Commit 566b3ceb authored by Graham McVicker's avatar Graham McVicker
Browse files

start, end, version constraints can be passed to overridden...

start, end, version constraints can be passed to overridden fetch_by_clone_accession method to speed up external queries
parent a073cdf1
......@@ -543,7 +543,8 @@ sub fetch_all_by_Clone {
}
if($self->_supported('CLONE')) {
return $self->fetch_all_by_clone_accession($clone->id);
return $self->fetch_all_by_clone_accession($clone->id, $clone->embl_acc,
$clone_start, $clone_end);
}
unless($self->_supported('CONTIG') ||
......@@ -577,12 +578,19 @@ sub fetch_all_by_Clone {
Arg [1] : string $acc
The EMBL accession number of the clone to fetch features from.
Arg [2] : (optional) string $ver
Arg [3] : (optional) int $start
Arg [4] : (optional) int $end
Example : @fs = @{$self->fetch_all_by_clone_accession('AC000093')};
Description: Retrieves features on the clone defined by the $acc arg in
Clone coordinates.
If this method is overridden then the coordinate_systems method
must return 'CLONE' as one of its values.
must return 'CLONE' as one of its values. The arguments
start, end, version are passed if this method is overridden and
can optionally be used to reduce the scope of the query and
improve performance.
If the fetch_all_by_Clone method has been overridden then this
method must also be overridden to chain calls to that method
......@@ -603,7 +611,7 @@ sub fetch_all_by_Clone {
=cut
sub fetch_all_by_clone_accession {
my ($self, $acc) = @_;
my ($self, $acc, $version, $start, $end) = @_;
unless($acc) {
$self->throw("clone accession argument not defined");
......
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