lightweight Ensembl feature object for Id mapping

modules/Bio/EnsEMBL/IdMapping/TinyFeature.pm

+package Bio::EnsEMBL::IdMapping::TinyFeature;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+sub new_fast {
+  my $class = shift;
+  my $array_ref = shift;
+  return bless $array_ref, $class;
+}
+
+
+sub id {
+  my $self = shift;
+  $self->[1] = shift if (@_);
+  return $self->[1];
+}
+
+
+sub stable_id {
+  my $self = shift;
+  $self->[2] = shift if (@_);
+  return $self->[2];
+}
+
+
+sub add_Transcript {
+  my $self = shift;
+  my $tr = shift;
+
+  unless ($self->[0] eq 'g' and $tr->[0] eq 'tr') {
+    throw('You can only add transcripts to a gene.');
+  }
+
+  push @{ $self->[9] }, $tr;
+}
+
+
+sub get_all_Transcripts {
+  my $self = shift;
+
+  throw('Only genes have transcripts.') unless ($self->[0] eq 'g'); 
+  
+  return $self->[9] || [];
+}
+
+
+sub add_Translation {
+  my $self = shift;
+  my $tl = shift;
+
+  unless ($self->[0] eq 'tr' and $tl->[0] eq 'tl') {
+    throw('You can only add a translation to a transcript.');
+  }
+
+  $self->[10] = $tl;
+}
+
+
+sub add_Exon {
+  my $self = shift;
+  my $exon = shift;
+
+  unless ($self->[0] eq 'tr' and $exon->[0] eq 'e') {
+    throw('You can only add exons to a transcript.');
+  }
+
+  push @{ $self->[11] }, $exon;
+}
+
+
+sub get_all_Exons {
+  my $self = shift;
+
+  throw('Only transcripts have exons.') unless ($self->[0] eq 'tr'); 
+  
+  return $self->[11] || [];
+}
+
+
+1;
+