SubSlicedFeature.pm

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=head1 LICENSE
 
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Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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     http://www.apache.org/licenses/LICENSE-2.0
 
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=cut
 
 
=head1 CONTACT
 
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=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
 
package Bio::EnsEMBL::SubSlicedFeature;
 
use strict;
use warnings;
 
use Bio::EnsEMBL::Utils::Argument qw/rearrange/;
use base qw/Bio::EnsEMBL::Utils::Proxy/;
 
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;