[Biojava-l] BioJava 1.3pre2

[Matthew Pocock]

Hi,

re gaps, the pure Gap must not be Attomic. Realy,
there are four classes of symbol

    Symbol --> BasisSymbol --> AttomicSymbol
         \--> Gap

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.

M

 --- "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.
> 	
> 	Fine.
> 	
> 	[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,
> dependency-fascist...]
> 	
> 	> I also made a major overhaul of the
> org.biojava.bio.proteomics
> 	> 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
> branch?
> 	
> 	> 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>).
> 	
> 	Thanks.
> 	
> 	> 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
> original
> 	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
> Singapore
> 	we agreed to make the datamodel interfaces in
> bio.search
> 	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.
> 	
> 	
> 	
> 	      Thomas.
> 	
> 
> 
>
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