I'm using biojava to parse an EMBL Flat file, modify it, and dump it out to file at the end. However when I used SeqIOTools.writeEmbl the file created, did not have correctly ordered and nested RN, RP, RX, RA, RT and RL lines. These lines should occur in repeated sets, one set for each reference in the flat file. I've modified some of the biojava classes and added 2 new classes to correct this. Everthing works fine now. I've put the modified classes and new classes here:
www.ebi.ac.uk/~lmorris/bioJavaFiles
Files modfied:
EmblLikeFormat EmblFileFormer SeqIOEventEmitter GenEmblPropertyComparator
Files added:
ReferenceAnnotation.java EmblReferenceComparator.java
If you need any more details on the changes I've made let me know. Thanks,
Lorna
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