2002-07-30  KATAYAMA Toshiaki  <k@bioruby.org>

	* BioRuby version 0.3.9 released.
	* lib/bio/location.rb:
	  * Locations#length (size) methods added (contributed by N. Goto)
	  * Locations#relative method added  (contributed by N. Goto)
	  * Locations#absolute method is renamed from offset
	  * Locations#offset, offset_aa methods removed
	    * use absolute/relative(n, :aa) for _aa
          * Locations#[], range methods added
	  * Location#range method added
	* lib/bio/db/embl.rb:
	  * fix accession method.
	* lib/bio/db/genpept.rb:
	  * temporally added - in the next release, we will make refactoring.
	* lib/bio/reference.rb:
	  * in bibtex and bibitem format, "PMIDnum" is changed to "PMID:num".
	* lib/bio/io/pubmed.rb:
	  * esearch, efetch methods are added.
	* lib/bio/db/aaindex.rb:
	  * fix serious bug in the index method to support negative values.
	* lib/bio/db.rb:
	  * fix fetch method to cut tag without fail.
	* lib/bio/extend.rb:
	  * added first_line_only option for the prefix in fill method.
	* doc/Tutorial.rd.ja:
	  * added docs on BibTeX etc.

2002-06-26  KATAYAMA Toshiaki  <k@bioruby.org>

	* BioRuby version 0.3.8 released.
	* lib/bio/sequence.rb:
	  * normalize! method added for clean up the object itself.
	  * 'to_seq' method was renamed to 'seq' (!)
	    * to_xxxx should be used when the class of the object changes.
	* lib/bio/appl/blast/xmparser.rb:
	  * each_iteration, each_hit, each, hits, statistics, message methods
	    are added in Report class.
	  * statistics, message methods are added in Iteration class.
	  * methods compatible with Fasta::Report::Hit are added in Hit class.
	* lib/bio/appl/blast/rexml.rb:
	  * many APIs were changed to follow the xmlparser.rb's. (!)
	* lib/bio/appl/{blast.rb,fasta.rb]:
	  * class method parser() is added for loading specified Report class.
	* etc/bioinformatics/seqdatabase.ini: added for OBDA (!)
	  * sample setup for BioRegistry - Open Bio Sequence Database Access.
	* lib/bio/extend.rb: added (!)
	  * This module adds some functionarity to the existing classes and
	    not loaded by default. User should require specifically if needed.
	* lib/bio/util/*: removed and merged into lib/bio/extend.rb (!)
	* lib/bio/id.rb: removed (!)
	* lib/bio/db/{embl.rb,sptr.rb,transfac.rb}: added entry_id
	* lib/bio/data/keggorg.rb: updated
	* sample/genes2* sample/genome2*: updated
	* doc/Tutrial.rd.ja: updated

2002-06-19  KATAYAMA Toshiaki  <k@bioruby.org>

	* BioRuby version 0.3.7 released.
	* lib/bio/sequence.rb: Sequence inherits String again (!)
	* lib/bio/db.rb, db/embl.rb, db/sptr.rb: moved EMBL specific methods

2002-06-18  KATAYAMA Toshiaki  <k@bioruby.org>

	* lib/bio/feature.rb: Bio::Feature#[] method added
	* doc/Tutrial.rd.ja: changed to use Feature class

2002-05-28  KATAYAMA Toshiaki  <k@bioruby.org>

	* lib/bio/appl/fasta.rb: parser separated, API renewal (!)
	  * lib/bio/appl/fasta/format10.rb: moved from fasta.rb

	* lib/bio/appl/blast.rb: parser separated, API renewal (!)
	  * lib/bio/appl/blast/format8.rb: newly added
	  * lib/bio/appl/blast/rexml.rb: newly added
	  * lib/bio/appl/blast/xmlparser.rb: moved from blast.rb

2002-05-16  KATAYAMA Toshiaki  <k@bioruby.org>

	* lib/bio/sequence.rb: added alias 'Seq' for class Sequence
	* lib/bio/db/fasta.rb: entry method added

2002-05-15  KATAYAMA Toshiaki  <k@bioruby.org>
	
	* lib/bio/io/dbget.rb: bug fixed for pfam (was wrongly skip # lines)
	* lib/bio/location.rb: offset method added, eased range check

2002-04-26  KATAYAMA Toshiaki  <k@bioruby.org>
	
	* sample/biofetch.rb: new 'info=' option added

2002-04-22  KATAYAMA Toshiaki  <k@bioruby.org>
	
	* lib/bio/appl/fasta.rb: follow changes made at fasta.genome.ad.jp
	* sample/gb2tab.rb: fixed to use authors.inspect for reference

2002-04-15  KATAYAMA Toshiaki  <k@bioruby.org>
	
	* sample/gb2fasta.rb: changed to follow new genbank.rb spec.
	* sample/gt2fasta.rb: changed to follow new genbank.rb spec.
	* sample/gbtab2mysql.rb: added for loading tab delimited data.

2002/04/08
	* version 0.3.6 released -k
	  * fixed inconsistency among db.rb, genbank.rb, genome.rb -k
	  * lib/bio/db/genbank.rb : serious bug fixed in locus method -k
	  * lib/bio/feature.rb : method name 'type' has changed -k

2002/03/27
	* sample/gb2tab.rb changed to follow new genbank.rb w/ new schema -k

2002/03/26
	* sample/gb2tab.rb use ruby instead of perl in the example -o
	* sample/gb2fasta.rb updated -o

2002/03/11
	* version 0.3.5 released -k

2002/03/04
	* lib/bio/sequence.rb to_a, to_ary methods renamed to names, codes -k
	* sample/biofetch.rb added for BioFetch server -k
	* bin/biofetch added for BioFetch client -k
	* lib/bio/io/fetch.rb added for BioFetch library -k
	* lib/bio/io/sql.rb added for BioSQL -k
	* lib/bio/io/registry.rb added for BioDirectory/Registry -k
	* lib/bio/feature.rb added for BioSQL, GenBank, EMBL etc. -k
	* lib/bio/db/genbank.rb rewrited to use Features, References -k
	* lib/bio/db/{genes,genome}.rb clean up -k
	* lib/bio/reference.rb added class References -k

2002/02/05
	* changed to use 'cgi' instead of 'cgi-lib' -n,k

2002/01/31
	* version 0.3.4 released -k
	  * lib/bio/db/genbank.rb -k
	    * fix for multiple 'allele' in the feature key. (thanx Lixin)

2002/01/07
	* lib/bio/appl/blast.rb -n
	  * remote blast support etc.

2001/12/18
	* lib/bio/id.rb -k
	  * newly created
	* lib/bio/io/brdb.rb -k
	  * newly created
	* lib/bio/db.rb -k
	  * template methods are deleted
	  * detailed docuement added
	* lib/bio/sequence.rb -k
	  * to_fasta, complement, translate fixed (due to the changes made
	    in 0.3.3)
	  * Sequence::NA#initialize doesn't replace 'u' with 't' any longer
	    * gc_percent, complement, translate, to_re, molecular_weight
	      methods are adapted to this change
	  * molecular_weight changed to calculate more precisely
	  * test code added 
	* lib/bio.rb -k
	  * rescue for require 'bio/appl/blast' is deleted

2001/12/15
	* lib/bio/sequence.rb -o
	  * Sequence#to_str added

2001/12/15
	* version 0.3.3 released -k

