[Biojava-l] BioJava 1.3pre2

Schreiber, Mark mark.schreiber at agresearch.co.nz
Sat May 3 13:14:03 EDT 2003

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, 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>).
	> 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.

Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.

More information about the Biojava-l mailing list