Revision history for Bioperl core modules

0.6.1  Sun April 2 2000

   o Sequences can have Sequence Features attached to them
        - The sequence features can be read from or written to
          EMBL and GenBank style flat files

   o Objects for Annotation, including References (but not
     full medline abstracts), Database links and Comments are

   o A Species object to represent nodes on a taxonomy tree
     is provided

   o The ability to parse HMMER and Sim4 output has been added

   o The Blast parsing has been improved, with better PSI-BLAST
     support and better overall behaviour.

   o Flat file indexed databases provide both random access 
     and sequential access to their component sequences.

   o A CodonTable object has been written with all known 
     CodonTables accessible.

   o A number of new lightweight analysis tools have been
     added, such as molecular weight determination.

    The 0.6 release also has improved software engineering
   o The sequence objects have been rewritten, providing more
     maintainable and easier to implement objects. These
     objects are backwardly compatible with the 0.05.1 objects

   o Many objects are defined in terms of interfaces and then  
     a Perl implementation has been provided. The interfaces
     are found in the 'I' files (module names ending in 'I').

     This means that it is possible to wrap C/CORBA/SQL access
     as true "bioperl" objects, compatible with the rest of

   o The SeqIO system has been overhauled to provide better
     processing and perl-like automatic interpretation of <>
     over arguments.

   o Many more tests have been added (a total of 172 automatic
     tests are now run before release).

0.05.1 Tue Jun 29 05:30:44 1999
        - Central distribution now requires Perl 5.004. This was
          done to get around 5.003-based problems in Bio/Index/* 
          and SimpleAlign.
        - Various bug fixes in the Bio::Tools::Blast modules
          including better exception handling and PSI-Blast 
          support. See Bio/Tools/Blast/CHANGES for more.
        - Fixed the Parse mechanism in to use readseq.
	  Follow the instructions in README for how to install
	  it (basically, you have to edit
        - Improved documentation of, indicating where 
          objects are returned and where strings are returned.
        - Fixed uninitialized warnings in
        - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.

0.05  Sun Apr 25 01:14:11 1999
        - Bio::Tools::Blast modules have less memory problems
          and faster parsing. Webblast uses LWP and supports
          more functionality. See Bio/Tools/Blast/CHANGES for more.
        - The Bio::SeqIO system has been started, moving the
          sequence reformatting code out of the sequence object
        - The Bio::Index:: system has been started, providing
          generic index capabilities and specifically works for
          Fasta formatted databases and EMBL .dat formatted 
        - The Bio::DB:: system started, providing access to 
          databases, both via flat file + index (see above) and
          via http to NCBI
        - The scripts/ directory, where industrial strength scripts
          are put has been started.
        - Many changes - a better distribution all round.

0.04.4  Wed Feb 17 02:20:13 1999
	- Bug fixes in the Bio::Tools::Blast modules and
	  (see Bio::Tools::Blast::CHANGES).
        - Fixed a bug in Bio::Tools::Fasta::num_seqs().
        - Beefed up the t/Fasta.t test script.
        - Small fix in Bio::Seq::type() (now always returns a string).
        - Changed Bio::Root::Utilities::get_newline_char() to 
          get_newline() since it could return more than one char.
        - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
        - Changed default timeout to 20 seconds (was 3).
        - Moved lengthy modification notes to the bottom of some files.
	- Fixed SimpleAlign write_fasta bug.
	- Beefed up SimpleAlign.t test

0.04.3  Thu Feb  4 07:48:53 1999
        - and now detect when
          script is run as a CGI and suppress output that is only
          appropriate when running interactively.
        - Bio::Root::Err::_set_context() adds name of script ($0).
        - Added comments in and
          regarding the use of the static objects via the qw(:obj) tag.
        - Fixed the ambiguous reverse calls in and to 
          CORE::reverse, avoiding Perl warnings.
        - Bug fixes in Bio::Tools::Blast modules (version 0.074) and 
          example scripts (see Bio::Tools::Blast::CHANGES).
        - examples/seq/ no longer always warns about using 
          -prot or -nucl command-line arguments; only when using the 
          -debug argument.
        - Methods added to Bio::Root::Utilities: create_filehandle(), 
          get_newline_char(), and taste_file() to generalize filehandle 
          creation and autodetect newline characters in files/streams
          (see bug report #19).
        - Bio::Root::IOManager::read() now handles timeouts and uses
        - uses Utilities::get_newline_char() instead
          of hardwiring in "\n".
        - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW

0.04.2  Wed Dec 30 02:27:36 1998
        - Bug fixes in Bio::Tools::Blast modules, version 0.073
          (see Bio::Tools::Blast::CHANGES).
        - Changed reverse calls in Bio/ and Bio/
          to CORE::reverse (prevents ambiguous warnings with 5.005).
        - Appending '.tmp.bioperl' to temporary files created by
          Bio::Root::Utilities::compress() or uncompress() to
          make it easy to identify & cleanup these files as needed.
        - Developers: Created CVS branch release-0-04-bug from
          release-0-04-1. Before making bug fixes to the 0.04.1 release,
          be sure to cvs checkout this branch into a clean area.

0.04.1  Wed Dec 16 05:39:15 1998
        - Bug fixes in Bio::Tools::Blast modules, version 0.072
          (see Bio::Tools::Blast::CHANGES).
        - Compile/SW/Makefile.PL now removes *.o and *.a files 
          with make clean.

0.04  Tue Dec  8 07:49:19 1998
        - Lots of new modules added including:
           * Ewan Birney's,,
             and Bio/Compile directory containing XS-linked C code for
             creating Smith-Waterman sequence alignments from within Perl.
           * Steve Chervitz's Blast distribution has been incorporated.
           * Georg Fuellen's for multiple alignment objects.
        - Bio/examples directory for demo scripts for all included modules.
        - Bio/t directory containing test suit for all included modules.
        - For changes specific to the Blast-related modules prior to
          incorporation in this central distribution, see the CHANGES
          file in the Bio/Tools/Blast directory.
0.01  Tue Sep  8 14:23:22 1998
        - original version from central CVS tree; created by h2xs 1.18