[Biojava-l] BioJava 1.3pre2

[Schreiber, Mark]

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. 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).
 
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).
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.
 
- Mark
 

	-----Original Message----- 
	From: Thomas Down [mailto:td2 at sanger.ac.uk] 
	Sent: Thu 1/05/2003 10:30 p.m. 
	To: biojava-l at biojava.org 
	Cc: 
	Subject: [Biojava-l] BioJava 1.3pre2
	
	

	Hi...
	
	I've just put up a (rather belated) BioJava 1.3pre2.  This includes
	a number of bug fixes since 1.3pre1, including fixes for the
	recent fasta parsing and ChangeEvent bugs.  Unless problems are
	reported, a 1.30-final release will be appearing shortly, so
	please get testing!
	
	For this release, I have provided two different binary .jar
	files, one compiled with J2SDK1.4.1 and one compiled with
	J2SDK1.3.1.  The JDK14 build includes some extra features which
	do not work with earlier java versions, but might give some
	strange errors if you try to run in with an old java runtime
	environment.
	
	Please note that BioJava 1.30 is likely to be the last release
	which supports JDK 1.2 and 1.3.  If anyone here thinks they will
	not be able to move to JDK1.4 over the coming months, it would
	be useful to hear about it now.
	
	Thanks,
	
	
	      Thomas.
	
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