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lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm  view on Meta::CPAN

      if ($Special_attributes{$tag}) {  # reserved attribute
	  push @{$reserved{$tag}},$value;
      } else {
	  push @{$unreserved{$tag}},$value;
      }
  }
  return (\%reserved,\%unreserved);
}

=item start_or_finish_sequence

  $loader->start_or_finish_sequence('Chr9')

This method is called at the beginning and end of a fasta section.

=cut

# sub start_or_finish_sequence { } inherited

=item load_sequence

  $loader->load_sequence('gatttcccaaa')

This method is called to load some amount of sequence after
start_or_finish_sequence() is first called.

=cut

# sub load_sequence { } inherited

=item open_fh

 my $io_file = $loader->open_fh($filehandle_or_path)

This method opens up the indicated file or pipe, using some
intelligence to recognized compressed files and URLs and doing the
right thing.

=cut

# sub open_fh { } inherited

# sub msg { } inherited

=item time

 my $time = $loader->time

This method returns the current time in seconds, using Time::HiRes if available.

=cut

# sub time { } inherited

=item unescape

 my $unescaped = GFF2Loader::unescape($escaped)

This is an internal utility.  It is the same as CGI::Util::unescape,
but doesn't change pluses into spaces and ignores unicode escapes.

=cut

# sub unescape { } inherited

1;
__END__

=back

=head1 BUGS

This is an early version, so there are certainly some bugs. Please
use the BioPerl bug tracking system to report bugs.

=head1 SEE ALSO

L<bioperl>,
L<Bio::DB::SeqFeature::Store>,
L<Bio::DB::SeqFeature::Segment>,
L<Bio::DB::SeqFeature::NormalizedFeature>,
L<Bio::DB::SeqFeature::GFF3Loader>,
L<Bio::DB::SeqFeature::Store::DBI::mysql>,
L<Bio::DB::SeqFeature::Store::berkeleydb>

=head1 AUTHOR

Lincoln Stein E<lt>lstein@cshl.orgE<gt>.

Copyright (c) 2006 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

=cut