[Biojava-dev] Re: biojava EMBL parser

[Lorna Morris]

Thankyou

I've put the new and modified files on this website:

http://www.ebi.ac.uk/~lmorris/bioJavaFilesJan04/


Here are some details:


Files added:

org.biojava.bio.seq.FeatureQualifier -  implements Comparable to specify 
the order of feature qualifiers within a feature

org.biojava.bio.seq.io.EmblGRFileFormer - overides addFeatureProperty 
(to use FeatureQualifier type as keys), overides formatQualifier() (to 
insert evidence tags after closing " in feature qualifiers).

Files changed:

AbstractGenEmblFileFormer - QUALIFIER_DATA changed from private to protected

EmblLikeFormat.writeSequence - changed to instantiate EmblGRFileFormer 
if the EMBL file is of the Genome Review sub-type

EmblProcessor - added a new Factory class GRFactory

FeatureTableParser.processAttribute - changed to check featureSource 
before calling addFeatureProperty

SeqIOEventEmitter.getSeqIOEvents - added new sorting method 
comparableList(Collection,SeqIOListener), added call to this new method

SeqIOTools - added new methods readEmblGR(OutputStream, SequenceIterator)
                     writeEmblGR(BufferedReader)
                     getEmblGRBuilderFactory()
               
           
I've added some javadoc and all my additions are marked with comment //lorna

If these changes could be added to biojava-live before the first release 
of EMBL Genome Reviews in mid February, that would be excellent. Paul 
Kersey (pkersey at ebi.ac.uk) will be looking after this whilst I'm away. 
Many thanks,

Lorna



Thomas Down wrote:

>On Mon, Jan 26, 2004 at 10:19:43AM +0000, Lorna Morris wrote:
>  
>
>>I thought I'd contact you directly because I'm away from tomorrow for a 
>>month and the first Genome Reviews release is due to be launched whilst 
>>I'm away. I will post the files to the mailing list later today or can 
>>pop over to talk to one of you at the Sanger if you need any further 
>>details.
>>    
>>
>
>The mailing list isn't very attachment-friendly -- could you put
>the files on a website somewhere, and we can fetch them from
>there?
>
>Thanks,
>
>     Thomas.
>  
>