From ecd21be477ae127db4a2c05b4bb5f914163a0c22 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 3 Jan 2007 13:34:48 +0000
Subject: [PATCH] Added optional argument to get_all_DBEntries and
get_all_DBLinks which is the database name. Use like in sql statment so
percentage sign can be used for wild cards etc.
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 25 ++++++++++------
modules/Bio/EnsEMBL/Gene.pm | 32 ++++++++++++++-------
modules/Bio/EnsEMBL/Transcript.pm | 21 +++++++++-----
modules/Bio/EnsEMBL/Translation.pm | 17 +++++++----
4 files changed, 64 insertions(+), 31 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index f0f80fafb5..e4994a6e5f 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -474,6 +474,7 @@ sub exists {
Arg [1] : Bio::EnsEMBL::Gene $gene
(The gene to retrieve DBEntries for)
+ Arg [2] : optional external database name
Example : @db_entries = @{$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
@@ -489,19 +490,20 @@ sub exists {
=cut
sub fetch_all_by_Gene {
- my ( $self, $gene ) = @_;
+ my ( $self, $gene, $ex_db_reg ) = @_;
if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw("Bio::EnsEMBL::Gene argument expected.");
}
- return $self->_fetch_by_object_type($gene->dbID(), 'Gene');
+ return $self->_fetch_by_object_type($gene->dbID(), 'Gene', $ex_db_reg);
}
=head2 fetch_all_by_Transcript
Arg [1] : Bio::EnsEMBL::Transcript
+ Arg [2] : optional external database name
Example : @db_entries = @{$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.
@@ -517,13 +519,13 @@ sub fetch_all_by_Gene {
=cut
sub fetch_all_by_Transcript {
- my ( $self, $trans ) = @_;
+ my ( $self, $trans, $ex_db_reg ) = @_;
if(!ref($trans) || !$trans->isa('Bio::EnsEMBL::Transcript')) {
throw("Bio::EnsEMBL::Transcript argument expected.");
}
- return $self->_fetch_by_object_type( $trans->dbID(), 'Transcript');
+ return $self->_fetch_by_object_type( $trans->dbID(), 'Transcript', $ex_db_reg);
}
@@ -531,6 +533,7 @@ sub fetch_all_by_Transcript {
Arg [1] : Bio::EnsEMBL::Translation $trans
(The translation to fetch database entries for)
+ Arg [2] : optional external database name
Example : @db_entries = @{$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
@@ -542,7 +545,7 @@ sub fetch_all_by_Transcript {
=cut
sub fetch_all_by_Translation {
- my ( $self, $trans ) = @_;
+ my ( $self, $trans, $ex_db_reg ) = @_;
if(!ref($trans) || !$trans->isa('Bio::EnsEMBL::Translation')) {
throw('Bio::EnsEMBL::Translation argument expected.');
@@ -551,7 +554,7 @@ sub fetch_all_by_Translation {
warning( "Cannot fetch_all_by_Translation without a dbID" );
return [];
}
- return $self->_fetch_by_object_type( $trans->dbID(), 'Translation' );
+ return $self->_fetch_by_object_type( $trans->dbID(), 'Translation', $ex_db_reg );
}
@@ -661,6 +664,7 @@ sub remove_from_object {
Arg [1] : string $ensID
Arg [2] : string $ensType
(object type to be returned)
+ Arg [3] : optional $exdbname (external database name)
Example : $self->_fetch_by_object_type( $translation_id, 'Translation' )
Description: Fetches DBEntry by Object type
Returntype : arrayref of DBEntry objects; may be of type IdentityXref if
@@ -674,7 +678,7 @@ sub remove_from_object {
=cut
sub _fetch_by_object_type {
- my ( $self, $ensID, $ensType ) = @_;
+ my ( $self, $ensID, $ensType, $exdbname ) = @_;
my @out;
if (!defined($ensID)) {
@@ -683,7 +687,8 @@ sub _fetch_by_object_type {
if (!defined($ensType)) {
throw("Can't fetch_by_EnsObject_type without a type");
}
- my $sth = $self->prepare("
+# my $sth = $self->prepare("
+ my $sql = (<<SSQL);
SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
@@ -703,7 +708,9 @@ sub _fetch_by_object_type {
AND xref.external_db_id = exDB.external_db_id
AND oxr.ensembl_id = ?
AND oxr.ensembl_object_type = ?
- ");
+SSQL
+ $sql .= " AND exDB.db_name like '".$exdbname."' " if($exdbname);
+ my $sth = $self->prepare($sql);
$sth->bind_param(1,$ensID,SQL_INTEGER);
$sth->bind_param(2,$ensType,SQL_VARCHAR);
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index cc863c5379..90c2564d15 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -435,23 +435,29 @@ sub add_DBEntry {
=cut
sub get_all_DBEntries {
- my $self = shift;
+ my ($self, $db_name_exp) = @_;
+ my $cache_name = "dbentries";
+ if(defined($db_name_exp)){
+ $cache_name .= $db_name_exp;
+ }
# if not cached, retrieve all of the xrefs for this gene
- if(!defined $self->{'dbentries'} && $self->adaptor()) {
- $self->{'dbentries'} =
- $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Gene($self);
+ if(!defined $self->{$cache_name} && $self->adaptor()) {
+ $self->{$cache_name} =
+ $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Gene($self,$db_name_exp);
}
- $self->{'dbentries'} ||= [];
+ $self->{$cache_name} ||= [];
- return $self->{'dbentries'};
+ return $self->{$cache_name};
}
=head2 get_all_DBLinks
Example : @dblinks = @{ $gene->get_all_DBLinks };
+ : @dblinks = @{ $gene->get_all_DBLinks("Uniprot%") };
+ Arg [1] : <optional> database name use % for wild card as sent to sql directly
Description: Retrieves _all_ related DBEntries for this gene. This includes
all DBEntries that are associated with the transcripts and
corresponding translations of this gene.
@@ -459,6 +465,11 @@ sub get_all_DBEntries {
If you only want to retrieve the DBEntries associated with the
gene (and not the transcript and translations) then you should
use the get_all_DBEntries call instead.
+
+ Note: Each entry may be listed more than once. No uniqueness checks are done.
+ Also if you put in an incorrect external database name no checks are done
+ to see if this exists, you will just get an empty list.
+
Returntype : Listref of Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : general
@@ -468,15 +479,16 @@ sub get_all_DBEntries {
sub get_all_DBLinks {
my $self = shift;
+ my $db_name_exp = shift;
- my @links = @{$self->get_all_DBEntries()};
+ my @links = @{$self->get_all_DBEntries($db_name_exp)};
# 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};
+ foreach my $transc (@{$self->get_all_Transcripts}) {
+ push @links, @{$transc->get_all_DBEntries($db_name_exp)};
my $transl = $transc->translation();
- push @links, @{$transl->get_all_DBEntries} if($transl);
+ push @links, @{$transl->get_all_DBEntries($db_name_exp)} if($transl);
}
return \@links;
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index c2a0ea680c..31ff92ffe2 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -180,13 +180,14 @@ sub new {
sub get_all_DBLinks {
my $self = shift;
+ my $ex_db_exp = shift;
my @links;
- push @links, @{$self->get_all_DBEntries};
+ push @links, @{$self->get_all_DBEntries($ex_db_exp)};
my $transl = $self->translation();
- push @links, @{$transl->get_all_DBEntries} if($transl);
+ push @links, @{$transl->get_all_DBEntries($ex_db_exp)} if($transl);
@links = sort {_compare_xrefs()} @links;
@@ -214,16 +215,22 @@ sub get_all_DBLinks {
sub get_all_DBEntries {
my $self = shift;
+ my $ex_db_exp = shift;
+ my $cache_name = "dbentries";
+
+ if(defined($ex_db_exp)){
+ $cache_name .= $ex_db_exp;
+ }
# if not cached, retrieve all of the xrefs for this gene
- if(!defined $self->{'dbentries'} && $self->adaptor()) {
- $self->{'dbentries'} =
- $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Transcript($self);
+ if(!defined $self->{$cache_name} && $self->adaptor()) {
+ $self->{$cache_name} =
+ $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Transcript($self, $ex_db_exp);
}
- $self->{'dbentries'} ||= [];
+ $self->{$cache_name} ||= [];
- return $self->{'dbentries'};
+ return $self->{$cache_name};
}
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index f0f3908483..5a218516e7 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -337,21 +337,28 @@ sub transform {
sub get_all_DBEntries {
my $self = shift;
+ my $ex_db_exp = shift;
+
+ my $cache_name = "dbentries";
+
+ if(defined($ex_db_exp)){
+ $cache_name .= $ex_db_exp;
+ }
#if not cached, retrieve all of the xrefs for this gene
- if(!defined $self->{'dbentries'}) {
+ if(!defined $self->{$cache_name}) {
my $adaptor = $self->adaptor();
my $dbID = $self->dbID();
return [] if(!$adaptor || !$dbID);
- $self->{'dbentries'} =
- $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self);
+ $self->{$cache_name} =
+ $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp);
}
- $self->{'dbentries'} ||= [];
+ $self->{$cache_name} ||= [];
- return $self->{'dbentries'};
+ return $self->{$cache_name};
}
--
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