in the tools
directory.. is this some where the problem is arising
.. if this is so adding resources deliberately to my
classpath wouldnt help i guess, but still i will check
it.however do u feel it is the problem with the
biojava.jar file? may be? or may be not? have you ever
faced such problems like the program getting compiled
well but still the unhealthy exceptions like the one i
get.
awaiting your help
from sarath
--- Matthew Pocock <mrp@sanger.ac.uk> wrote:
> 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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