Core 0.4.2 0.4.3 delta

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These are detailed notes on changes made between release-0-04-2 and release-0-04-3.

Bio::Root::Err
Added support for CGI scripts in Global.pm and Object.pm. Added name of executed script to Err::_set_context().
Incremented version number to 0.041.
Bio::Root::Global
Added support for CGI scripts in Global.pm and Object.pm. Added name of executed script to Err::_set_context().
Bio::Root::IOManager
Added timeout support to read().
Added new methods create_filehandle(), get_newline_char(), and taste_file(). create_filehandle() contains functionality that was formerly in IOManager::read(). Extracted it since get_newline_char() needs it.
Bio::Root::Object
Added support for CGI scripts in Global.pm and Object.pm. Added name of executed script to Err::_set_context().
Incremented version number to 0.041.
Comments added. Minor touch-ups.
Bio::Root::Utilities
Added/clarified comments regarding the use of the static objects imported by the :obj tag.
Added new methods create_filehandle(), get_newline_char(), and taste_file(). create_filehandle() contains functionality that was formerly in IOManager::read(). Extracted it since get_newline_char() needs it.
Bio::Seq
Added trunc function and exceptions to t/Seq.t
Migrating the CORE::reverse modification that were made in the main trunk into the 0.04 branch.
Bio::Tools::Blast
Adjusted the regexps used in _parse_hsp_string() to fix bug in recognition of HSP alignment data. Changed _display_hits() to use table_tiled() avoiding the buggy Sbjct::_display_stats(). Added deprecated note in Sbjct::display() and _display_stats().
Changed docs regarding latest version of BLAST-GP supported (2.0.8)
Bio::Tools::Fasta
_parse_seq_stream() now uses Bio::Root::Utilities::get_newline_char() instead of hardwiring.
Bio::Tools::Sigcleave
Adding to repository. Sigcleave.pm --> egcg sigcleave emulation code
Fixed some stuff so that warnings go away during 'make test'
Put old-school method for calculating weight table back in. The 'new' way was not generating accurate results. Oh well,at the expense of some speed we get more accurate scores.
Added Sigcleave.pm to the bioperl-0-04-bug branch
Removed all things associated with Sigcleave.pm from this bug branch :)
Bio::Tools::WWW
Added URL for Presage. Added distinct URLs for Pfam's US and UK locations.
Added/clarified comments regarding the use of the static objects imported by the :obj tag.
Method calls that return a Not_found_url also generate warnings to this effect.
Bio::Tools::pSW
Fixed documentation bug
Bio::UnivAln
Migrating the CORE::reverse modification that were made in the main trunk into the 0.04 branch.
Added a 1; before the token for safety. Added Georg Fuellen's disclaimer comment.
Makefile.PL
Added some changes and text for the next maintenance release, 0.04.3.
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