2003-10-13  KATAYAMA Toshiaki <k@bioruby.org>

	* BioRuby 0.5.3 released.

	  Fixed bugs in Blast XML parsers: xmlparser.rb is fixed not to
	  omit the string after ' and " in sequence definitions,
	  rexml.rb is fixed not to raise NoMethodError as "undefined
	  method `each_element_with_text' for nil:NilClass".

2003-10-07  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>

	* lib/bio/db/nbrf.rb

	  Newly added NBRF/PIR flatfile sequence format class.

2003-09-30  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>

	* lib/bio/db/pdb.rb

	  Newly added PDB database flatfile format class.
	  This is pre-alpha version, specs shall be changed frequently.

2003-08-22  KATAYAMA Toshiaki <k@bioruby.org>

	* BioRuby 0.5.2 released.

	  Fixed to be loaded in Ruby 1.8.0 without warnings.

	* doc/KEGG_API.rd.ja:

	  Newly added a Japanese document on the KEGG API.

2003-08-12  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>

	* lib/bio/appl/blast/format0.rb

	  Newly added NCBI BLAST default (-m 0) output parser,
	  which may be 5-10x faster than BioPerl's parser.
	  This is alpha version, specs may be frequently changed.
	  PHI-BLAST support is still incomplete.
	  Ruby 1.8 recommended. In ruby 1.6, you need strscan.

	* lib/bio/appl/blast/wublast.rb

	  Newly added WU-BLAST default output parser.
	  This is alpha version, specs may be frequently changed.
	  Support for parameters and statistics are still incomplete.
	  Ruby 1.8 recommended. In ruby 1.6, you need strscan.

2003-07-25  GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>

	* lib/bio/alignment.rb:

	  Newly added multiple sequence alignment class.

	* lib/bio/appl/alignfactory.rb:

	  Newly added template class for multiple alignment software.

	* lib/bio/appl/clustalw.rb:

	  Newly added CLUSTAL W wrapper.
	  <http://www.ebk.ac.uk/clustalw/>
	  <ftp://ftp.ebk.ac.uk/pub/software/unix/clustalw/>

	* lib/bio/appl/clustalw/report.rb:

	  Newly added CLUSTAL W result data (*.aln file) parser.

	* lib/bio/appl/mafft.rb, lib/bio/appl/mafft/report.rb:

	  Newly added MAFFT wrapper and report parser.
	  (MAFFT is a multiple sequence alignment program based on FFT.)
	  <http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/>

2003-07-16  KATAYAMA Toshiaki  <k@bioruby.org>

	* BioRuby version 0.5.1 released.

	* lib/bio/sequence.rb: some methods (using 'rna?' internally) were
	  temporally unusable by the changes in 0.5.0 is fixed.

	* lib/bio/io/flatfile.rb: autodetection failure of the fasta entry
	  without sequence is fixed.  FlatFile.auto method is added.

	* lib/bio/db.rb: sugtag2array fixed.  DB.open now accepts IO/ARGF.

	* lib/bio/db/embl.rb: references method is added.


2003-06-25  KATAYAMA Toshiaki  <k@bioruby.org>

	* BioRuby version 0.5.0 released.

	* lib/bio/appl/blast/report.rb:

	    Refactored from xmlparser.rb, rexml.rb, and format8.rb files.
	    Formats are auto detected and parsers are automatically
	    selected by checking whether XMLParser or REXML are installed.
	    You can call simply as
	      Bio::Blast::Report.new(blastoutput)
	    or you can choose parsers/format explicitly by
	      Bio::Blast::Report.xmlparser(format7blastoutput)
	      Bio::Blast::Report.rexml(fomat7blastoutput)
	      Bio::Blast::Report.tab(format8blastoutput)
	    You can also use newly added class method reports for multiple
	    xml blast output.
	      Bio::Blast.reports(output) # output can be IO or String

	* lib/bio/appl/fasta/report.rb:

	    Refactored from format10.rb, format6.rb and sample/* files.

	* lib/bio/appl/hmmer/report.rb:

	    Bug fix and clean up.

	* bin/biogetseq:

	    Newly added OBDA (BioRegistry) entry retrieval command.

	* etc/bioinformatics/seqdatabase.ini, lib/bio/io/registry.rb:
	    Updated for new OBDA spec (Singapore version).
	    Including config file versioning and changes in tag names,
	    support for OBDA_SEARCH_PATH environmental variable.

	* lib/bio/io/keggapi.rb:

	    Newly added KEGG API client library.
	    <http://www.genome.ad.jp/kegg/soap/>

	* lib/bio/io/ddbjxml.rb:

	    Newly added DDBJ XML client library (test needed).
	    <http://xml.nig.ac.jp/>

	* lib/bio/io/das.rb:

	    Newly added BioDAS client library.

	* lib/bio/db/gff.rb:

	    Newly added GFF format parser/store library.

	* lib/bio/appl/tmhmm/report.rb:

	    Newly added TMHMM report parser.
	    <http://www.cbs.dtu.dk/services/TMHMM/>

	* lib/bio/appl/targetp/report.rb:

	    Newly added TargetP report parser.
	    <http://www.cbs.dtu.dk/services/TargetP/>

	* lib/bio/appl/sosui/report.rb:

	    Newly added SOSUI report parser.
	    <http://sosui.proteome.bio.tuat.ac.jp/cgi-bin/sosui.cgi>

	* lib/bio/appl/psort/report.rb:

	    Newly added PSORT report parser.
	    <http://www.psort.org/>, <http://psort.ims.u-tokyo.ac.jp/>

	* lib/bio/appl/genscan/report.rb:

	    Newly added GENSCAN report parser.
	    <http://genes.mit.edu/GENSCAN.html>

	* lib/bio/db/prosite.rb: bug fix in ps2re method.

	* lib/bio/db/fantom.rb:

	    Newly added FANTOM database parser (XML).
	    <http://fantom2.gsc.riken.go.jp/>

	* lib/bio/db/go.rb:

	    Newly added GO parser.
	    <http://www.geneontology.org/>

	* lib/bio/feature.rb:
	
	    'each' method now accepts an argument to select specific feature.

	* lib/bio/db/fasta.rb: definition=, data= to change comment line.

	* lib/bio/db/genbank.rb:
	
	    References and features now accept a block. 'acc_version' method
	    is added to return the Accsession.Version string.
	    'accession' method now returns Accession part of the acc_version.
	    'version' method now returns Version part of the acc_version as
	    an integer.

	* lib/bio/db/keggtab.rb:

	    Rewrited for bug fix and clean up (note: some methods renamed!)
	    * gsub('abrev', 'abbrev') in method names
	    * db_path_by_keggorg is changed to db_path_by_abbrev
	    * @bio_root is changed to @bioroot (ENV['BIOROOT'] overrides)
	    * Bio::KEGG::DBname is changed to Bio::KEGG::Keggtab::DB
	      * @database is added (a hash with its key db_abbreb)
	      * database, name, path methods added with its argument db_abbreb

	* lib/bio/io/flatfile.rb:

	   Enumerable mix-in is included.

	* lib/bio/io/flatfile/indexer.rb:

	    Indexing of the FASTA format file is now supported with various
	    type of definition line.

	* bin/dbget:

	    Removed (moved under sample directory because the port of the
	    dbget server is now closed).

	* install.rb:

	    Changed to use setup 3.1.4 to avoid installing CVS/ directory.

	* sample/goslim.rb:

	    Added a sample to generate histogram from GO slim.

	* sample/tdiary.rb:

	    Added for tDiary <http://www.tdiary.org/> users. have fun. :)

2003-01-28  KATAYAMA Toshiaki  <k@bioruby.org>

	* BioRuby version 0.4.0 released.
	* bin/bioflat:
	  * newly added for the BioFlat indexing
	* lib/bio/io/flatfile.rb, flatfile/{indexer.rb,index.rb,bdb.rb}:
	  * flatfile indexing is supported by N. Goto
	* lib/bio/db/genbank.rb: changed to contain common methods only
	  * lib/bio/db/genbank/genbank.rb
	  * lib/bio/db/genbank/genpept.rb
	  * lib/bio/db/genbank/refseq.rb
	  * lib/bio/db/genbank/ddbj.rb
	* lib/bio/db/embl.rb: changed to contain common methods only
	  * lib/bio/db/embl/embl.rb
	  * lib/bio/db/embl/sptr.rb
	  * lib/bio/db/embl/swissprot.rb
	  * lib/bio/db/embl/trembl.rb
	* lib/bio/appl/emboss.rb:
	  * added - just a generic wrapper, no specific parsers yet.
	* lib/bio/appl/hmmer.rb:
	  * added - execution wrapper
	* lib/bio/appl/hmmer/report.rb:
	  * added - parsers for hmmsearch, hmmpfam contributed by H. Suga
	* lib/bio/db.rb: open method added for easy use of flatfile.
	* lib/bio/db/kegg/genes.rb:
	  * fixed bug in codon_usage method in the case of long sequence >999
	  * eclinks, splinks, pathways, gbposition, chromosome methods added
	* lib/bio/db/aaindex.rb:
	  * adapted for the new AAindex2 format (release >= 6.0).
	* lib/bio/db/fasta.rb: entry_id is changed to return first word	only
	* lib/bio/data/na.rb, aa.rb, keggorg.rb:
	  * moved under class NucleicAcid, AminoAcid, KEGG (!)
	* in the test codes, DBGET is replaced by BioFetch

2002-08-30  Yoshinori K. Okuji  <okuji@enbug.org>

	* lib/bio/matrix.rb: Removed.
	* lib/bio/db/aaindex.rb: Require matrix instead of bio/matrix.
	* lib/bio/db/transfac.rb: Likewise.
	* lib/bio/pathway.rb: Likewise.
	  (Pathway#dump_matrix): Don't use Matrix#dump.

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

