[Biojava-l] Parsing INSDseq Sequences (1.3 & 1.4)

[Seth Johnson]

Hi Richard,

I still cannot locate the GI number for the main sequence.  After I parse it
with readINSDseqDNA, I then use:

                Note [] myAccs =
((RichAnnotation)rs.getAnnotation()).getProperties(
Terms.getAdditionalAccessionTerm());

However, the 'myAccs' appears to be empty.  Am I on the wrong track to get
to other-seqids???

On 6/6/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
>
> GenBank has a separate line for GI number, so it can be parsed out
> nicely. INSDseq does not, so you have to rely on the other-seqids tag
> and hope that one of them is the GI number. However it seems I have not
> included that tag in the parser, so I will include it. This will make
> the other-seqids values available through the notes with the term
> Terms.getAdditionalAccessionTerm(), but getIdentifier() will remain
> null.
>
> For your second question, the tutorial makes the mistake in several
> places of saying getNoteSet(Terms.blahblah()). This was shorthand for:
>
> rs.getAnnotation().getProperty(Terms.blahblah())
>         (for single values)
>
> or
>
> ((RichAnnotation)rs.getAnnotation()).getProperties(Terms.blahblah())
>         (for multiple values)
>
> but never got expanded. Maybe someone can fix that one day... :)ded...
>
> I'm just updating INSDseq to 1.4 now. The guys next door gave me the
> details of the changes, and told me that 1.3 is actually no longer
> supported by them after Friday this week! So I'll make it 1.4 only.
>
> cheers,
> Richard
>
>