[Bioperl-l] New code

[Steve Chervitz]

Bioperlers,

I just committed a bunch of code on the main trunk.
I've tried to add sufficient documentation to the modules as well as
sample code to make things clear. More will be added in the future,
particularly in the area of test code in the t/ directory.

Here are the areas of my additions/changes. Consult the docs in the
modules as well as the cvs logs for details.

Bio::Root::Interface
Bio::Root::Exception
Bio::Root::Root  - Added transparent support for exception throwing with
                   Graham Barr's Error.pm

Bio::Tools
  Bio::Tools::StateMachine
  Bio::Tools::StateMachine::AbstractStateMachine
  Bio::Tools::StateMachine::IOStatemachine

Bio::
  Bio::AnalysisParserI
  Bio::AnalysisResultI

Bio::SearchIO
  Bio::SearchIO::psiblast
  Bio::SearchIO::SearchWriterI
  Bio::SearchIO::Writer
  Bio::SearchIO::Writer::HSPTableWriter.pm
  Bio::SearchIO::Writer::HitTableWriter.pm
  Bio::SearchIO::Writer::ResultTableWriter.pm

Bio::Search:
  Bio::Search::DatabaseI
  Bio::Search::GenericDatabase
  Bio::Search::BlastUtils
  Bio::Search::Result::ResultI
  Bio::Search::Result::BlastResult
  Bio::Search::Hit::HitI
  Bio::Search::Hit::BlastHit
  Bio::Search::HSP::BlastHSP
  Bio::Search::HSP::HSPI

Bio::Factory:
  Bio::Factory::HitFactoryI.pm
  Bio::Factory::BlastHitFactory.pm
  Bio::Factory::ResultFactoryI.pm
  Bio::Factory::BlastResultFactory.pm

examples/searchio/
examples/searchio/writer
  Examples for using the Bio::SearchIO::Writer:: modules

examples/exception/
  Examples for using the new exception throwing capabilities
  added to Bio::Root::Root, and for using Error.pm in general.


If anything seems unclear or appears to be broken, don't hesitate to let
me know. (Note: I won't be able to respond to any emails until after 12/30).

Happy Holidays All,

Steve
steve_chervitz@affymetrix.com