Core 0.4.2 0.4.3 delta

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.