Raw content of Bio::EnsEMBL::Funcgen::AnnotatedFeature
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Funcgen::AnnotatedFeature
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::AnnotatedFeature - A module to represent a feature mapping as
predicted by the eFG pipeline.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::AnnotatedFeature;
my $feature = Bio::EnsEMBL::Funcgen::AnnotatedFeature->new(
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
-STRAND => -1,
-DISPLAY_LABEL => $text,
-SCORE => $score,
-FEATURE_SET => $fset,
);
=head1 DESCRIPTION
A AnnotatedFeature object represents the genomic placement of a prediction
generated by the eFG analysis pipeline, which may have originated from one or many
separate experiments.
=head1 AUTHOR
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::AnnotatedFeature;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Funcgen::SetFeature;
use Bio::EnsEMBL::Funcgen::FeatureType;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Funcgen::SetFeature);
=head2 new
Arg [-SCORE]: (optional) int - Score assigned by analysis pipeline
Arg [-ANALYSIS] : Bio::EnsEMBL::Analysis
Arg [-SLICE] : Bio::EnsEMBL::Slice - The slice on which this feature is.
Arg [-START] : int - The start coordinate of this feature relative to the start of the slice
it is sitting on. Coordinates start at 1 and are inclusive.
Arg [-END] : int -The end coordinate of this feature relative to the start of the slice
it is sitting on. Coordinates start at 1 and are inclusive.
Arg [-DISPLAY_LABEL]: string - Display label for this feature
Arg [-STRAND] : int - The orientation of this feature. Valid values are 1, -1 and 0.
Arg [-dbID] : (optional) int - Internal database ID.
Arg [-ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor - Database adaptor.
Example : my $feature = Bio::EnsEMBL::Funcgen::AnnotatedFeature->new(
-SLICE => $chr_1_slice,
-START => 1_000_000,
-END => 1_000_024,
-STRAND => -1,
-DISPLAY_LABEL => $text,
-SCORE => $score,
-FEATURE_SET => $fset,
);
Description: Constructor for AnnotatedFeature objects.
Returntype : Bio::EnsEMBL::Funcgen::AnnotatedFeature
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($score,)
= rearrange(['SCORE'], @_);
$self->score($score) if $score;
return $self;
}
=head2 score
Arg [1] : (optional) int - score
Example : my $score = $feature->score();
Description: Getter and setter for the score attribute for this feature.
Returntype : int
Exceptions : None
Caller : General
Status : Low Risk
=cut
sub score {
my $self = shift;
$self->{'score'} = shift if @_;
return $self->{'score'};
}
=head2 display_label
Arg [1] : string - display label
Example : my $label = $feature->display_label();
Description: Getter and setter for the display label of this feature.
Returntype : str
Exceptions : None
Caller : General
Status : Medium Risk
=cut
#Can This be mirrored in AnnotatedFeatureSet?
#this will over ride individual display_label for annotated features.
#set label could be used as track name and feature label used in zmenu?
#These should therefore be called track_label and display_label
sub display_label {
my $self = shift;
$self->{'display_label'} = shift if @_;
#auto generate here if not set in table
#need to go with one or other, or can we have both, split into diplay_name and display_label?
if(! $self->{'display_label'} && $self->adaptor()){
$self->{'display_label'} = $self->feature_type->name()." -";
$self->{'display_label'} .= " ".$self->cell_type->name();# if $self->cell_type->display_name();
$self->{'display_label'} .= " Enriched Site";
}
return $self->{'display_label'};
}
1;
]]>