[Biojava-l] BioJava 1.3pre2
matthew_pocock at yahoo.co.uk
Sun May 4 13:41:04 EDT 2003
re gaps, the pure Gap must not be Attomic. Realy,
there are four classes of symbol
Symbol --> BasisSymbol --> AttomicSymbol
And BasisSymbol lists must be over BasisSymbol or Gap.
Unfortunately, that's not quite what we have in the
code-base. Anyway, if there is a tiny bit of special
case code, we can get away with Gap being a
BasisSymbol, but we can't get away with it being
Attomic - bad things will happen.
--- "Schreiber, Mark"
<mark.schreiber at agresearch.co.nz> wrote: > Hi -
> I vote in favour of removing the uneeded dependency
> from the head. Could we possibly also merge in any
> changes to the head that aren't new packages?
> - Mark
> -----Original Message-----
> From: Thomas Down [mailto:thomas at derkholm.net]
> Sent: Fri 2/05/2003 8:57 p.m.
> To: Schreiber, Mark
> Cc: Thomas Down; biojava-l at biojava.org
> Subject: Re: [Biojava-l] BioJava 1.3pre2
> Once upon a time, on a computer far far away,
> Schreiber, Mark wrote:
> > Hi -
> > I know of two additions that I made to
> biojava-live that would be
> > good in bj1.3. I made some additions to
> SeqIOTools which makes the
> > new fileToBiojava and biojavaToFile easier and
> more flexible to use.
> [Aside: if BioJava after 1.3 is going to be
> JDK1.4-only, can we dump
> the use of jakarta-regexp on the HEAD and use the
> standard Java APIs
> instead? You local, friendly,
> > I also made a major overhaul of the
> > package which would be useful to merge in
> (alternatively that
> > package should be dropped from 1.3 as its non
> biojava-live form
> > is buggy and unreliable).
> It's a bit hard to tell what's happened just by
> diffing the
> code, since it got reformatted too. But I couldn't
> see anything
> objectionable. Shall we merge this up on the 1.3
> > I also know of three recent bug reports that
> haven't been resolved (too my knowledge).
> > 1 Problems with printing CircularLocations (I'll
> try and cover this
> > in the next few days <sigh>).
> > 2 Gap Symbol needs to be Atomic?? (not sure of
> the details on this
> > but its a fairly recent post).
> I'm not sure about this one. I though that the
> plan was that any
> cross-products symbols which include gaps do not
> acually occupy
> any `volume' in symbol-space. But I'll re-read the
> message and make sure I'm not missing anything. It
> would be good
> to have a few words from Matthew about this one.
> > 3 Upgrade the Blast result system. Not really a
> bug, just the addition
> > of the ability to get all the information made
> available by the
> > BlastLikeSAXParser events.
> No, that's not been done yet. As I remember it, at
> we agreed to make the datamodel interfaces in
> annotatable, so that aligner-specific bits of data
> can be
> shoved into an annotation bundle. But were we
> going to add
> any other methods? I know percentage identity has
> come up
> on a few occasions.
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