=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::SubSlicedFeature
=head1 SYNOPSIS
my $truncated_gene = Bio::EnsEMBL::Utils::SubSlicedFeature->new(
-start => 300,
-end => 10000,
-feature => $gene);
my $transcripts = $truncated_gene->get_all_Transcripts();
# list of transcripts is limited to those within the coordinates, rather
# than the original feature Slice.
=head1 DESCRIPTION
Alters the behaviour of a normal Feature object to act within a user-specified
sub-slice of of its boundaries. As it stands, this only affects get_all_*
methods, meaning that seq_region_start() and project() will work on original
coordinates.
=cut
$Bio::EnsEMBL::SubSlicedFeature::VERSION = '112.0_55'; # TRIAL
$Bio::EnsEMBL::SubSlicedFeature::VERSION = '112.055';
use strict;
sub new {
my ($class, @args) = @_;
my ($start,$end,$original_feature) = rearrange([qw/start end feature/], @args);
my $self = $class->SUPER::new($original_feature);
$self->{'start'} = $start;
$self->{'end'} = $end;
return $self;
}
# Required by Proxy to control scope of the autoloaded methods.
# Also intercepts calls to get methods that would access Slice
sub __resolver {
my ($self, $package_name, $method) = @_;
if ($method =~ /^get_all_/) {
# Call original method and filter results to Proxy coordinates
return sub {
my ($local_self, @args) = @_;
my $feature_list = $local_self->__proxy()->$method(@args);
my @short_list;
foreach my $feature (@$feature_list) {
if ($feature->start > $local_self->{'start'}
&& $feature->end < $local_self->{'end'}) {
push @short_list,$feature;
}
}
return \@short_list;
}
} else {
# No intervention required, call original object method
return sub {
my ($local_self, @args) = @_;
return $local_self->__proxy()->$method(@args);
};
}
}
1;