[Biojava-l] BioJava 1.3pre2

[Schreiber, Mark]

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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