[Biojava-l] EmblFileFormer

[Schreiber, Mark]

Hi Lorna,

This is really good. Writing files correctly has been a weak point in biojava. I have committed your changes to the 1.3.1 branch and I will put them on the biojava-live branch shortly.

If there are any volunteers the writing of GenPept and SwissProt files also sucks badly. International fame and adoration await the person who fixes them :)

- mark


> -----Original Message-----
> From: Lorna Morris [mailto:lmorris at ebi.ac.uk] 
> Sent: Tuesday, 25 November 2003 3:38 a.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] EmblFileFormer
> 
> 
> Hello
> 
> 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'm attatching the classes to this mail.
> 
> 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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