Commit e8cb5843 authored by Alistair Rust's avatar Alistair Rust
Browse files

- Removed delete_by_RawContig_id method.

- Replaced with remove_RawContig.
parent 4ed92b29
......@@ -499,26 +499,26 @@ sub remove {
=head2 delete_by_RawContig_id
Arg [1] : string $contig_id
Example : $feature_adaptor->delete_by_RawContig_id($contig_id);
Description: This removes a feature from the database. The table the
feature is removed from is defined by the abstract method
_tablename, and the primary key of the table is assumed
to be contig_id.
=head2 remove_RawContig
Arg [1] : Bio::Ensembl::RawContig $contig
Example : $feature_adaptor->remove_RawContig($contig);
Description: This removes features from the database which lie on a removed
contig. The table the features are removed from is defined by
the abstract method_tablename, and the primary key of the table
is assumed to be contig_id.
Returntype : none
Exceptions : thrown if no contig_id is supplied
Exceptions : thrown if no contig is supplied
Caller : general
=cut
sub delete_by_RawContig_id {
my ($self, $contig_id) = @_;
sub remove_RawContig {
my ($self, $contig) = @_;
unless($contig_id) {
$self->throw("BaseFeatureAdaptor::delete_by_RawContig_id - no contig_id defined: ".
"Deletion of feature failed.");
unless($contig) {
$self->throw("BaseFeatureAdaptor::remove - no contig supplied: ".
"Deletion of features failed.");
}
my $table = $self->_tablename();
......@@ -537,7 +537,7 @@ sub delete_by_RawContig_id {
my ($actual_table) = $table_name =~ /(^\w+)/; # lose the table alias, if there is one
my $sth = $self->prepare("DELETE FROM $actual_table WHERE contig_id = ?");
$sth->execute($contig_id);
$sth->execute($contig->dbID);
}
return;
......
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