Revision history for Bioperl core modules

0.04.3  Thu Feb  4 07:48:53 1999
        - Bio::Root::Object.pm and Global.pm 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 Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
          regarding the use of the static objects via the qw(:obj) tag.
        - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm 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/seqtools.pl 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
          Utilities::create_filehandle().
        - Bio::Tools::Fasta.pm 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/Seq.pm and Bio/UnivAln.pm
          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 Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
             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 Bio::UnivAln.pm 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