From ec038cbb7aff7ae3a103ea16381bee02856d0954 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 12 Oct 2006 14:53:44 +0000
Subject: [PATCH] Removed xref priority.
---
modules/Bio/EnsEMBL/DBEntry.pm | 40 +++------------------
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 32 +++++++----------
modules/t/dbEntries.t | 22 ++++--------
3 files changed, 24 insertions(+), 70 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBEntry.pm b/modules/Bio/EnsEMBL/DBEntry.pm
index 2dc2a846b6..adcedbd995 100644
--- a/modules/Bio/EnsEMBL/DBEntry.pm
+++ b/modules/Bio/EnsEMBL/DBEntry.pm
@@ -84,15 +84,14 @@ sub new_fast {
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
- -info_text => $info_text,
- -xref_priority => $xref_priority);
+ -info_text => $info_text);
Description: Creates a new DBEntry object
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : Bio::EnsEMBL::DBEntryAdaptor
Status : At Risk
Due to 'PRIMARY_ID_LINKABLE','DISPLAY_ID_LINKABLE','PRIORITY',
- 'INFO_TYPE', 'INFO_TEXT', ''DB_DISPLAY_NAME', 'XREF_PRIORITY'
+ 'INFO_TYPE', 'INFO_TEXT', ''DB_DISPLAY_NAME'
being under development - if you don't use any of these the
method can be considered Stable
@@ -106,12 +105,11 @@ sub new {
my ( $adaptor, $dbID, $primary_id, $version,
$dbname, $release, $display_id, $description,
$primary_id_linkable, $display_id_linkable, $priority,
- $db_display_name, $info_type, $info_text, $xref_priority) =
+ $db_display_name, $info_type, $info_text) =
rearrange ( ['ADAPTOR','DBID','PRIMARY_ID','VERSION',
'DBNAME','RELEASE','DISPLAY_ID','DESCRIPTION',
'PRIMARY_ID_LINKABLE','DISPLAY_ID_LINKABLE','PRIORITY',
- 'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT',
- 'XREF_PRIORITY'], @args );
+ 'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT'], @args );
$self->{'adaptor'} = $adaptor;
$self->{'dbID'} = $dbID;
@@ -129,7 +127,6 @@ sub new {
if( defined $db_display_name) { $self->db_display_name($db_display_name) }
if( defined $info_type) { $self->info_type($info_type) }
if( defined $info_text) { $self->info_text($info_text) }
- if( defined $xref_priority) { $self->xref_priority($xref_priority) }
return $self;
}
@@ -380,9 +377,7 @@ sub display_id_linkable {
Arg [1] : int $priority
Example : none
Priority : Getter/setter for attribute 'priority'. Note this
- is the priority from the external_db table; if you
- require the priority from the xref table, us the
- xref_priority attribute instead.
+ is the priority from the external_db table.
Returntype : String
Exceptions : none
Caller : general
@@ -556,31 +551,6 @@ sub status{
return $self->{status};
}
-
-=head2 xref_priority
-
- Arg [1] : int $xref_priority
- Example : none
- Priority : Getter/setter for attribute 'xref_priority'. Note
- that this is the priority from the xref table; if
- you require the priority from the external_db table,
- use the priority attribute instead.
- Returntype : String
- Exceptions : none
- Caller : general
- Status : At Risk
- : due to it being under development
-
-=cut
-
-sub xref_priority {
- my ( $self, $arg ) = @_;
- if( defined $arg ) {
- $self->{xref_priority} = $arg;
- }
- return $self->{xref_priority};
-}
-
=head1 DEPRECATED METHODS
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 077c6299e4..f0f80fafb5 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -67,7 +67,7 @@ sub fetch_by_dbID {
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
- xref.info_type, xref.info_text, xref.priority
+ xref.info_type, xref.info_text
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.xref_id = ?
@@ -82,7 +82,7 @@ sub fetch_by_dbID {
my ( $refID, $dbprimaryId, $displayid, $version, $desc,
$primary_id_linkable, $display_id_linkable, $priority,
$dbname, $db_display_name, $release, $synonym,
- $info_type, $info_text, $xref_priority) = @$arrayref;
+ $info_type, $info_text) = @$arrayref;
if(!$exDB) {
$exDB = Bio::EnsEMBL::DBEntry->new
@@ -98,8 +98,7 @@ sub fetch_by_dbID {
-priority => $priority,
-db_display_name => $db_display_name,
-info_type => $info_type,
- -info_text => $info_text,
- -xref_priority => $xref_priority);
+ -info_text => $info_text);
$exDB->description( $desc ) if ( $desc );
}
@@ -142,7 +141,7 @@ sub fetch_by_db_accession {
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
- xref.info_type, xref.info_text, xref.priority
+ xref.info_type, xref.info_text
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.dbprimary_acc = ?
@@ -173,7 +172,7 @@ sub fetch_by_db_accession {
while ( my $arrayref = $sth->fetchrow_arrayref()){
my ( $dbID, $dbprimaryId, $displayid, $version, $desc,
$primary_id_linkable, $display_id_linkable, $priority, $dbname, $db_display_name,
- $release, $synonym, $info_type, $info_text, $xref_priority) = @$arrayref;
+ $release, $synonym, $info_type, $info_text) = @$arrayref;
if(!$exDB) {
$exDB = Bio::EnsEMBL::DBEntry->new
@@ -189,8 +188,7 @@ sub fetch_by_db_accession {
-priority => $priority,
-db_display_name=>$db_display_name,
-info_type => $info_type,
- -info_text => $info_text,
- -xref_priority => $xref_priority);
+ -info_text => $info_text);
$exDB->description( $desc ) if ( $desc );
}
@@ -309,8 +307,7 @@ sub store {
description = ?,
external_db_id = ?,
info_type = ?,
- info_text = ?,
- priority = ?");
+ info_text = ?");
$sth->bind_param(1, $exObj->primary_id,SQL_VARCHAR);
$sth->bind_param(2, $exObj->display_id,SQL_VARCHAR);
$sth->bind_param(3, $exObj->version,SQL_VARCHAR);
@@ -318,7 +315,6 @@ sub store {
$sth->bind_param(5, $dbRef,SQL_INTEGER);
$sth->bind_param(6, $exObj->info_type, SQL_VARCHAR);
$sth->bind_param(7, $exObj->info_text, SQL_VARCHAR);
- $sth->bind_param(8, 1,SQL_INTEGER); # XXX remove this!
$sth->execute();
@@ -698,7 +694,7 @@ sub _fetch_by_object_type {
idt.hit_end, idt.translation_start, idt.translation_end,
idt.cigar_line, idt.score, idt.evalue, idt.analysis_id,
gx.linkage_type,
- xref.info_type, xref.info_text, xref.priority
+ xref.info_type, xref.info_text
FROM (xref xref, external_db exDB, object_xref oxr)
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
@@ -722,7 +718,7 @@ sub _fetch_by_object_type {
$synonym, $queryid, $targetid, $query_start, $query_end,
$translation_start, $translation_end, $cigar_line,
$score, $evalue, $analysis_id, $linkage_type,
- $info_type, $info_text, $xref_priority) = @$arrRef;
+ $info_type, $info_text) = @$arrRef;
my %obj_hash = (
'adaptor' => $self,
@@ -774,7 +770,6 @@ sub _fetch_by_object_type {
$exDB->db_display_name($exDB_db_display_name);
$exDB->info_type($info_type);
$exDB->info_text($info_text);
- $exDB->xref_priority($xref_priority);
push( @out, $exDB );
$seen{$refID} = $exDB;
@@ -1101,10 +1096,10 @@ sub fetch_all_by_description {
xref.version, xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
- xref.info_type, xref.info_text, xref.priority
+ xref.info_type, xref.info_text
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
- WHERE xref.description like ?
+ WHERE xref.description like ?
AND xref.external_db_id = exDB.external_db_id";
if(defined($dbname)){
@@ -1120,7 +1115,7 @@ sub fetch_all_by_description {
while ( my $arrayref = $sth->fetchrow_arrayref()){
my ( $dbID, $dbprimaryId, $displayid, $version, $desc,
$primary_id_linkable, $display_id_linkable, $priority, $dbname,$db_display_name,
- $release, $synonym, $info_type, $info_text, $xref_priority) = @$arrayref;
+ $release, $synonym, $info_type, $info_text) = @$arrayref;
my $exDB = Bio::EnsEMBL::DBEntry->new
( -adaptor => $self,
@@ -1135,8 +1130,7 @@ sub fetch_all_by_description {
-priority => $priority,
-db_display_name=>$db_display_name,
-info_type => $info_type,
- -info_text => $info_text,
- -xref_priority => $xref_priority);
+ -info_text => $info_text);
$exDB->description( $desc ) if ( $desc );
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index e07e7a6372..e37adb17b5 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -91,8 +91,7 @@ my $xref = Bio::EnsEMBL::DBEntry->new
-priority => "5",
-db_display_name => "Nice friendly name",
-info_type => "PROJECTION",
- -info_text => "from human gene ENSG0000011111",
- -xref_priority => "2"
+ -info_text => "from human gene ENSG0000011111"
);
@@ -125,22 +124,16 @@ $multi->hide( "core", "object_xref", "xref", "identity_xref", "go_xref" );
my $gene = $ga->fetch_by_dbID( $all_gene_ids->[0] );
my $tr = $gene->get_all_Transcripts()->[0];
-print STDERR "transcript ".$tr->dbID."\n";
my $tl = $tr->translation();
-print STDERR "\ndb1=".$dbEntryAdaptor->store( $xref, $gene->dbID, "Gene" )."\n";
my $oxr_count = count_rows($db, 'object_xref');
-print STDERR "\n1 count is actually".$oxr_count."\n";
-print STDERR "\ndb2=".$dbEntryAdaptor->store( $xref, $tr->dbID, "Transcript" );
+$dbEntryAdaptor->store( $xref, $tr->dbID, "Transcript" );
$oxr_count = count_rows($db, 'object_xref');
-print STDERR "\n2 count is avctually".$oxr_count."\n";
-print STDERR "\ndb3=".$dbEntryAdaptor->store( $goref, $tl->dbID, "Translation" );
+$dbEntryAdaptor->store( $goref, $tl->dbID, "Translation" );
$oxr_count = count_rows($db, 'object_xref');
-print STDERR "\n3 count is actually".$oxr_count."\n";
-print STDERR "\ndb4=".$dbEntryAdaptor->store( $ident_xref, $tl->dbID, "Translation" );
+$dbEntryAdaptor->store( $ident_xref, $tl->dbID, "Translation" );
$oxr_count = count_rows($db, 'object_xref');
-print STDERR "\n4 count is actually".$oxr_count."\n";
-print STDERR "\ndb5=".$dbEntryAdaptor->store( $ident_xref, $tr->dbID, "Transcript" );
+$dbEntryAdaptor->store( $ident_xref, $tr->dbID, "Transcript" );
my ($go_count );
$oxr_count = count_rows($db, 'object_xref');
@@ -148,8 +141,7 @@ $oxr_count = count_rows($db, 'object_xref');
# 6 right number of object xrefs in db
#
debug( "object_xref_count = $oxr_count" );
-print STDERR "\n5 count is actually".$oxr_count."\n";
-ok( $oxr_count == 5 );
+ok( $oxr_count == 4 );
$xref_count = count_rows($db, 'xref');
$sth->finish();
@@ -176,8 +168,6 @@ $ident_count = count_rows($db, 'identity_xref');
debug( "Number of identity_xrefs = $ident_count" );
ok( $ident_count == 2 );
-ok($xref->xref_priority() == 2);
-
$multi->restore();
--
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