2006-02-27  Toshiaki Katayama <k@bioruby.org>

	* BioRuby 1.0.0 released

2006-02-10  Toshiaki Katayama <k@bioruby.org>

	* BioRuby shell is changed to use session/ directory under the current
	  or specified directory to store the session information instead of
	  ./.bioruby directory.

2006-02-05  Toshiaki Katayama <k@bioruby.org>

	* License to be changed to Ruby's (not yet completed).

2006-02-01  Trevor Wennblom <trevor@corevx.com>

	* Bio::RestrictionEnzyme first commit for comments.
	  * See lib/bio/util/restriction_enzyme.rb and
	    test/unit/bio/util/restriction_enzyme

2006-01-28  Toshiaki Katayama <k@bioruby.org>

	* lib/bio/appl/emboss.rb

          EMBOSS USA format is now accepted via seqret/entret commands
	  and also utilized in the BioRuby shell (lib/bio/shell.rb,
	  plugin/entry.rb, plugin/emboss.rb).

	* lib/bio/io/brdb.rb is removed - unused Bio::BRDB (BioRuby DB)

2006-01-23  Toshiaki Katayama <k@bioruby.org>

	* lib/bio/sequence.rb

	  Bio::Sequence is refactored to be a container class for
	  any sequence annotations.  Functionality is separared into
	  several files under the lib/bio/sequence/ direcotry as
	  common.rb, compat.rb, aa.rb, na.rb, format.rb

2006-01-20  Toshiaki Katayama <k@bioruby.org>

	* BioRuby 0.7.1 is released.

2006-01-12  Toshiaki Katayama <k@bioruby.org>

	* lib/bio/db.ra: fixed a bug of the tag_cut method introduced in 0.7.0
	  (reported by Alex Gutteridge)

2006-01-04  Naohisa Goto <ng@bioruby.org>

	* Bio::PDB is refactored.  See doc/Changes-0.7 for more details.

2005-12-19  Toshiaki Katayama <k@bioruby.org>

	* BioRuby 0.7.0 is released.

	  See doc/Changes-0.7.rd file for major and incompatible changes.

2005-12-19  Naohisa Goto <ng@bioruby.org>

	* lib/bio/db/pdb.rb, lib/bio/db/pdb/pdb.rb, lib/bio/db/pdb/*.rb
	  * Many changes have been made.
	  * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
            changed. Now, Record is changed from hash to Struct, and
            method_missing is no longer used.
          * In the "MODEL" record, model_serial is changed to serial.
	  * In any records, record_type is changed to record_name.
	  * In most records contains real numbers, changed to return
	    float values instead of strings.
	  * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
	    Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
	    Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
	    Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
	    Bio::PDB::DataType.
	  * There are more and more changes to be written...

	* lib/bio/db/pdb/atom.rb
	  * Bio::PDB::Atom is removed.
	    Instead, please use Bio::PDB::Record::ATOM and
            Bio::PDB::Record::HETATM.

2005-12-02  Naohisa Goto <ng:bioruby.org>

	* lib/bio/alignment.rb
	  * Old Bio::Alignment class is renamed to
	    Bio::Alignment::OriginalAlignment.
	    Now, new Bio::Alignment is a module. However,
	    you don't mind so much because most of the class methods
	    previously existed are defined to delegate to the new
	    Bio::Alignment::OriginalAlignment class,
            for keeping backward compatibility.
	  * New classes and modules are introduced. Please refer RDoc.
	  * each_site and some methods changed to return Bio::Alignment::Site,
	    which inherits Array (previously returned Array).
	  * consensus_iupac now returns only standard bases
	    'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
	    'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
	    '?' (or missing_char, in EnumerableExtension#consensus_iupac).
	    Note that consensus_iupac now does not return u and invalid
	    letters not defined in IUPAC standard even if all bases
	    are equal.
	  * There are more and more changes to be written...

2005-11-05  Toshiaki Katayama <k@bioruby.org>

	* lib/bio/sequence.rb

	  Bio::Sequence.auto(str) method is added which auto detect the
	  molecular type of the string and then returns the
	  Bio::Sequence::NA or Bio::Sequence::AA object.
	  
	  Bio::Sequence#blast and Bio::Sequence#fasta methods are removed.

	* lib/bio/shell/plugin/codon.rb

	  Newly added plugin to treat codon table.
	  ColoredCodonTable is ported from the codontable.rb

2005-11-01  Toshiaki Katayama <k@bioruby.org>

	* bin/bioruby, lib/bio/shell/

	  All methods are changed to private methods to avoid adding them
	  in top level binding, which caused many unexpected behaviors,
	  as adviced by Koichi Sasada.

	  The MIDI plugin is now able to select musical scales.
	
2005-10-23  Toshiaki Katayama <k@bioruby.org>

	* lib/bio/util/color_scheme

	  Newly contributed Bio::ColorScheme

	* lib/bio/db/kegg/kgml.rb

	  Newly added KEGG KGML parser.

2005-10-05  Toshiaki Katayama <k@bioruby.org>

	* lib/bio/shell/plugin/midi.rb

	  Sequcne to MIDI plugin is contributed by Natsuhiro Ichinose

2005-09-25  Toshiaki Katayama <k@bioruby.org>

	* README.DEV

	  Newly added guideline document for the contributors.

	* README

	  Updated and added instructions on RubyGems.

2005-09-23  Toshiaki Katayama <k@bioruby.org>

	* bin/bioruby, lib/bio/shell.rb, lib/bio/shell/core.rb,
	  lib/bio/shell/session.rb, lib/bio/shell/plugin/seq.rb,
	  lib/bio/shell/flatfile.rb, lib/bio/shell/obda.rb

	  Newly added BioRuby shell, the command line user interface.
	  Try 'bioruby' command in your terminal.

	* doc/Changes-0.7.rd

	  Newly added document describing incompatible and important
	  changes between the BioRuby 0.6 and 0.7 versions.

	* lib/bio/sequence.rb

	  Bio::Sequence.guess, Bio::Sequence#guess methods are added
	  which guess the sequence type by following fomula (default
	  value for the threshold is 0.9).

	              number of ATGC
	  --------------------------------------- > threshold
	    number of other chars - number of N

2005-09-10  Naohisa Goto <ng@bioruby.org>

	* lib/bio.rb, lib/bio/appl/blast.rb, lib/bio/appl/blast/format0.rb,
	  lib/bio/appl/blast/report.rb, lib/bio/appl/clustalw.rb,
	  lib/bio/appl/fasta.rb, lib/bio/appl/fasta/format10.rb,
	  lib/bio/appl/hmmer.rb, lib/bio/appl/hmmer/report.rb,
	  lib/bio/appl/mafft.rb, lib/bio/appl/psort.rb,
	  lib/bio/appl/psort/report.rb, lib/bio/appl/sim4.rb,
	  lib/bio/db/genbank/ddbj.rb, lib/bio/io/flatfile/bdb.rb,
	  lib/bio/io/flatfile/index.rb, lib/bio/io/flatfile/indexer.rb

	  fixed autoload problem

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

	  Bio::Blast.reports method was moved from lib/bio/appl/blast/report.rb
	  to lib/bio/appl/blast.rb for autoload.

2005-08-31  Toshiaki Katayama <k@bioryby.org>

	* BioRuby 0.6.4 is released.

	* doc/KEGG_API.rd

	  Newly added English version of the KEGG API manual.

	* lib/bio/aa.rb

	  the 'one2name' method introduced in 0.6.3 is fixed and added 'one'
	  and 'three' methods as aliases for 'to_1' and 'to_3' methods.

2005-08-31  Naohisa Goto <ng@bioruby.org>

	* removed unused file lib/bio/appl/factory.rb
	  (the functionality had been integrated into lib/bio/command.rb)

	* doc/Tutorial.rd

	  Newly added an English translation of the Japanese tutorial.

2005-08-16  Naohisa Goto <ng@bioruby.org>

	* lib/bio/command.rb

	  Newly added Bio::Command::Tools module.
	  Bio::Command::Tools is a collection of useful methods
	  for execution of external commands.

	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
	  lib/bio/appl/hmmer.rb, lib/bio/io/fastacmd.rb

	  For security reason, shell special characters are escaped.

	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb, lib/bio/appl/hmmer.rb

	  Options are stored with an array (@options).
	  #options and #opions= methods are added.

	* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb

	  Bio::Blast.remote and Bio::Fasta.remote is fixed to work
	  with the recent change of the GenomeNet.

2005-08-11  Toshiaki Katayama <k@bioruby.org>

	* Sequence#to_re method to have compatibility with 0.6.2 for RNA

	* Fixed Bio::Fastacmd#fetch to work

	* Bio::Fastacmd and Bio::Bl2seq classes (introduced in 0.6.3) are
	  renamed to Bio::Blast::Fastacmd, Bio::Blast::Bl2seq respectively.

2005-08-09  Toshiaki Katayama <k@bioruby.org>

	* BioRuby 0.6.3 is released.

	  This version would be the final release to support Ruby 1.6 series
	  (as long as no serious bug is found:).

	* lib/bio/util/sirna.rb:

	  Newly added method for desing of siRNA, contributed by
	  Itoshi Nikaido.  The lib/bio/util/ directory if reserved
	  for bioinfomatics algorithms implemented by pure Ruby.

	* lib/bio/io/fastacmd.rb:

	  Newly added wrapper for NCBI fastacmd program, contributed by
	  Shinji Shigenobu.

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

	  Bug fixed by Masashi Fujita when the position of sequence
	  rarely becomes '-' instead of digits.

2005-08-08  Mitsuteru Nakao <n@bioruby.org>

        * lib/bio/db/embl/sptr.rb:

          Added Bio::SPTR#protein_name and Bio::SPTR#synoyms methods. 
          contributed by Luca Pireddu.

          Changed Bio::SPTR#gn, Bio::SPTR#gene_name and 
          Bio::SPTR#gene_names methods. contributed by Luca Pireddu.

2005-08-08  Naohisa Goto <ng@bioruby.org>

	* lib/bio/appl/bl2seq/report.rb:

	  Newly added bl2seq (BLAST 2 sequences) output parser.

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

	  Added `self.class::` before F0dbstat.new for bl2seq/report.rb

2005-08-07  Toshiaki Katayama <k@bioruby.org>

	* lib/bio/sequence.rb, lib/bio/data/na.rb, lib/bio/data/aa.rb:

	  Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have
	  Data module, and this module is included and extended to make
	  all methods as both of instance methods and class methods.

	  Bio::Sequence::NA and AA classes are rewrited (molecular_weight,
	  to_re methods) to use Bio::NucleicAcid.

	  Bio::Sequence::NA#molecular_weight method is fixed to subtract
	  two hydrogens per each base.

	* lib/bio/db/medline.rb: publication_type (pt) method is added.

2005-08-07  Naohisa Goto <ng@bioruby.org>

	* lib/bio/db/genbank/common.rb:

	  Avoid NoMethodError (private method `chomp` called for nil:NilClass)
	  when parsing features of

	    ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
            Salmonella_typhimurium_LT2/AE006468.gbk

2005-07-11  Toshiaki Katayama <k@bioruby.org>

	* bin/br_pmfetch.rb:

	  Added sort by page option (--sort page)

	* lib/io/higet.rb:

	  Newly added Bio::HGC::HiGet class for HiGet SOAP service.

2005-06-28  Toshiaki Katayama <k@bioruby.org>

	* gemspec.rb: newly added RubyGems spec file.

2005-06-21  Naohisa Goto <ng@bioruby.org>

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

	  Newly added support for reading BLAST -m 7 result files
	  through Bio::FlatFile by adding
	  DELIMITER = "</BlastOutput>\n" to Bio::Blast::Report class.
	  (Note that tab-delimited format (-m 8 and -m 9) are not yet
	  supported by Bio::FlatFile)

	* lib/bio/io/flatfile.rb:

	  Added file format autodetection of BLAST XML format.

2005-06-20  Naohisa Goto <ng@bioruby.org>

	* lib/bio/appl/blast/format0.rb: added 'to_s' to store original entry

2005-04-04  Mitsuteru Nakao <n@bioruby.org>

        * lib/bio/db/go.rb:

          Newly added Bio::GO::External2go class for parsing external2go file.

2005-03-10  Naohisa Goto <ng@bioruby.org>

	* lib/bio/io/flatfile.rb:

	  Added file format autodetection of Spidey (Bio::Spidey::Report).

2005-03-10  Naohisa Goto <ng@bioruby.org>

	* lib/bio/io/flatfile.rb:

	  Added file format autodetection for Bio::KEGG::KO,
	  Bio::KEGG::GLYCAN, Bio::KEGG::REACTION, Bio::Blat::Report
	  and Bio::Sim4::Report.

	  In order to distinguish Bio::KEGG::REACTION and 
	  Bio::KEGG::COMPOUND, autodetection regexp. of
	  Bio::KEGG::COMPOUND were modified.

2005-02-09  KATAYAMA Toshiaki <k@bioruby.org>

	* lib/bio/db/kegg/genes.rb:

	  Added cu method which returns codon usage in Hash for the
	  convenience (codon_usage method returns in Array or Fixnum).

2004-12-13  KATAYAMA Toshiaki <k@bioruby.org>

	* BioRuby 0.6.2 released.

	* test/all_tests.rb:

	  Unit tests for some classes are newly incorporated by
	  Moses Hohman.  You can try it by 'ruby install.rb test'

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

	  Newly added Spidey result parser class.

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

	  Newly added BLAT result parser class.

	* fixes and improvements:
	  * lib/bio/appl/blast/blast/format0.rb
	    * minor fix for the Blast default format parser
	  * lib/bio/alignment.rb
	    * Alignment class
	  * lib/bio/db/prosite.rb
	    * bug reported by Rolv Seehuus is fixed
	    * some methods are added

2004-10-25  KATAYAMA Toshiaki <k@bioruby.org>

	* lib/bio/db/{compound.rb,reaction.rb,glycan.rb}:

	  Newly added parser for KEGG REACTION and KEGG GLYCAN database
	  entries, fix for KEGG COMPOUND parser to support the new format.

2004-10-09  GOTO Naohisa <ng@bioruby.org>

	* lib/bio/appl/sim4.rb

	  Newly added sim4 wrapper class.
	  This is test version, specs would be changed frequently.

	* lib/bio/appl/sim4/report.rb

	  Newly added sim4 result parser class.

2004-08-25  KATAYAMA Toshiaki <k@bioruby.org>

	* BioRuby 0.6.1 released.
	  * fix for the packaging miss of 0.6.0
	  * bin/*.rb are renamed to bin/br_*.rb (similar to the BioPerl's
	    convention: bp_*.pl)

2004-08-24  KATAYAMA Toshiaki <k@bioruby.org>

	* BioRuby 0.6.0 released.
	  * many fixes for Ruby 1.8
	  * updated for genome.ad.jp -> genome.jp transition

	* lib/bio/db/pdb.rb

	  Newly added parser for PDB contributed by Alex Gutteridge (EBI).

	* lib/bio/data/codontable.rb

	  Bio::CodonTable is rewrited to be a class instead of static variable.
	  Now it can hold table definition, start codons, stop codons and
	  added methods to detect start/stop codons and reverse translation.

	  Also includes sample code to show codon table in ANSI colored
	  ascii art, have fun.

	* lib/bio/sequence.rb

	  Bio::Sequence::NA#translate is rewrited to accept an user defined
	  codon table as a Bio::CodonTable object and any character can be
	  specified for the unknown codon.  This method runs about 30% faster
	  than ever before.

	  Bio::Sequence::AA#to_re method is added for the symmetry.

	  Bio::Seq will be changed to hold generic rich sequence features.
	  This means Bio::Seq is no longer an alias of Bio::Sequence but
	  is a sequence object model, something like contents of a GenBank
	  entry, common in BioPerl, BioJava etc.

	* lib/bio/io/soapwsdl.rb

	  Newly added common interface for SOAP/WSDL in BioRuby
	  used by keggapi.rb, ddbjxml.rb.

	* lib/bio/io/keggapi.rb

	  Completely rewrited to support KEGG API v3.0

	* lib/bio/io/esoap.rb

	  Newly added client library for Entrez Utilities SOAP interface.

	* lib/bio/db/genbank, lib/bio/db/embl

	  Refactored to use common.rb as a common module.

	* bin/pmfetch.rb

	  Newly added command to search PubMed.

	* bin/biofetch.rb, flatfile.rb, biogetseq.rb

	  Renamed to have .rb suffix.

	* sample/biofetch.rb

	  Rewrited to use KEGG API instead of DBGET


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

