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Bio/SeqFeature/Lite.pm  view on Meta::CPAN

All methods are as described in L<Bio::SeqFeatureI> with the following additions:

=head2 The new() Constructor

 $feature = Bio::SeqFeature::Lite->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:

  -seq_id      the reference sequence
  -start       the start position of the feature
  -end         the stop position of the feature
  -stop        an alias for end
  -name        the feature name (returned by seqname())
  -type        the feature type (returned by primary_tag())
  -primary_tag the same as -type
  -source      the source tag
  -score       the feature score (for GFF compatibility)
  -desc        a description of the feature
  -segments    a list of subfeatures (see below)
  -subtype     the type to use when creating subfeatures
  -strand      the strand of the feature (one of -1, 0 or +1)
  -phase       the phase of the feature (0..2)
  -seq         a dna or protein sequence string to attach to feature
  -id          an alias for -name
  -seqname     an alias for -name
  -display_id  an alias for -name
  -display_name an alias for -name  (do you get the idea the API has changed?)
  -primary_id  unique database ID
  -url         a URL to link to when rendered with Bio::Graphics
  -attributes  a hashref of tag value attributes, in which the key is the tag
               and the value is an array reference of values
  -factory     a reference to a feature factory, used for compatibility with
               more obscure parts of Bio::DB::GFF

The subfeatures passed in -segments may be an array of
Bio::SeqFeature::Lite 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".

=head2 Non-SeqFeatureI methods

A number of new methods are provided for compatibility with
Ace::Sequence, which has a slightly different API from SeqFeatureI:

=over 4

=item url()

Get/set the URL that the graphical rendering of this feature will link to.

=item add_segment(@segments)

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.

=item segments()

An alias for sub_SeqFeature().

=item get_SeqFeatures()

Alias for sub_SeqFeature()

=item get_all_SeqFeatures()

Alias for sub_SeqFeature()

=item merged_segments()

Another alias for sub_SeqFeature().

=item stop()

An alias for end().

=item name()

An alias for seqname().

=item exons()

An alias for sub_SeqFeature() (you don't want to know why!)

=back

=cut

use strict;

use base qw(Bio::Root::Root Bio::SeqFeatureI Bio::LocationI Bio::SeqI);

*stop        = \&end;
*info        = \&name;
*seqname     = \&name;
*exons       = *sub_SeqFeature = *merged_segments = \&segments;
*get_all_SeqFeatures = *get_SeqFeatures = \&segments;
*method         = \&primary_tag;
*source         = \&source_tag;
*get_tag_values = \&each_tag_value;
*add_SeqFeature = \&add_segment;
*get_all_tags   = \&all_tags;
*abs_ref        = \&ref;

# implement Bio::SeqI and FeatureHolderI interface

sub primary_seq { return $_[0] }
sub annotation { 
    my ($obj,$value) = @_;
    if( defined $value ) {
	$obj->throw("object of class ".ref($value)." does not implement ".
		    "Bio::AnnotationCollectionI. Too bad.")
	    unless $value->isa("Bio::AnnotationCollectionI");
	$obj->{'_annotation'} = $value;
    } elsif( ! defined $obj->{'_annotation'}) {