[Fwd: [Biojava-l] packages under construction]

[Gerald Loeffler]

fyi (the response was sent by accident to me privately):

	gerald

Matthew Pocock wrote:
> 
> oops - could you forward that mail to the mailing list? I hit 'r' not 'R'
> 
> Matthew Pocock wrote:
> 
> > Hi.
> >
> > Gerald Loeffler wrote:
> >
> > > Hi!
> > >
> > > Matthew Pocock wrote:
> > > > We should add some class or package javadoc tag - like @construction,
> > > > @stable to indicate this.
> > >
> > > I didn't know that javadoc is able to process custom tags...sounds good!
> >
> > We would have to extend the standard doclet a little, but it pays in spades.
> >
> > >
> > >
> > > >
> > > > The seq package and sub packages are fairly solid. We need to get alignments
> > > > finnished (this means gapped sequences), and I guess the feature strategy
> > > > may change, but this package is ready for use today.
> > >
> > > Hmm...changing the feature strategy sounds like a pretty fundamental
> > > change to me. To what will it be changed - what is the current model
> > > missing?
> >
> > I have spoken to Michel about this now. Feature is missing a score field, which I
> > hadn't considered to be important but actualy is.
> >
> > We have also discussed representing complicated things like sequences that don't
> > stoor any actual sequence, just features (useful for things like blast hits) &
> > features that are accross multiple sequences (like genes in unfinnished genomes).
> > I think we can handle all of this without rezorting to changing the API, so it
> > looks like features will remain stable for now. Hura.
> >
> > >
> > >
> > >         cheers,
> > >         gerald
> > >
> > > --
> > > Gerald.Loeffler@vienna.at
> > > Tel.: +43 676 3289588
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l

-- 
 Gerald Loeffler - Daemonstration Software Consulting
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 Email: Gerald.Loeffler@vienna.at
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           DNA Chip Technology, Computational Biology