Commit 5fb74911 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

deprecated broken method

parent ce0593ce
...@@ -145,6 +145,7 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP ...@@ -145,6 +145,7 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP
### Removed in Ensembl Release 84 ### ### Removed in Ensembl Release 84 ###
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_by_attrib()* - Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_by_attrib()*
- Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_all_by_attrib()* - Bio::EnsEMBL::DBSQL::**CoordSystemAdaptor**::*_fetch_all_by_attrib()*
- Bio::EnsEMBL::DBSQL::**SliceAdaptor**::*fetch_by_band()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_short_name()* - Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_short_name()*
- Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_max_assembly_contig()* - Bio::EnsEMBL::DBSQL::**MetaContainer**::*get_max_assembly_contig()*
- Bio::EnsEMBL::**Exon**::*_get_stable_entry_info()* - Bio::EnsEMBL::**Exon**::*_get_stable_entry_info()*
......
...@@ -1487,34 +1487,14 @@ sub is_circular { ...@@ -1487,34 +1487,14 @@ sub is_circular {
=head2 fetch_by_band =head2 fetch_by_band
Title : fetch_by_band Description : DEPRECATED. Use fetch_by_chr_band instead
Usage :
Function: Does not work please use fetch_by_chr_band
Example :
Returns : Bio::EnsEMBL::Slice
Args : the band name
Status : AT RISK
=cut =cut
sub fetch_by_band { sub fetch_by_band {
my ($self,$band) = @_; my ($self,$band) = @_;
my $sth = $self->dbc->prepare deprecate("fetch_by_band is deprecated and will be removed in e84. Please use fetch_by_chr_band instead.");
("select s.name,max(k.seq_region_id)-min(k.seq_region_id, min(k.seq_region_start), max(k.seq_region_id) " .
"from karyotype as k " .
"where k.band like ? and k.seq_region_id = s.seq_region_id");
$sth->bind_param(1,"$band%",SQL_VARCHAR);
$sth->execute();
my ( $seq_region_name, $discrepancy, $seq_region_start, $seq_region_end) = $sth->fetchrow_array;
if($seq_region_name && $discrepancy>0) {
throw("Band maps to multiple seq_regions");
} else {
return $self->fetch_by_region('toplevel',$seq_region_name,$seq_region_start,$seq_region_end);
}
throw("Band not recognised in database");
} }
=head2 fetch_by_chr_band =head2 fetch_by_chr_band
......
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