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Ace/Sequence/GappedAlignment.pm  view on Meta::CPAN

Ace::Sequence::GappedAlignment - Gapped alignment object

=head1 SYNOPSIS

    # open database connection and get an Ace::Sequence object
    use Ace::Sequence;

    # get a megabase from the middle of chromosome I
    $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                              -db     => $db,
			      -offset => 3_000_000,
			      -length => 1_000_000);

    # get all the gapped alignments
    @alignments = $seq->alignments('EST_GENOME');

    # get the aligned segments from the first one
    @segs = $alignments[0]->segments;

    # get the position of the first aligned segment on the
    # source sequence:
    ($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);

    # get the target position for the first aligned segment
    ($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);

=head1 DESCRIPTION

Ace::Sequence::GappedAlignment is a subclass of
Ace::Sequence::Feature.  It inherits all the methods of
Ace::Sequence::Feature, but adds the ability to retrieve the positions
of the aligned segments.  Each segment is an Ace::Sequence::Feature,
from which you can retrieve the source and target coordinates.

=head1  OBJECT CREATION

You will not ordinarily create an I<Ace::Sequence::GappedAlignment>
object directly.  Instead, objects will be created in response to a
alignments() call to an I<Ace::Sequence> object.

=head1 OBJECT METHODS

Most methods are inherited from I<Ace::Sequence::Feature>.  The
following methods are also supported:

=over 4

=item segments()

  @segments = $gene->segments;

Return a list of Ace::Sequence::Feature objects corresponding to
similar segments.

=item relative()

  $relative = $gene->relative;
  $gene->relative(1);

This turns on and off relative coordinates.  By default, the exons and
intron features will be returned in the coordinate system used by the
gene.  If relative() is set to a true value, then coordinates will be
expressed as relative to the start of the gene.  The first exon will
(usually) be 1.

=head1 SEE ALSO

L<Ace>, L<Ace::Object>, L<Ace::Sequence>,L<Ace::Sequence::Homol>,
L<Ace::Sequence::Feature>, L<Ace::Sequence::FeatureList>, L<GFF>

=head1 AUTHOR

Lincoln Stein <lstein@cshl.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

Copyright (c) 1999, Lincoln D. Stein

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut