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lib/Bio/Das/ProServer/SourceAdaptor/simpledb.pm  view on Meta::CPAN

=head1 NAME

Bio::Das::ProServer::SourceAdaptor::simpledb - Builds simple DAS features from a database

=head1 VERSION

$LastChangedRevision: 687 $

=head1 SYNOPSIS

  Build simple segment:start:stop features from a basic database table structure:

  segmentid,featureid,start,end,type,note,link

=head1 DESCRIPTION

=head1 SUBROUTINES/METHODS

=head2 capabilities

=head2 build_features - Return an array of features based on a query given in the config file

  my @aFeatures = $oSourceAdaptor->build_features({
                                                   segment => $sSegmentId,
                                                   start   => $iSegmentStart, # Optional
                                                   end     => $iSegmentEnd,   # Optional
                                                   dsn     => $sDSN,          # if used as part of a hydra
                                                  });
=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

  [mysource]
  adaptor   = simpledb
  transport = dbi
  dbhost    = mysql.example.com
  dbport    = 3308
  dbname    = proserver
  dbuser    = proserverro
  dbpass    = topsecret
  dbtable   = mytable

  Or for SourceHydra use:
  [mysimplehydra]
  adaptor   = simpledb           # SourceAdaptor to clone
  hydra     = dbi                # Hydra implementation to use
  transport = dbi
  basename  = hydra              # dbi: basename for db tables containing servable data
  dbname    = proserver
  dbhost    = mysql.example.com
  dbuser    = proserverro
  dbpass    = topscret

=head1 DEPENDENCIES

 Bio::Das::ProServer::SourceAdaptor

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: Roger M Pettett$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

=cut