[Biojava-l] Remote location exception
Keith James
kdj@sanger.ac.uk
22 Aug 2001 09:54:14 +0100
>>>>> "Michael" == Michael Muratet <michael.muratet@invitrogen.com> writes:
Ack! HTML...
Michael> <!doctype html public "-//w3c//dtd html 4.0
Michael> transitional//en"> <html> Greetings All <p>I've
Michael> encountered my first sequence which contains a "join" in
Michael> a cds feature. I'm using the latest release version
Michael> of biojava, with some code that looks like:
Michael> <p>
Michael> StreamReader stream = new StreamReader(new
Michael> BufferedReader(new InputStreamReader(inputStream)),
[...]
Michael> <p>I can live with this, but I would like to catch the
Michael> exception in my code so that I can skip further
Michael> calculations. The exception is apparently caught
Michael> somewhere in biojava. I've tried working backwards from
Michael> the EmblLikeLocationParser class, but I can't find
Michael> it. Does anyone have any clues?
>From memory this is happening in EmblProcessor (SwissprotProcessor
does the same), allowing reading past unsupported features.
I think what we need is a SeqIOErrorHandler analagous to the XML
ErrorHandler so that a choice could be made between swallowing the
errors and throwing Exceptions?
I'll do this if there is some general support for the idea.
To avoid breaking existing code I'm thinking of registering a default
error handler which emulates current behaviour.
--
-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA