Commit b58ad16c authored by Elia Stupka's avatar Elia Stupka
Browse files

Changed all DBSQL to DBOLD in code

parent c72c775d
#
# BioPerl module for Bio::EnsEMBL::DBSQL::BaseAdaptor
# BioPerl module for Bio::EnsEMBL::DBOLD::BaseAdaptor
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
......@@ -12,7 +12,7 @@
=head1 NAME
Bio::EnsEMBL::DBSQL::BaseAdaptor - Base Adaptor for DBSQL adaptors
Bio::EnsEMBL::DBOLD::BaseAdaptor - Base Adaptor for DBOLD adaptors
=head1 SYNOPSIS
......@@ -28,11 +28,11 @@ Bio::EnsEMBL::DBSQL::BaseAdaptor - Base Adaptor for DBSQL adaptors
$adaptor->deleteObj();
# constructor, ok for inheritence
$adaptor = Bio::EnsEMBL::DBSQL::ClassWhichInheritsFromBaseAdaptor->new($dbobj)
$adaptor = Bio::EnsEMBL::DBOLD::ClassWhichInheritsFromBaseAdaptor->new($dbobj)
=head1 DESCRIPTION
This is a true base class for Adaptors in the Ensembl DBSQL
This is a true base class for Adaptors in the Ensembl DBOLD
system. Original idea from Arne
=head1 CONTACT
......@@ -49,7 +49,7 @@ The rest of the documentation details each of the object methods. Internal metho
# Let the code begin...
package Bio::EnsEMBL::DBSQL::BaseAdaptor;
package Bio::EnsEMBL::DBOLD::BaseAdaptor;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
......
......@@ -42,16 +42,16 @@ The rest of the documentation details each of the object methods. Internal metho
# Let the code begin...
package Bio::EnsEMBL::DBSQL::Clone;
package Bio::EnsEMBL::DBOLD::Clone;
use vars qw(@ISA);
use strict;
# Object preamble - inheriets from Bio::Root::Object
use Bio::Root::Object;
use Bio::EnsEMBL::DBSQL::RawContig;
use Bio::EnsEMBL::DBSQL::Feature_Obj;
use Bio::EnsEMBL::DBSQL::Gene_Obj;
use Bio::EnsEMBL::DBOLD::RawContig;
use Bio::EnsEMBL::DBOLD::Feature_Obj;
use Bio::EnsEMBL::DBOLD::Gene_Obj;
use Bio::EnsEMBL::DB::CloneI;
@ISA = qw(Bio::Root::Object Bio::EnsEMBL::DB::CloneI);
......@@ -71,7 +71,7 @@ sub _initialize {
$id || $self->throw("Cannot make clone db object without id");
$dbobj || $self->throw("Cannot make clone db object without db object");
$dbobj->isa('Bio::EnsEMBL::DBSQL::Obj') || $self->throw("Cannot make clone db object with a $dbobj object");
$dbobj->isa('Bio::EnsEMBL::DBOLD::Obj') || $self->throw("Cannot make clone db object with a $dbobj object");
$self->id($id);
$self->_db_obj($dbobj);
......@@ -172,7 +172,7 @@ sub delete {
my $sth = $self->_db_obj->prepare("delete from contig where internal_id = '$contig'");
my $res = $sth->execute;
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self->_db_obj);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self->_db_obj);
$feature_obj->delete($contig);
}
......@@ -229,7 +229,7 @@ sub get_all_Genes {
if( ! exists $got{$rowhash->{'gene'}}) {
my $gene_obj = Bio::EnsEMBL::DBSQL::Gene_Obj->new($self->_db_obj);
my $gene_obj = Bio::EnsEMBL::DBOLD::Gene_Obj->new($self->_db_obj);
my $gene = $gene_obj->get($rowhash->{'gene'}, $supporting);
if ($gene) {
push(@out, $gene);
......
#
# Ensembl module for Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor
# Ensembl module for Bio::EnsEMBL::DBOLD::CrossMatchDBAdaptor
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
......@@ -12,13 +12,13 @@
=head1 NAME
Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor - DESCRIPTION of Object
Bio::EnsEMBL::DBOLD::CrossMatchDBAdaptor - DESCRIPTION of Object
=head1 SYNOPSIS
my $db=Bio::EnsEMBL::DBSQL::Obj->new(-dbname=>'july_dna',-host=>'ecs1c',-user=>'ensadmin');
my $db=Bio::EnsEMBL::DBOLD::Obj->new(-dbname=>'july_dna',-host=>'ecs1c',-user=>'ensadmin');
my $cross=Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor->new(-dbname=>'crossmatch',-host=>'ecs1c',-user=>'ensadmin');
my $cross=Bio::EnsEMBL::DBOLD::CrossMatchDBAdaptor->new(-dbname=>'crossmatch',-host=>'ecs1c',-user=>'ensadmin');
$db->_crossdb($cross);
......@@ -42,14 +42,14 @@ The rest of the documentation details each of the object methods. Internal metho
# Let the code begin...
package Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor;
package Bio::EnsEMBL::DBOLD::CrossMatchDBAdaptor;
use vars qw(@ISA);
use strict;
# Object preamble - inheriets from Bio::Root::RootI
use DBI;
use Bio::Root::RootI;
use Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer;
use Bio::EnsEMBL::DBOLD::SymmetricContigFeatureContainer;
use Bio::EnsEMBL::DBLoader;
@ISA = qw(Bio::Root::RootI);
......@@ -93,7 +93,7 @@ sub new {
Usage : $crossdb->new_dbobj
Function: reads the dblocation table to load the new db
Example : $crossdb->new_dbobj()
Returns : Bio::EnsEMBL::DBSQL::Obj
Returns : Bio::EnsEMBL::DBOLD::Obj
Args : none
......@@ -126,7 +126,7 @@ sub new_dbobj{
Usage : $crossdb->old_dbobj
Function: reads the dblocation table to load the old db
Example : $crossdb->old_dbobj()
Returns : Bio::EnsEMBL::DBSQL::Obj
Returns : Bio::EnsEMBL::DBOLD::Obj
Args : none
......@@ -154,9 +154,9 @@ sub old_dbobj{
Title : get_SymmetricContigFeatureContainer
Usage : $crossdb->get_SymmetricContigFeatureContainer
Function: Gets a Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer
Function: Gets a Bio::EnsEMBL::DBOLD::SymmetricContigFeatureContainer
Example : $crossdb->get_SymmetricContigFeatureContainer
Returns : Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer
Returns : Bio::EnsEMBL::DBOLD::SymmetricContigFeatureContainer
Args : none
......@@ -165,7 +165,7 @@ sub old_dbobj{
sub get_SymmetricContigFeatureContainer{
my ($self) = @_;
return Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer->new($self);
return Bio::EnsEMBL::DBOLD::SymmetricContigFeatureContainer->new($self);
}
=head2 get_clonelist
......
......@@ -44,7 +44,7 @@ Internal methods are usually preceded with a _
# Let the code begin...
package Bio::EnsEMBL::DBSQL::DBPrimarySeq;
package Bio::EnsEMBL::DBOLD::DBPrimarySeq;
use vars qw(@ISA);
use strict;
......
......@@ -12,7 +12,7 @@
=head1 NAME
Bio::EnsEMBL::DBSQL::DummyStatement - Dummy statement object for debugging
Bio::EnsEMBL::DBOLD::DummyStatement - Dummy statement object for debugging
=head1 SYNOPSIS
......@@ -37,7 +37,7 @@ The rest of the documentation details each of the object methods. Internal metho
# Let the code begin...
package Bio::EnsEMBL::DBSQL::DummyStatement;
package Bio::EnsEMBL::DBOLD::DummyStatement;
use vars qw($AUTOLOAD @ISA);
use strict;
......
#
# EnsEMBL module for Bio::EnsEMBL::DBSQL::Feature_Obj
# EnsEMBL module for Bio::EnsEMBL::DBOLD::Feature_Obj
#
# Cared for by Elia Stupka <elia@ebi.ac.uk>
#
......@@ -11,14 +11,14 @@
=head1 NAME
Bio::EnsEMBL::DBSQL::Feature_Obj - MySQL database adapter class for EnsEMBL Feature Objects
Bio::EnsEMBL::DBOLD::Feature_Obj - MySQL database adapter class for EnsEMBL Feature Objects
=head1 SYNOPSIS
use Bio::EnsEMBL::DBSQL::Obj;
use Bio::EnsEMBL::DBSQL::Feature_Obj;
use Bio::EnsEMBL::DBOLD::Obj;
use Bio::EnsEMBL::DBOLD::Feature_Obj;
$db = new Bio::EnsEMBL::DBSQL::Obj( -user => 'root', -db => 'pog' , -host => 'caldy' , -driver => 'mysql' );
$db = new Bio::EnsEMBL::DBOLD::Obj( -user => 'root', -db => 'pog' , -host => 'caldy' , -driver => 'mysql' );
my $feature_obj=Bio::EnsEMBL::Feature_Obj->new($obj);
#Check if a feature exists
......@@ -26,7 +26,7 @@ Bio::EnsEMBL::DBSQL::Feature_Obj - MySQL database adapter class for EnsEMBL Feat
=head1 DESCRIPTION
This is one of the objects contained in Bio:EnsEMBL::DBSQL::Obj, dealing with
This is one of the objects contained in Bio:EnsEMBL::DBOLD::Obj, dealing with
feature objects.
The Obj object represents a database that is implemented somehow (you shouldn\'t
......@@ -46,7 +46,7 @@ usually preceded with a _
# Let the code begin...
package Bio::EnsEMBL::DBSQL::Feature_Obj;
package Bio::EnsEMBL::DBOLD::Feature_Obj;
use vars qw(@ISA);
use strict;
......@@ -54,7 +54,7 @@ use strict;
# Object preamble - inheriets from Bio::Root::Object
use Bio::Root::Object;
#use Bio::EnsEMBL::DBSQL::Obj;
#use Bio::EnsEMBL::DBOLD::Obj;
use Bio::EnsEMBL::Ghost;
use Bio::EnsEMBL::Gene;
......@@ -62,8 +62,8 @@ use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::FeatureFactory;
use DBI;
use Bio::EnsEMBL::DBSQL::Utils;
use Bio::EnsEMBL::DBSQL::DummyStatement;
use Bio::EnsEMBL::DBOLD::Utils;
use Bio::EnsEMBL::DBOLD::DummyStatement;
......@@ -402,7 +402,7 @@ sub get_Protein_annseq{
my $res = $sth->execute();
my $rowhash = $sth->fetchrow_hashref;
my $gene_obj=Bio::EnsEMBL::DBSQL::Gene_Obj->new($self->_db_obj);
my $gene_obj=Bio::EnsEMBL::DBOLD::Gene_Obj->new($self->_db_obj);
my $transcript = $gene_obj->get_Transcript($rowhash->{'id'});
my $translation = $gene_obj->get_Translation($ENSP);
......@@ -850,7 +850,7 @@ sub get_PredictionFeature_as_Transcript{
my $ft=$self->get_PredictionFeature_by_id($genscan_id);
my $contig=$self->_db_obj->get_Contig($ft->seqname);
&Bio::EnsEMBL::DBSQL::Utils::fset2transcript($ft,$contig);
&Bio::EnsEMBL::DBOLD::Utils::fset2transcript($ft,$contig);
}
......
#
# Ensembl module for Bio::EnsEMBL::DBSQL::GapContig
# Ensembl module for Bio::EnsEMBL::DBOLD::GapContig
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
......@@ -12,7 +12,7 @@
=head1 NAME
Bio::EnsEMBL::DBSQL::GapContig - DESCRIPTION of Object
Bio::EnsEMBL::DBOLD::GapContig - DESCRIPTION of Object
=head1 SYNOPSIS
......@@ -40,7 +40,7 @@ The rest of the documentation details each of the object methods. Internal metho
# Let the code begin...
package Bio::EnsEMBL::DBSQL::GapContig;
package Bio::EnsEMBL::DBOLD::GapContig;
use vars qw(@ISA);
use strict;
......
This diff is collapsed.
#
# BioPerl module for DBSQL::Obj
# BioPerl module for DBOLD::Obj
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
......@@ -11,11 +11,11 @@
=head1 NAME
Bio::EnsEMBL::DBSQL::Obj - Object representing an instance of an EnsEMBL DB
Bio::EnsEMBL::DBOLD::Obj - Object representing an instance of an EnsEMBL DB
=head1 SYNOPSIS
$db = Bio::EnsEMBL::DBSQL::Obj->new(
$db = Bio::EnsEMBL::DBOLD::Obj->new(
-user => 'root',
-dbname => 'pog',
-host => 'caldy',
......@@ -52,7 +52,7 @@ The rest of the documentation details each of the object methods. Internal metho
# Let the code begin...
package Bio::EnsEMBL::DBSQL::Obj;
package Bio::EnsEMBL::DBOLD::Obj;
use vars qw(@ISA);
use strict;
......@@ -62,21 +62,21 @@ use strict;
use Bio::Root::RootI;
use Bio::EnsEMBL::DB::ObjI;
use Bio::EnsEMBL::DBSQL::Gene_Obj;
use Bio::EnsEMBL::DBSQL::Update_Obj;
use Bio::EnsEMBL::DBSQL::Feature_Obj;
use Bio::EnsEMBL::DBSQL::RawContig;
use Bio::EnsEMBL::DBSQL::GapContig;
use Bio::EnsEMBL::DBOLD::Gene_Obj;
use Bio::EnsEMBL::DBOLD::Update_Obj;
use Bio::EnsEMBL::DBOLD::Feature_Obj;
use Bio::EnsEMBL::DBOLD::RawContig;
use Bio::EnsEMBL::DBOLD::GapContig;
use Bio::EnsEMBL::DBSQL::Clone;
use Bio::EnsEMBL::DBOLD::Clone;
use Bio::EnsEMBL::FeatureFactory;
use Bio::EnsEMBL::Chromosome;
use DBI;
use Bio::EnsEMBL::DB::ObjI;
use Bio::EnsEMBL::DBSQL::StaticGoldenPathAdaptor;
use Bio::EnsEMBL::DBOLD::StaticGoldenPathAdaptor;
use Bio::EnsEMBL::DBSQL::DummyStatement;
use Bio::EnsEMBL::DBOLD::DummyStatement;
@ISA = qw(Bio::EnsEMBL::DB::ObjI Bio::Root::RootI);
......@@ -245,7 +245,7 @@ sub mapdbname {
sub get_Update_Obj {
my ($self) = @_;
my $update_obj = Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj = Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj;
}
......@@ -430,7 +430,7 @@ sub write_Contig {
# write sequence features. We write all of them together as it
# is more efficient
my @features = $contig->get_all_SeqFeatures;
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
$feature_obj->write($contig, @features);
return 1;
......@@ -523,13 +523,13 @@ sub write_Chromosome {
my $mapdb = $obj->mapdb;
Sets or gets a mapdb connection, which is a
C<Bio::EnsEMBL::Map::DBSQL::Obj> object.
C<Bio::EnsEMBL::Map::DBOLD::Obj> object.
If a mapdb connection doesn't exist, a new
connection is made using the information provided
to the C<_initialize> method. This will produce
an exception if the
C<Bio::EnsEMBL::Map::DBSQL::Obj> module can't be
C<Bio::EnsEMBL::Map::DBOLD::Obj> module can't be
found.
=cut
......@@ -539,7 +539,7 @@ sub mapdb {
if ($value) {
$self->throw("$value is not a valid mapdb object")
unless $value->isa("Bio::EnsEMBL::Map::DBSQL::Obj");
unless $value->isa("Bio::EnsEMBL::Map::DBOLD::Obj");
$self->{'_mapdb'} = $value;
}
else {
......@@ -549,8 +549,8 @@ sub mapdb {
# If $map is just an unblessed hash (first time
# mapdb is called), connect to the map database.
if (ref($map) eq 'HASH') {
require Bio::EnsEMBL::Map::DBSQL::Obj;
$self->{'_mapdb'} = Bio::EnsEMBL::Map::DBSQL::Obj->new(%$map);
require Bio::EnsEMBL::Map::DBOLD::Obj;
$self->{'_mapdb'} = Bio::EnsEMBL::Map::DBOLD::Obj->new(%$map);
}
}
return $self->{'_mapdb'};
......@@ -737,7 +737,7 @@ sub prepare {
if( $self->_debug > 10 ) {
print STDERR "Prepared statement $string\n";
my $st = Bio::EnsEMBL::DBSQL::DummyStatement->new();
my $st = Bio::EnsEMBL::DBOLD::DummyStatement->new();
$st->_fileh(\*STDERR);
$st->_statement($string);
return $st;
......@@ -1180,7 +1180,7 @@ sub get_donor_locator {
$self->warn("Obj->get_donor_locator is a deprecated method!
Calling Update_Obj->get_donor_locator instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_donor_locator();
}
......@@ -1201,7 +1201,7 @@ sub get_last_update_offset{
$self->warn("Obj->get_last_update_offset is a deprecated method!
Calling Update_Obj->get_last_update_offset instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_last_update_offset();
}
......@@ -1223,7 +1223,7 @@ sub get_last_update{
$self->warn("Obj->get_last_update is a deprecated method!
Calling Update_Obj->get_last_update_offset instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_last_update_offset();
}
......@@ -1246,7 +1246,7 @@ sub get_now_offset{
$self->warn("Obj->get_now_offset is a deprecated method!
Calling Update_Obj->get_now_offset instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_now_offset();
}
......@@ -1288,7 +1288,7 @@ sub get_Protein_annseq{
$self->warn("Obj->get_Protein_annseq is a deprecated method!
Calling Feature_Obj->get_Protein_annseq instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->get_Protein_annseq($ENSP);
}
......@@ -1418,7 +1418,7 @@ sub get_updated_Clone_id {
$self->warn("Obj->get_updated_Clone_id is a deprecated method!
Calling Update_Obj->get_updated_Clone_id instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_updated_Clone_id($last_offset, $now_offset);
}
......@@ -1442,7 +1442,7 @@ sub get_updated_Objects{
$self->warn("Obj->get_updated_Objects is a deprecated method!
Calling Update_Obj->get_updated_Objects instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_updated_Objects($last_offset,$now_offset);
}
......@@ -1466,7 +1466,7 @@ sub get_updated_Ghosts{
$self->warn("Obj->get_updated_Ghosts is a deprecated method!
Calling Update_Obj->get_updated_Ghosts instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_updated_Ghosts($last_offset, $now_offset);
}
......@@ -1487,7 +1487,7 @@ sub get_Ghost{
$self->warn("Obj->get_Ghost is a deprecated method!
Calling Update_Obj->get_Ghost instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->get_Ghost($ghost_id,$ghost_type);
}
......@@ -1509,7 +1509,7 @@ sub write_Ghost{
$self->warn("Obj->write_Ghost is a deprecated method!
Calling Update_Obj->write_Ghost instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->write_Ghost($ghost);
}
......@@ -1533,7 +1533,7 @@ sub archive_Gene {
$self->warn("Obj->archive_Gene is a deprecated method!
Calling Update_Obj->archive_Gene instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->archive_Gene($gene,$arc_db);
}
......@@ -1597,7 +1597,7 @@ sub delete_Features {
$self->warn("Obj->delete_Features is a deprecated method!
Calling Feature_Obj->delete instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->delete($contig);
}
......@@ -1659,7 +1659,7 @@ sub replace_last_update {
$self->warn("Obj->replace_last_update is a deprecated method!
Calling Update_Obj->replace_last_update instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->replace_last_update($now_offset);
}
......@@ -1680,7 +1680,7 @@ sub current_update {
$self->warn("Obj->current_update is a deprecated method!
Calling Update_Obj->current_update instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->current_update();
}
......@@ -1701,7 +1701,7 @@ sub start_update {
$self->warn("Obj->start_update is a deprecated method!
Calling Update_Obj->start_update instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->start_update($start,$end);
}
......@@ -1722,7 +1722,7 @@ sub finish_update {
$self->warn("Obj->finish_update is a deprecated method!
Calling Update_Obj->finish_update instead!");
my $update_obj=Bio::EnsEMBL::DBSQL::Update_Obj->new($self);
my $update_obj=Bio::EnsEMBL::DBOLD::Update_Obj->new($self);
return $update_obj->finish_update();
}
......@@ -1767,7 +1767,7 @@ sub write_all_Protein_features {
$self->warn("Obj->write_all_Protein_features is a deprecated method!
Calling Feature_Obj->write_all_Protein_features instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->write_all_Protein_features($prot_annseq,$ENSP);
}
......@@ -1790,7 +1790,7 @@ sub write_Protein_feature {
$self->warn("Obj->write_Protein_feature is a deprecated method!
Calling Feature_Obj->write_Protein_feature instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->write_Protein_feature($ENSP,$feature);
}
......@@ -1812,7 +1812,7 @@ sub write_Feature {
$self->warn("Obj->write_Feature is a deprecated method!
Calling Feature_Obj->write_Feature instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->write($contig,@features);
}
......@@ -1877,7 +1877,7 @@ sub write_Analysis {
$self->warn("Obj->write_Analysis is a deprecated method!
Calling Feature_Obj->write_Analysis instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->write_Analysis($analysis);
}
......@@ -1899,7 +1899,7 @@ sub exists_Homol_Feature {
$self->warn("Obj->exists_Homol_Feature is a deprecated method!
Calling Feature_Obj->exists_Homol_Feature instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->exists($feature,$analysisid,$contig);
}
......@@ -1921,7 +1921,7 @@ sub get_Analysis {
$self->warn("Obj->get_Analysis is a deprecated method!
Calling Feature_Obj->get_Analysis instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->get_Analysis($id);
}
......@@ -1943,7 +1943,7 @@ sub exists_Analysis {
$self->warn("Obj->exists_Analysis is a deprecated method!
Calling Feature_Obj->exists_Analysis instead!");
my $feature_obj=Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
my $feature_obj=Bio::EnsEMBL::DBOLD::Feature_Obj->new($self);
return $feature_obj->exists_Analysis($analysis);
}
......@@ -2032,7 +2032,7 @@ sub get_Clone {
#$self->warn("Obj->get_Clone is a deprecated method!
#Calling Clone->fetch instead!");
my $clone = new Bio::EnsEMBL::DBSQL::Clone( -id => $id,
my $clone = new Bio::EnsEMBL::DBOLD::Clone( -id => $id,
-dbobj => $self );
return $clone->fetch();
......@@ -2057,10 +2057,10 @@ sub get_Contig{
#Calling Contig->fetch instead!");
if( $id eq 'gapcontig' ) {
my $contig = new Bio::EnsEMBL::DBSQL::GapContig;
my $contig = new Bio::EnsEMBL::DBOLD::GapContig;