NAME

       Ace::Sequence::GappedAlignment - Gapped alignment object

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);

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.

OBJECT CREATION

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

OBJECT METHODS

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

       segments()
             @segments = $gene->segments;

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

       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.

SEE ALSO

       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature,
       Ace::Sequence::FeatureList, GFF

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.

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 166:
           You forgot a '=back' before '=head1'