Bio-Das-ProServer

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  return keys %segs;
}

1;
__END__

=head1 NAME

Bio::Das::ProServer::SourceAdaptor::simple

=head1 VERSION

$Revision: 687 $

=head1 SYNOPSIS

Builds das from parser genesat tab-delimited flat files of the form:

 gene.name	gene.id

=head1 DESCRIPTION

=head1 SUBROUTINES/METHODS

=head2 init - Initialise capabilities for this source

  $oSourceAdaptor->init();

=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
                                                  });
  my @aFeatures = $oSourceAdaptor->build_features({
                                                   'feature_id' => $sFeatureId,
                                                  });

=head2 das_stylesheet - Return a DAS XML stylesheet

  Overrides the superclass method to return a hardcoded XML DAS stylesheet.

=head2 known_segments - Return a list of known entry point segment IDs

  Returns a list of all segment identifiers in the file.

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

 Bio::Das::ProServer::SourceAdaptor
 Carp
 POSIX

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

=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



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