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Ace::Sequence::GappedAlignment(3pm)			User Contributed Perl Documentation		       Ace::Sequence::GappedAlignment(3pm)

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'

perl v5.14.2							    2001-11-10				       Ace::Sequence::GappedAlignment(3pm)