Raw content of Bio::EnsEMBL::ExternalData::DAS::FeatureGroup
<![CDATA[#
# EnsEMBL module for Bio::EnsEMBL::ExternalData::DAS::FeatureGroup
#
#
=head1 NAME
Bio::EnsEMBL::ExternalData::DAS::FeatureGroup
=head1 SYNOPSIS
my $g = Bio::EnsEMBL::ExternalData::DAS::FeatureGroup->new( {
'group_id' => 'group1',
'group_label' => 'Group 1',
'group_type' => 'transcript',
'note' => [ 'Something interesting' ],
'link' => [
{ 'href' => 'http://...',
'txt' => 'Group Link' }
],
'target' => [
{ 'target_id' => 'Seq 1',
'target_start' => '400',
'target_stop' => '800' }
]
} );
printf "Group ID: %s\n", $g->display_id();
printf "Group Label: %s\n", $g->display_label();
printf "Group Type: %s\n", $g->type_label();
for my $l ( @{ $g->links() } ) {
printf "Group Link: %s -> %s\n", $l->{'href'}, $l->{'txt'};
}
for my $n ( @{ $g->notes() } ) {
printf "Group Note: %s\n", $n;
}
for my $t ( @{ $g->targets() } ) {
printf "Group Target: %s:%s,%s\n", $t->{'target_id'},
$t->{'target_start'},
$t->{'target_stop'};
}
=head1 DESCRIPTION
An object representation of a DAS feature group.
The constructor is designed to work with the output of the DAS features command,
as obtained from the Bio::Das::Lite module.
See L<http://www.biodas.org/documents/spec.html> for more information about DAS
and its data types.
=head1 AUTHOR
Andy Jenkinson
=head1 CONTACT
Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
package Bio::EnsEMBL::ExternalData::DAS::FeatureGroup;
use strict;
use warnings;
=head2 new
Arg [1] : Hash reference (see SYNOPSIS for details and example)
Description: Constructs a new Bio::EnsEMBL::ExternalData::DAS::FeatureGroup.
Returntype : Bio::EnsEMBL::ExternalData::DAS::FeatureGroup
Exceptions : none
Caller : Bio::EnsEMBL::ExternalData::DAS::Feature
Status : Stable
=cut
sub new {
my $proto = shift;
my $class = ref $proto || $proto;
my $raw = shift;
my $self = {};
for my $key qw( group_id group_label
group_type
note link target ) {
$self->{$key} = $raw->{$key} if exists $raw->{$key};
}
bless $self, $class;
return $self;
}
=head2 display_id
Arg [1] : none
Example : print $g->display_id();
Description: This method returns the DAS group identifier.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub display_id {
my $self = shift;
return $self->{'group_id'};
}
=head2 display_label
Arg [1] : none
Example : print $g->display_label();
Description: This method returns the DAS group label.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub display_label {
my $self = shift;
return $self->{'group_label'} || $self->display_id;
}
=head2 type_label
Arg [1] : none
Example : print $g->type_label();
Description: This method returns the DAS group type label.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub type_label {
my $self = shift;
return $self->{'group_type'};
}
# The following are zero-to-many, thus return arrayrefs:
=head2 notes
Arg [1] : none
Example : @notes = @{ $g->notes() };
Description: This method returns the DAS group notes.
Returntype : arrayref of strings
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub notes {
my $self = shift;
return $self->{'note'} || [];
}
=head2 links
Arg [1] : none
Example : @links = @{ $g->links() };
Description: This method returns the DAS group external links.
Returntype : arrayref of { href=>$, txt=>$ } hashes
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub links {
my $self = shift;
return $self->{'link'} || [];
}
=head2 targets
Arg [1] : none
Example : @targets = @{ $g->targets() };
Description: This method returns the DAS group targets.
Returntype : arrayref of { target_id=>$, target_start=>$, target_stop=>$ } hashes
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub targets {
my $self = shift;
return $self->{'target'} || [];
}
1;]]>