Hi Torsten 

Thanks for that. I have fixed that and I hope to get that in the development
version in the next few days.

However, there is still a problem that has been mentioned before on the list
in that Artemis does not yet take into account column 1 in GFF3 (the "ID of
the landmark used to establish the coordinate system"). This means feature
positions that are not on the first sequence are wrong. I hope to get this
fixed soon as well.


On 3/11/09 12:28 AM, "Torsten Seemann"
<torsten.seem...@infotech.monash.edu.au> wrote:

> I've been migrating most of my software/scripts over to GFF3, and have
> encountered a possible bug with Artemis (v11) on Linux x86_64.
> When the GFF3 has multiple sequences in the ##FASTA section, Artemis dies
> with:
> Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException:
> uk.ac.sanger.artemis.io.EmblStreamFeature
> at 
> uk.ac.sanger.artemis.io.GFFDocumentEntry.combineGeneFeatures(GFFDocumentEntry.
> java:166)
> at uk.ac.sanger.artemis.io.GFFDocumentEntry.<init>(GFFDocumentEntry.java:75)
> However, if i REMOVE the >region00001 sequence so there is only the
> one >Seq sequence, all is ok. The extra sequences in the ##FASTA
> section are commonly used to store CDS translations, or when the GFF
> covers lots of sequences eg. contigs in an assembly.
> I have attached a .GFF3 file which causes this (and inlined it below
> for completeness).
> ##gff-version 3
> Seq vbc region 20 60 . + . ID=region00001;product=Junk DNA
>> Seq
> GC
>> region00001
> Thank you.

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