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.\" ========================================================================
.\"
.IX Title "Ace::Sequence::GappedAlignment 3pm"
.TH Ace::Sequence::GappedAlignment 3pm "2018-11-01" "perl v5.28.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Ace::Sequence::GappedAlignment \- Gapped alignment object
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    # 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   => \*(AqCHROMOSOME_I,
\&                              \-db     => $db,
\&                              \-offset => 3_000_000,
\&                              \-length => 1_000_000);
\&
\&    # get all the gapped alignments
\&    @alignments = $seq\->alignments(\*(AqEST_GENOME\*(Aq);
\&
\&    # 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);
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "OBJECT CREATION"
.IX Header "OBJECT CREATION"
You will not ordinarily create an \fIAce::Sequence::GappedAlignment\fR
object directly.  Instead, objects will be created in response to a
\&\fBalignments()\fR call to an \fIAce::Sequence\fR object.
.SH "OBJECT METHODS"
.IX Header "OBJECT METHODS"
Most methods are inherited from \fIAce::Sequence::Feature\fR.  The
following methods are also supported:
.IP "\fBsegments()\fR" 4
.IX Item "segments()"
.Vb 1
\&  @segments = $gene\->segments;
.Ve
.Sp
Return a list of Ace::Sequence::Feature objects corresponding to
similar segments.
.IP "\fBrelative()\fR" 4
.IX Item "relative()"
.Vb 2
\&  $relative = $gene\->relative;
\&  $gene\->relative(1);
.Ve
.Sp
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 \fBrelative()\fR 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.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
Ace::Sequence::Feature, Ace::Sequence::FeatureList, \s-1GFF\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs\-mop.fr>
.PP
Copyright (c) 1999, Lincoln D. Stein
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 166:" 4
.IX Item "Around line 166:"
You forgot a '=back' before '=head1'