Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none
Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel
use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => 'transcript', -name => 'alpha-1 antitrypsin' ); # create a feature composed of multiple segments, all of type "similarity" $f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]], -name => 'ABC-3', -type => 'gapped_alignment', -subtype => 'similarity'); # build up a gene exon by exon $e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>'exon'); $e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>'exon'); $e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>'exon'); $f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>'gene');
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.
All methods are as described in Bio::SeqFeatureI with the following additions:
$feature = Bio::Graphics::Feature->new(@args);
This method creates a new feature object. You can create a simple feature that contains no subfeatures, or a hierarchically nested object.
Arguments are as follows:
-start the start position of the feature -stop the stop position of the feature -end an alias for stop -name the feature name (returned by seqname()) -type the feature type (returned by primary_tag()) -source the source tag -segments a list of subfeatures (see below) -subtype the type to use when creating subfeatures
The subfeatures passed in -segments may be an array of Bio::Graphics::Feature objects, or an array of [$start,$stop] pairs. Each pair should be a two-element array reference. In the latter case, the feature type passed in -subtype will be used when creating the subfeatures.
If no feature type is passed, then it defaults to "feature".
A number of new methods are provided for compatibility with Ace::Sequence, which has a slightly different API from SeqFeatureI:
Add one or more segments (a subfeature). Segments can either be Feature objects, or [start,stop] arrays, as in the -segments argument to new(). The feature endpoints are automatically adjusted.
An alias for sub_SeqFeature().
Another alias for sub_SeqFeature().
An alias for end().
An alias for seqname().
An alias for sub_SeqFeature() (you don't want to know why!)
Lincoln Stein <firstname.lastname@example.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
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.