[Biojava-l] IllegalArgumentException when parsing an embl file

Kalle Näslund kalle.naslund at genpat.uu.se
Thu Jan 13 05:06:17 EST 2005

mark.schreiber at group.novartis.com wrote:

>Hi Anna -
>It seems the problem may be with the EMBL file.
>java.lang.IllegalArgumentException: Location [1045891,1046196] is outside
>This part indicates BioJava is trying to make a Feature with the Location [1045891,1046196] which is outside the bounds of the available sequence. It is not allowed 
>to create features outside of the available Sequence. Apparently BioJava 
>is able to find 1000000 bases. Is there actually more sequence than this in the EMBL file?
Just a quick observation that might be relevant, it seems that the only 
place in SimpleFeature that throws an IllegalArgumentException
due to the range being outside the sequence is commented out since some 
time, with the cvs comment "Various modifications to make
life easier" ( SimpleFeature rev 1.22 ). So this problem seems to have 
occured for more people, and a quick dirty solution was found.

So, i guess, if Anna is aware of the consequences, ( things might go bad 
if you want to use these Features ) a solution might be to try
an up to date biojava cvs build. 

mvh Kalle

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