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Commit a27ef2e0 authored by Ian Longden's avatar Ian Longden
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allow option info_type in getting xrefs

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modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+ 13
− 9
View file @ a27ef2e0
......@@ -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, $exDB );
......
modules/Bio/EnsEMBL/Gene.pm
+ 9
− 5
View file @ a27ef2e0
......@@ -435,16 +435,19 @@ sub add_DBEntry {
=cut
sub get_all_DBEntries {
my ($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;
......
modules/Bio/EnsEMBL/Transcript.pm
+ 7
− 2
View file @ a27ef2e0
......@@ -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} =
......
modules/Bio/EnsEMBL/Translation.pm
+ 5
− 1
View file @ a27ef2e0
......@@ -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} ||= [];
......
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