diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 0788283e4661bbbe72f2cc9aa35fbe6ef20d8d17..68edddc686e5548d0e7e1f7f1a9be10c6e3038d1 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -447,7 +447,7 @@ sub store {
$sth->finish();
#
# store the synonyms for the new xref
- #
+ #
my $synonym_check_sth = $self->prepare(
"SELECT xref_id, synonym
FROM external_synonym
@@ -463,7 +463,7 @@ sub store {
$synonym_check_sth->bind_param(1,$dbX,SQL_INTEGER);
$synonym_check_sth->bind_param(2,$syn,SQL_VARCHAR);
$synonym_check_sth->execute();
- my ($dbSyn) = $synonym_check_sth->fetchrow_array();
+ my ($dbSyn) = $synonym_check_sth->fetchrow_array();
$synonym_store_sth->bind_param(1,$dbX,SQL_INTEGER);
$synonym_store_sth->bind_param(2,$syn,SQL_VARCHAR);
$synonym_store_sth->execute() if(!$dbSyn);
@@ -521,7 +521,7 @@ INSERT IGNORE INTO object_xref
$sth->bind_param( 3, $ensembl_id, SQL_INTEGER );
$sth->bind_param( 4, $exObj->linkage_annotation(), SQL_VARCHAR );
$sth->bind_param( 5, $analysis_id, SQL_INTEGER);
-
+
#print "stored xref id $dbX in obejct_xref\n";
$sth->execute();
$exObj->dbID($dbX);
@@ -565,7 +565,7 @@ INSERT IGNORE INTO object_xref
foreach my $info (@{$exObj->get_all_linkage_info()}) {
my( $lt, $sourceXref ) = @{$info};
my $sourceXid = undef;
- if( $sourceXref ){
+ if( $sourceXref ){
$sourceXref->is_stored($self->dbc) || $sourceXref->store;
$sourceXid = $sourceXref->dbID;
}
@@ -575,7 +575,7 @@ INSERT IGNORE INTO object_xref
$sth->execute();
}
}
- }
+ }
return $dbX;
}
@@ -585,7 +585,7 @@ INSERT IGNORE INTO object_xref
Arg [1] : Bio::EnsEMBL::DBEntry $dbe
Example : if($dbID = $db_entry_adaptor->exists($dbe)) { do stuff; }
Description: Returns the db id of this DBEntry if it exists in this database
- otherwise returns undef. Exists is defined as an entry with
+ otherwise returns undef. Exists is defined as an entry with
the same external_db and display_id
Returntype : int
Exceptions : thrown on incorrect args
@@ -601,7 +601,7 @@ sub exists {
throw("arg must be a Bio::EnsEMBL::DBEntry not [$dbe]");
}
- my $sth = $self->prepare('SELECT x.xref_id
+ my $sth = $self->prepare('SELECT x.xref_id
FROM xref x, external_db xdb
WHERE x.external_db_id = xdb.external_db_id
AND x.display_label = ?
@@ -623,10 +623,10 @@ sub exists {
=head2 fetch_all_by_Gene
- Arg [1] : Bio::EnsEMBL::Gene $gene
+ Arg [1] : Bio::EnsEMBL::Gene $gene
(The gene to retrieve DBEntries for)
Arg [2] : optional external database name
- Arg [3] : optional external_db type
+ Arg [3] : optional external_db type
Example : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($gene)};
Description: This returns a list of DBEntries associated with this gene.
Note that this method was changed in release 15. Previously
@@ -656,9 +656,9 @@ sub fetch_all_by_Gene {
Arg [1] : Bio::EnsEMBL::Transcript
Arg [2] : optional external database name
- Arg [3] : optional external_db type
+ Arg [3] : optional external_db type
Example : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($trans)};
- Description: This returns a list of DBEntries associated with this
+ Description: This returns a list of DBEntries associated with this
transcript. Note that this method was changed in release 15.
Previously it set the DBLinks attribute of the gene passed in
to contain all of the gene, transcript, and translation xrefs
@@ -687,7 +687,7 @@ sub fetch_all_by_Transcript {
Arg [1] : Bio::EnsEMBL::Translation $trans
(The translation to fetch database entries for)
Arg [2] : optional external database name
- Arg [3] : optional externaldb type
+ Arg [3] : optional externaldb type
Example : @db_entries = @{$db_entry_adptr->fetch_all_by_Translation($trans)};
Description: Retrieves external database entries for an EnsEMBL translation
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
@@ -704,7 +704,7 @@ sub fetch_all_by_Translation {
if(!ref($trans) || !$trans->isa('Bio::EnsEMBL::Translation')) {
throw('Bio::EnsEMBL::Translation argument expected.');
}
- if( ! $trans->dbID ){
+ if( ! $trans->dbID ){
warning( "Cannot fetch_all_by_Translation without a dbID" );
return [];
}
@@ -818,15 +818,20 @@ sub remove_from_object {
=head2 _fetch_by_object_type
Arg [1] : string $ensID
- Arg [2] : string $ensType
- (object type to be returned)
+ Arg [2] : string $ensType (object type to be returned)
Arg [3] : optional $exdbname (external database name)
- Arf [4] : optional $exdb_type (external database type)
+ (may be an SQL pattern containing '%' which matches any
+ number of characters)
+ Arg [4] : optional $exdb_type (external database type)
+ (may be an SQL pattern containing '%' which matches any
+ number of characters)
Example : $self->_fetch_by_object_type( $translation_id, 'Translation' )
Description: Fetches DBEntry by Object type
NOTE: In a multi-species database, this method will
return all the entries matching the search criteria, not
just the ones associated with the current species.
+
+
Returntype : arrayref of DBEntry objects; may be of type IdentityXref if
there is mapping data, or OntologyXref if there is linkage data.
Exceptions : none
@@ -866,16 +871,35 @@ sub _fetch_by_object_type {
xref.info_type, xref.info_text, exDB.type, gx.source_xref_id,
oxr.linkage_annotation, xref.description
FROM (xref xref, external_db exDB, object_xref oxr)
- LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
+ LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
LEFT JOIN ontology_xref gx on gx.object_xref_id = oxr.object_xref_id
WHERE xref.xref_id = oxr.xref_id
- AND xref.external_db_id = exDB.external_db_id
+ 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);
- $sql .= " AND exDB.type like '" . $exdb_type . "' " if ($exdb_type);
+
+ if ( defined($exdbname) ) {
+ if ( index( $exdbname, '%' ) != -1 ) {
+ $sql .= " AND exDB.db_name = "
+ . $self->dbc()->db_handle()->quote( $exdbname, SQL_VARCHAR );
+ } else {
+ $sql .= " AND exDB.db_name LIKE "
+ . $self->dbc()->db_handle()->quote( $exdbname, SQL_VARCHAR );
+ }
+ }
+
+ if ( defined($exdb_type) ) {
+ if ( index( $exdb_type, '%' ) != -1 ) {
+ $sql .= " AND exDB.type = "
+ . $self->dbc()->db_handle()->quote( $exdb_type, SQL_VARCHAR );
+ } else {
+ $sql .= " AND exDB.type LIKE "
+ . $self->dbc()->db_handle()->quote( $exdb_type, SQL_VARCHAR );
+ }
+ }
+
my $sth = $self->prepare($sql);
$sth->bind_param( 1, $ensID, SQL_INTEGER );
@@ -1040,9 +1064,9 @@ sub list_gene_ids_by_external_db_id{
Arg [1] : string $external_name
Arg [2] : (optional) string $external_db_name
Example : @gene_ids = $dbea->list_gene_ids_by_extids('CDPX');
- Description: Retrieve a list of geneid by an external identifier that is
- linked to any of the genes transcripts, translations or the
- gene itself
+ Description: Retrieve a list of geneid by an external identifier that is
+ linked to any of the genes transcripts, translations or the
+ gene itself
Returntype : list of ints
Exceptions : none
Caller : unknown
@@ -1070,9 +1094,9 @@ sub list_gene_ids_by_extids {
Arg [1] : string $external_name
Arg [2] : (optional) string $external_db_name
Example : @tr_ids = $dbea->list_transcript_ids_by_extids('BCRA2');
- Description: Retrieve a list transcript ids by an external identifier that
- is linked to any of the genes transcripts, translations or the
- gene itself
+ Description: Retrieve a list transcript ids by an external identifier that
+ is linked to any of the genes transcripts, translations or the
+ gene itself
Returntype : list of ints
Exceptions : none
Caller : unknown
@@ -1276,7 +1300,7 @@ sub _type_by_external_id {
=head2 _type_by_external_db_id
- Arg [1] : string $type - external_db type
+ Arg [1] : integer $type - external_db_id
Arg [2] : string $ensType - ensembl_object_type
Arg [3] : (optional) string $extraType
other object type to be returned
@@ -1337,7 +1361,7 @@ sub _type_by_external_db_id{
);
}
- my $query =
+ my $query =
"SELECT $ID_sql
FROM $from_sql xref x, object_xref oxr
WHERE $where_sql x.external_db_id = ? AND
@@ -1460,7 +1484,7 @@ sub fetch_all_by_description {
if you want to use SQL patterns
Example : @unigene_refs = @{$db_entry_adaptor->fetch_all_by_source("%unigene%")};
- Description: Retrieves DBEntrys that match the source name.
+ Description: Retrieves DBEntrys that match the source name.
Returntype : ref to array of Bio::EnsEMBL::DBSQL::DBEntry
Exceptions : None.
Caller : General