diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 2ae8b8c9809b687dca2a0d78118d2f357a7173ba..1aba840199dbc21902837ff7692e9bcf8afbeb65 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -477,6 +477,7 @@ sub exists {
Arg [1] : Bio::EnsEMBL::Gene $gene
(The gene to retrieve DBEntries for)
Arg [2] : optional external database name
+ Arg [3] : optional info type
Example : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($gene)};
Description: This returns a list of DBEntries associated with this gene.
Note that this method was changed in release 15. Previously
@@ -492,13 +493,13 @@ sub exists {
=cut
sub fetch_all_by_Gene {
- my ( $self, $gene, $ex_db_reg ) = @_;
+ my ( $self, $gene, $ex_db_reg, $info_type ) = @_;
if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw("Bio::EnsEMBL::Gene argument expected.");
}
- return $self->_fetch_by_object_type($gene->dbID(), 'Gene', $ex_db_reg);
+ return $self->_fetch_by_object_type($gene->dbID(), 'Gene', $ex_db_reg, $info_type);
}
@@ -506,6 +507,7 @@ sub fetch_all_by_Gene {
Arg [1] : Bio::EnsEMBL::Transcript
Arg [2] : optional external database name
+ Arg [3] : optional info type
Example : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($trans)};
Description: This returns a list of DBEntries associated with this
transcript. Note that this method was changed in release 15.
@@ -521,13 +523,13 @@ sub fetch_all_by_Gene {
=cut
sub fetch_all_by_Transcript {
- my ( $self, $trans, $ex_db_reg ) = @_;
+ my ( $self, $trans, $ex_db_reg, $info_type ) = @_;
if(!ref($trans) || !$trans->isa('Bio::EnsEMBL::Transcript')) {
throw("Bio::EnsEMBL::Transcript argument expected.");
}
- return $self->_fetch_by_object_type( $trans->dbID(), 'Transcript', $ex_db_reg);
+ return $self->_fetch_by_object_type( $trans->dbID(), 'Transcript', $ex_db_reg, $info_type);
}
@@ -536,6 +538,7 @@ sub fetch_all_by_Transcript {
Arg [1] : Bio::EnsEMBL::Translation $trans
(The translation to fetch database entries for)
Arg [2] : optional external database name
+ Arg [3] : optional info type
Example : @db_entries = @{$db_entry_adptr->fetch_by_Translation($trans)};
Description: Retrieves external database entries for an EnsEMBL translation
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
@@ -547,7 +550,7 @@ sub fetch_all_by_Transcript {
=cut
sub fetch_all_by_Translation {
- my ( $self, $trans, $ex_db_reg ) = @_;
+ my ( $self, $trans, $ex_db_reg, $info_type ) = @_;
if(!ref($trans) || !$trans->isa('Bio::EnsEMBL::Translation')) {
throw('Bio::EnsEMBL::Translation argument expected.');
@@ -557,7 +560,7 @@ sub fetch_all_by_Translation {
return [];
}
- return $self->_fetch_by_object_type( $trans->dbID(), 'Translation', $ex_db_reg );
+ return $self->_fetch_by_object_type( $trans->dbID(), 'Translation', $ex_db_reg, $info_type );
}
@@ -681,7 +684,7 @@ sub remove_from_object {
=cut
sub _fetch_by_object_type {
- my ( $self, $ensID, $ensType, $exdbname ) = @_;
+ my ( $self, $ensID, $ensType, $exdbname, $infotype ) = @_;
my @out;
if (!defined($ensID)) {
@@ -713,6 +716,7 @@ sub _fetch_by_object_type {
AND oxr.ensembl_object_type = ?
SSQL
$sql .= " AND exDB.db_name like '".$exdbname."' " if($exdbname);
+ $sql .= " AND xref.info_type like '".$infotype."' " if($infotype);
my $sth = $self->prepare($sql);
$sth->bind_param(1,$ensID,SQL_INTEGER);
@@ -737,6 +741,8 @@ SSQL
'display_id' => $displayid,
'version' => $version,
'release' => $release,
+ 'info_type' => $info_type,
+ 'info_text' => $info_text,
'dbname' => $dbname );
@@ -778,8 +784,6 @@ SSQL
$exDB->display_id_linkable($display_id_linkable);
$exDB->priority($priority);
$exDB->db_display_name($exDB_db_display_name);
- $exDB->info_type($info_type);
- $exDB->info_text($info_text);
$exDB->type($type);
push( @out, $exDB );
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index ab32eb847e63abf89d82a601054c5e431b0bc512..155a50770d1d2439e1f5b26e8a38b0c4ecc7f8ab 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -435,16 +435,19 @@ sub add_DBEntry {
=cut
sub get_all_DBEntries {
- my ($self, $db_name_exp) = @_;
+ my ($self, $db_name_exp, $info_type) = @_;
my $cache_name = "dbentries";
if(defined($db_name_exp)){
$cache_name .= $db_name_exp;
}
+ if(defined($info_type)){
+ $cache_name .= $info_type;
+ }
# if not cached, retrieve all of the xrefs for this gene
if(!defined $self->{$cache_name} && $self->adaptor()) {
$self->{$cache_name} =
- $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Gene($self,$db_name_exp);
+ $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Gene($self,$db_name_exp,, $info_type);
}
$self->{$cache_name} ||= [];
@@ -480,15 +483,16 @@ sub get_all_DBEntries {
sub get_all_DBLinks {
my $self = shift;
my $db_name_exp = shift;
+ my $info_type = shift;
- my @links = @{$self->get_all_DBEntries($db_name_exp)};
+ my @links = @{$self->get_all_DBEntries($db_name_exp, $info_type)};
# add all of the transcript and translation xrefs to the return list
foreach my $transc (@{$self->get_all_Transcripts}) {
- push @links, @{$transc->get_all_DBEntries($db_name_exp)};
+ push @links, @{$transc->get_all_DBEntries($db_name_exp, $info_type)};
my $transl = $transc->translation();
- push @links, @{$transl->get_all_DBEntries($db_name_exp)} if($transl);
+ push @links, @{$transl->get_all_DBEntries($db_name_exp, $info_type)} if($transl);
}
return \@links;
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 76824ba7eec65c4edf3f92e2e8125cbe0ce7e24c..523735b36066e9d10f3a9aaa51298d93ad2909d9 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -181,13 +181,14 @@ sub new {
sub get_all_DBLinks {
my $self = shift;
my $ex_db_exp = shift;
+ my $info_type = shift;
my @links;
- push @links, @{$self->get_all_DBEntries($ex_db_exp)};
+ push @links, @{$self->get_all_DBEntries($ex_db_exp, $info_type)};
my $transl = $self->translation();
- push @links, @{$transl->get_all_DBEntries($ex_db_exp)} if($transl);
+ push @links, @{$transl->get_all_DBEntries($ex_db_exp, $info_type)} if($transl);
@links = sort {_compare_xrefs()} @links;
@@ -216,12 +217,16 @@ sub get_all_DBLinks {
sub get_all_DBEntries {
my $self = shift;
my $ex_db_exp = shift;
+ my $info_type = shift;
my $cache_name = "dbentries";
if(defined($ex_db_exp)){
$cache_name .= $ex_db_exp;
}
+ if(defined($info_type)){
+ $cache_name .= $info_type;
+ }
# if not cached, retrieve all of the xrefs for this gene
if(!defined $self->{$cache_name} && $self->adaptor()) {
$self->{$cache_name} =
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index b8e273b4c9509fb6d1bf1c72f1f4f348ad80dfec..cb5109328241f4fe1f5054cea7e7fb312389d167 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -512,12 +512,16 @@ sub transform {
sub get_all_DBEntries {
my $self = shift;
my $ex_db_exp = shift;
+ my $info_type = shift;
my $cache_name = "dbentries";
if(defined($ex_db_exp)){
$cache_name .= $ex_db_exp;
}
+ if(defined($info_type)){
+ $cache_name .= $info_type;
+ }
# if not cached, retrieve all of the xrefs for this gene
if(!defined $self->{$cache_name}) {
@@ -527,7 +531,7 @@ sub get_all_DBEntries {
return [] if(!$adaptor || !$dbID);
$self->{$cache_name} =
- $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp);
+ $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp, $info_type);
}
$self->{$cache_name} ||= [];