Raw content of Bio::EnsEMBL::Translation
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Translation - A class representing the translation of a
transcript
=head1 SYNOPSIS
my $translation = Bio::EnsEMBL::Translation->new(
-START_EXON => $exon1,
-END_EXON => $exon2,
-SEQ_START => 98,
-SEQ_END => 39
);
# stable ID setter
$translation->stable_id('ENSP00053458');
# get start and end position in start/end exons
my $start = $translation->start;
my $end = $translation->end;
=head1 DESCRIPTION
A Translation object defines the CDS and UTR regions of a Transcript
through the use of start_Exon/end_Exon, and start/end attributes.
=cut
package Bio::EnsEMBL::Translation;
use vars qw($AUTOLOAD @ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Storable;
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [-START_EXON] : The Exon object in which the translation (CDS) starts
Arg [-END_EXON] : The Exon object in which the translation (CDS) ends
Arg [-SEQ_START] : The offset in the start_Exon indicating the start
position of the CDS.
Arg [-SEQ_END] : The offset in the end_Exon indicating the end
position of the CDS.
Arg [-STABLE_ID] : The stable identifier for this Translation
Arg [-VERSION] : The version of the stable identifier
Arg [-DBID] : The internal identifier of this Translation
Arg [-ADAPTOR] : The TranslationAdaptor for this Translation
Arg [-SEQ] : Manually sets the peptide sequence of this translation.
May be useful if this translation is not stored in
a database.
Arg [-CREATED_DATE]: the date the translation was created
Arg [-MODIFIED_DATE]: the date the translation was modified
Example : my $tl = Bio::EnsEMBL::Translation->new
(-START_EXON => $ex1,
-END_EXON => $ex2,
-SEQ_START => 98,
-SEQ_END => 39);
Description: Constructor. Creates a new Translation object
Returntype : Bio::EnsEMBL::Translation
Exceptions : none
Caller : general
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my ( $start_exon, $end_exon, $seq_start, $seq_end,
$stable_id, $version, $dbID, $adaptor, $seq,
$created_date, $modified_date ) =
rearrange( [ "START_EXON", "END_EXON", "SEQ_START", "SEQ_END",
"STABLE_ID", "VERSION", "DBID", "ADAPTOR",
"SEQ", "CREATED_DATE", "MODIFIED_DATE" ], @_ );
my $self = bless {
'start_exon' => $start_exon,
'end_exon' => $end_exon,
'adaptor' => $adaptor,
'dbID' => $dbID,
'start' => $seq_start,
'end' => $seq_end,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date,
'modified_date' => $modified_date,
'seq' => $seq
}, $class;
return $self;
}
=head2 new_fast
Arg [1] : hashref to be blessed
Description: Construct a new Bio::EnsEMBL::Translation using the hashref.
Exceptions : none
Returntype : Bio::EnsEMBL::Translation
Caller : general, subclass constructors
Status : Stable
=cut
sub new_fast {
my $class = shift;
my $hashref = shift;
return bless $hashref, $class;
}
=head2 start
Arg [1] : (optional) int $start - start position to set
Example : $translation->start(17);
Description: Getter/setter for the value of start, which is a position within
the exon given by start_Exon.
If you need genomic coordinates, use the genomic_start()
method.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub start{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'start'} = $value;
}
return $obj->{'start'};
}
=head2 end
Arg [1] : (optional) int $end - end position to set
Example : $translation->end(8);
Description: Getter/setter for the value of end, which is a position within
the exon given by end_Exon.
If you need genomic coordinates, use the genomic_end()
method.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub end {
my $self = shift;
if( @_ ) {
my $value = shift;
$self->{'end'} = $value;
}
return $self->{'end'};
}
=head2 start_Exon
Arg [1] : (optional) Bio::EnsEMBL::Exon - start exon to assign
Example : $translation->start_Exon($exon1);
Description: Getter/setter for the value of start_Exon, which denotes the
exon at which translation starts (and within this exon, at the
position indicated by start, see above).
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
Status : Stable
=cut
sub start_Exon {
my $self = shift;
if( @_ ) {
my $value = shift;
if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
throw("Got to have an Exon object, not a $value");
}
$self->{'start_exon'} = $value;
}
return $self->{'start_exon'};
}
=head2 end_Exon
Arg [1] : (optional) Bio::EnsEMBL::Exon - start exon to assign
Example : $translation->start_Exon($exon1);
Description: Getter/setter for the value of end_Exon, which denotes the
exon at which translation ends (and within this exon, at the
position indicated by end, see above).
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
Status : Stable
=cut
sub end_Exon {
my $self = shift;
if( @_ ) {
my $value = shift;
if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
throw("Got to have an Exon object, not a $value");
}
$self->{'end_exon'} = $value;
}
return $self->{'end_exon'};
}
=head2 cdna_start
Arg [1] : (optional) Bio::EnsEMBL::Transcript $transcript
The transcript which this is a translation of.
Example : $translation_cdna_start = $translation->cdna_start();
Description : Returns the start position of the translation in cDNA
coordinates.
If no transcript is given, the method will use
TranscriptAdaptor->fetch_by_translation_id() to locate
the correct transcript.
Return type : Integer
Exceptions : Throws if the given (optional) argument is not a
transcript.
Caller : General
Status : At Risk (Under Development)
=cut
sub cdna_start {
my $self = shift;
my ($transcript) = @_;
if ( defined $transcript
&& ( !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
{
throw("Argument is not a transcript");
}
if ( !exists $self->{'cdna_start'} ) {
if ( !defined $transcript ) {
# We were not given a transcript, get the transcript out of
# the database.
my $transcript_adaptor =
$self->adaptor()->db()->get_TranscriptAdaptor();
$transcript =
$transcript_adaptor->fetch_by_translation_id(
$self->dbID() );
}
$self->{'cdna_start'} =
$self->start_Exon()->cdna_coding_start($transcript);
}
return $self->{'cdna_start'};
} ## end sub cdna_start
=head2 cdna_end
Arg [1] : (optional) Bio::EnsEMBL::Transcript $transcript
The transcript which this is a translation of.
Example : $translation_cdna_end = $translation->cdna_end();
Description : Returns the end position of the translation in cDNA
coordinates.
If no transcript is given, the method will use
TranscriptAdaptor->fetch_by_translation_id() to locate
the correct transcript.
Return type : Integer
Exceptions : Throws if the given (optional) argument is not a
transcript.
Caller : General
Status : At Risk (Under Development)
=cut
sub cdna_end {
my $self = shift;
my ($transcript) = @_;
if ( defined $transcript
&& ( !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
{
throw("Argument is not a transcript");
}
if ( !exists $self->{'cdna_end'} ) {
if ( !defined $transcript ) {
# We were not given a transcript, get the transcript out of
# the database.
my $transcript_adaptor =
$self->adaptor()->db()->get_TranscriptAdaptor();
$transcript =
$transcript_adaptor->fetch_by_translation_id(
$self->dbID() );
}
$self->{'cdna_end'} =
$self->end_Exon()->cdna_coding_end($transcript);
}
return $self->{'cdna_end'};
} ## end sub cdna_end
=head2 genomic_start
Args : None
Example : $translation_genomic_start =
$translation->genomic_start();
Description : Returns the start position of the translation in
genomic coordinates on the forward strand.
Return type : Integer
Exceptions : None
Caller : General
Status : At Risk (Under Development)
=cut
sub genomic_start {
my $self = shift;
if ( !exists $self->{'genomic_start'} ) {
if ( $self->start_Exon()->strand() >= 0 ) {
$self->{'genomic_start'} =
$self->start_Exon()->start() + ( $self->start() - 1 );
} else {
$self->{'genomic_start'} =
$self->end_Exon()->end() - ( $self->end() - 1 );
}
}
return $self->{'genomic_start'};
}
=head2 genomic_end
Args : None
Example : $translation_genomic_end = $translation->genomic_end();
Description : Returns the end position of the translation in genomic
coordinates on the forward strand.
Return type : Integer
Exceptions : None
Caller : General
Status : At Risk (Under Development)
=cut
sub genomic_end {
my $self = shift;
if ( !exists $self->{'genomic_end'} ) {
if ( $self->end_Exon()->strand() >= 0 ) {
$self->{'genomic_end'} =
$self->end_Exon()->start() + ( $self->end() - 1 );
} else {
$self->{'genomic_end'} =
$self->start_Exon()->end() - ( $self->start() - 1 );
}
}
return $self->{'genomic_end'};
}
=head2 version
Arg [1] : (optional) string $version - version to set
Example : $translation->version(2);
Description: Getter/setter for attribute version
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub version {
my $self = shift;
$self->{'version'} = shift if( @_ );
return $self->{'version'};
}
=head2 stable_id
Arg [1] : (optional) string $stable_id - stable ID to set
Example : $translation->stable_id('ENSP0059890');
Description: Getter/setter for attribute stable_id
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub stable_id {
my $self = shift;
$self->{'stable_id'} = shift if( @_ );
return $self->{'stable_id'};
}
=head2 created_date
Arg [1] : (optional) string $created_date - created date to set
Example : $translation->created_date('2007-01-10 20:52:00');
Description: Getter/setter for attribute created date
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub created_date {
my $self = shift;
$self->{'created_date'} = shift if ( @_ );
return $self->{'created_date'};
}
=head2 modified_date
Arg [1] : (optional) string $modified_date - modification date to set
Example : $translation->modified_date('2007-01-10 20:52:00');
Description: Getter/setter for attribute modified date
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub modified_date {
my $self = shift;
$self->{'modified_date'} = shift if ( @_ );
return $self->{'modified_date'};
}
=head2 transform
Arg [1] : hashref $old_new_exon_map
a hash that maps old to new exons for a whole gene
Description: maps start end end exon according to mapping table.
If an exon is not mapped, just keep the old one.
Returntype: none
Exceptions : none
Caller : Transcript->transform()
Status : Stable
=cut
sub transform {
my $self = shift;
my $href_exons = shift;
my $start_exon = $self->start_Exon();
my $end_exon = $self->end_Exon();
if ( exists $href_exons->{$start_exon} ) {
$self->start_Exon($href_exons->{$start_exon});
} else {
# do nothing, the start exon wasnt mapped
}
if ( exists $href_exons->{$end_exon} ) {
$self->end_Exon($href_exons->{$end_exon});
} else {
# do nothing, the end exon wasnt mapped
}
}
=head2 get_all_DBEntries
Arg [1] : (optional) $ex_db_exp - external db name
Example : @dbentries = @{$translation->get_all_DBEntries()};
Description: Retrieves DBEntries (xrefs) for this translation.
This method will attempt to lazy-load DBEntries from a
database if an adaptor is available and no DBEntries are present
on the translation (i.e. they have not already been added or
loaded).
Returntype : list reference to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : get_all_DBLinks, TranslationAdaptor::store
Status : Stable
=cut
sub get_all_DBEntries {
my $self = shift;
my $ex_db_exp = shift;
my $ex_db_type = shift;
my $cache_name = "dbentries";
if(defined($ex_db_exp)){
$cache_name .= $ex_db_exp;
}
if(defined($ex_db_type)){
$cache_name .= $ex_db_type;
}
# if not cached, retrieve all of the xrefs for this gene
if(!defined $self->{$cache_name}) {
my $adaptor = $self->adaptor();
my $dbID = $self->dbID();
return [] if(!$adaptor || !$dbID);
$self->{$cache_name} =
$self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp, $ex_db_type);
}
$self->{$cache_name} ||= [];
return $self->{$cache_name};
}
=head2 add_DBEntry
Arg [1] : Bio::EnsEMBL::DBEntry $dbe
The dbEntry to be added
Example : $translation->add_DBEntry($xref);
Description: Associates a DBEntry with this translation. Note that adding
DBEntries will prevent future lazy-loading of DBEntries for this
translation (see get_all_DBEntries).
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
Status : Stable
=cut
sub add_DBEntry {
my $self = shift;
my $dbe = shift;
unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
throw('Expected DBEntry argument');
}
$self->{'dbentries'} ||= [];
push @{$self->{'dbentries'}}, $dbe;
}
=head2 get_all_DBLinks
Arg [1] : see get_all_DBEntries
Example : see get_all_DBEntries
Description: This is here for consistancy with the Transcript and Gene
classes. It is a synonym for the get_all_DBEntries method.
Returntype : see get_all_DBEntries
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_DBLinks {
my $self = shift;
return $self->get_all_DBEntries(@_);
}
=head2 get_all_ProteinFeatures
Arg [1] : (optional) string $logic_name
The analysis logic_name of the features to retrieve. If not
specified, all features are retrieved instead.
Example : $features = $self->get_all_ProteinFeatures('PFam');
Description: Retrieves all ProteinFeatures associated with this
Translation. If a logic_name is specified, only features with
that logic_name are returned. If no logic_name is provided all
associated protein_features are returned.
ProteinFeatures are lazy-loaded from the database unless they
added manually to the Translation or had already been loaded.
Returntype : Bio::EnsEMBL::ProteinFeature
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_ProteinFeatures {
my $self = shift;
my $logic_name = shift;
if(!$self->{'protein_features'}) {
my $adaptor = $self->adaptor();
my $dbID = $self->dbID();
return [] if (!$adaptor || !$dbID);
my %hash;
$self->{'protein_features'} = \%hash;
my $pfa = $adaptor->db()->get_ProteinFeatureAdaptor();
my $name;
foreach my $f (@{$pfa->fetch_all_by_translation_id($dbID)}) {
my $analysis = $f->analysis();
if($analysis) {
$name = lc($f->analysis->logic_name());
} else {
warning("ProteinFeature has no attached analysis\n");
$name = '';
}
$hash{$name} ||= [];
push @{$hash{$name}}, $f;
}
}
# a specific type of protein feature was requested
if(defined($logic_name)) {
$logic_name = lc($logic_name);
return $self->{'protein_features'}->{$logic_name} || [];
}
my @features = ();
# all protein features were requested
foreach my $type (keys %{$self->{'protein_features'}}) {
push @features, @{$self->{'protein_features'}->{$type}};
}
return \@features;
}
=head2 get_all_DomainFeatures
Example : @domain_feats = @{$translation->get_all_DomainFeatures};
Description: A convenience method which retrieves all protein features
that are considered to be 'Domain' features. Features which
are 'domain' features are those with analysis logic names:
'pfscan', 'scanprosite', 'superfamily', 'pfam', 'prints',
'smart', 'pirsf', 'tigrfam'.
Returntype : listref of Bio::EnsEMBL::ProteinFeatures
Exceptions : none
Caller : webcode (protview)
Status : Stable
=cut
sub get_all_DomainFeatures{
my ($self) = @_;
my @features;
my @types = ('pfscan', #profile (prosite or pfam motifs)
'scanprosite', #prosite
'superfamily',
'pfam',
'smart',
'tigrfam',
'pirsf',
'prints');
foreach my $type (@types) {
push @features, @{$self->get_all_ProteinFeatures($type)};
}
return \@features;
}
=head2 add_ProteinFeature
Arg [1] : Bio::EnsEMBL::ProteinFeature $pf
The ProteinFeature to be added
Example : $translation->add_ProteinFeature($pf);
Description: Associates a ProteinFeature with this translation. Note that
adding ProteinFeatures will prevent future lazy-loading of
ProteinFeatures for this translation (see
get_all_ProteinFeatures).
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
Status : Stable
=cut
sub add_ProteinFeature {
my $self = shift;
my $pf = shift;
unless ($pf && ref($pf) && $pf->isa('Bio::EnsEMBL::ProteinFeature')) {
throw('Expected ProteinFeature argument');
}
my $analysis = $pf->analysis;
throw("ProteinFeature has no attached Analysis.") unless $analysis;
push @{ $self->{'protein_features'}->{$analysis->logic_name} }, $pf;
}
=head2 display_id
Example : print $translation->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For translations this is (depending on
availability and in this order) the stable Id, the dbID or an
empty string.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
=cut
sub display_id {
my $self = shift;
return $self->{'stable_id'} || $self->dbID || '';
}
=head2 length
Example : print "Peptide length =", $translation->length();
Description: Retrieves the length of the peptide sequence (i.e. number of
amino acids) represented by this Translation object.
Returntype : int
Exceptions : none
Caller : webcode (protview etc.)
Status : Stable
=cut
sub length {
my $self = shift;
my $seq = $self->seq();
return ($seq) ? CORE::length($seq) : 0;
}
=head2 seq
Example : print $translation->seq();
Description: Retrieves a string representation of the peptide sequence
of this Translation. This retrieves the transcript from the
database and gets its sequence, or retrieves the sequence which
was set via the constructor.
Returntype : string
Exceptions : warning if the sequence is not set and cannot be retrieved from
the database.
Caller : webcode (protview etc.)
Status : Stable
=cut
sub seq {
my $self = shift;
if(@_) {
$self->{'seq'} = shift;
return $self->{'seq'};
}
return $self->{'seq'} if($self->{'seq'});
my $adaptor = $self->{'adaptor'};
if(!$adaptor) {
warning("Cannot retrieve sequence from Translation - adaptor is not set.");
}
my $dbID = $self->{'dbID'};
if(!$dbID) {
warning("Cannot retrieve sequence from Translation - dbID is not set.");
}
my $tr_adaptor = $self->{'adaptor'}->db()->get_TranscriptAdaptor;
my $seq = $tr_adaptor->fetch_by_translation_id($dbID)->translate();
if($seq){
$self->{'seq'} = $seq->seq();
return $self->{'seq'};
}
else{
return ''; #empty string
}
}
=head2 get_all_Attributes
Arg [1] : optional string $attrib_code
The code of the attribute type to retrieve values for.
Example : ($sc_attr) = @{$tl->get_all_Attributes('_selenocysteine')};
@tl_attributes = @{$translation->get_all_Attributes()};
Description: Gets a list of Attributes of this translation.
Optionally just get Attrubutes for given code.
Recognized attribute "_selenocysteine"
Returntype : listref Bio::EnsEMBL::Attribute
Exceptions : warning if translation does not have attached adaptor and
attempts lazy load.
Caller : general, modify_translation
Status : Stable
=cut
sub get_all_Attributes {
my $self = shift;
my $attrib_code = shift;
if( ! exists $self->{'attributes' } ) {
if(!$self->adaptor() ) {
# warning('Cannot get attributes without an adaptor.');
return [];
}
my $aa = $self->adaptor->db->get_AttributeAdaptor();
$self->{'attributes'} = $aa->fetch_all_by_Translation( $self );
}
if( defined $attrib_code ) {
my @results = grep { uc($_->code()) eq uc($attrib_code) }
@{$self->{'attributes'}};
return \@results;
} else {
return $self->{'attributes'};
}
}
=head2 add_Attributes
Arg [1..N] : Bio::EnsEMBL::Attribute $attribute
Attributes to add.
Example : $translation->add_Attributes($selenocysteine_attribute);
Description: Adds an Attribute to the Translation. Usefull to
do _selenocysteine.
If you add an attribute before you retrieve any from database,
lazy load will be disabled.
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
Status : Stable
=cut
sub add_Attributes {
my $self = shift;
my @attribs = @_;
if( ! exists $self->{'attributes'} ) {
$self->{'attributes'} = [];
}
for my $attrib ( @attribs ) {
if( ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
throw( "Argument to add_Attribute must be a Bio::EnsEMBL::Attribute" );
}
push( @{$self->{'attributes'}}, $attrib );
$self->{seq}=undef;
}
}
=head2 get_all_SeqEdits
Example : my @seqeds = @{$transcript->get_all_SeqEdits()};
Description: Retrieves all post transcriptional sequence modifications for
this transcript.
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : none
Caller : spliced_seq()
Status : Stable
=cut
sub get_all_SeqEdits {
my $self = shift;
my @seqeds;
my $attribs;
my @edits = ('initial_met', '_selenocysteine', 'amino_acid_sub');
foreach my $edit(@edits){
$attribs = $self->get_all_Attributes($edit);
# convert attributes to SeqEdit objects
foreach my $a (@$attribs) {
push @seqeds, Bio::EnsEMBL::SeqEdit->new(-ATTRIB => $a);
}
}
return \@seqeds;
}
=head2 modify_translation
Arg [1] : Bio::Seq $peptide
Example : my $seq = Bio::Seq->new(-SEQ => $dna)->translate();
$translation->modify_translation($seq);
Description: Applies sequence edits such as selenocysteines to the Bio::Seq
peptide thats passed in
Returntype : Bio::Seq
Exceptions : none
Caller : Bio::EnsEMBL::Transcript->translate
Status : Stable
=cut
sub modify_translation {
my ($self, $seq) = @_;
my @seqeds = @{$self->get_all_SeqEdits()};
# sort in reverse order to avoid complication of adjusting downstream edits
@seqeds = sort {$b <=> $a} @seqeds;
# apply all edits
my $peptide = $seq->seq();
foreach my $se (@seqeds) {
$se->apply_edit(\$peptide);
}
$seq->seq($peptide);
return $seq;
}
=head2 temporary_id
Description: DEPRECATED This method should not be needed. Use dbID,
stable_id or something else.
=cut
sub temporary_id {
my $self = shift;
deprecate( "I cant see what a temporary_id is good for, please use " .
"dbID or stableID or\n try without an id." );
$self->{'temporary_id'} = shift if( @_ );
return $self->{'temporary_id'};
}
=head2 get_all_DASFactories
Function : Retrieves a listref of registered DAS objects
Returntype: DAS objects
Exceptions: none
Caller : webcode
Example : $dasref = $prot->get_all_DASFactories;
Status : Stable
=cut
sub get_all_DASFactories {
my $self = shift;
return [ $self->adaptor()->db()->_each_DASFeatureFactory ];
}
=head2 get_all_DAS_Features
Example : $features = $prot->get_all_DAS_Features;
Description: Retreives a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
(2) a pointer to the DAS stylesheet
Returntype : hashref of Bio::SeqFeatures
Exceptions : none
Caller : webcode
Status : Stable
=cut
sub get_all_DAS_Features{
my $self = shift;
my $db = $self->adaptor->db;
my $GeneAdaptor = $db->get_GeneAdaptor;
my $Gene = $GeneAdaptor->fetch_by_translation_stable_id($self->stable_id) || return;
my $slice = $Gene->feature_Slice;
return $self->SUPER::get_all_DAS_Features($slice);
}
1;
]]>