Commit 577d4ff0 authored by Graham McVicker's avatar Graham McVicker
Browse files

removed fetch_all_by_Slice_and_type method, extended fetch_all_by_Slice method...

removed fetch_all_by_Slice_and_type method, extended fetch_all_by_Slice method to take additional type arg
parent a3f8ec70
......@@ -48,36 +48,39 @@ use vars qw(@ISA);
=head2 fetch_all_by_Slice_and_type
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
Arg [2] : String $type
Example : none
Description: uses optional type to retrieve repeat features
uses BaseFeatureAdaptor fetch_all_by_Slice_constraint
Returntype : listref Bio::EnsEMBL::RepeatFeature
Exceptions :
Caller : general
Arg [2] : (optional) string $logic_name
Limits RepeatFeatures obtained to those having an Analysis with
of the specified logic_name. If no logic name is specified
Repeats of all analysis types are retrieved.
Arg [3] : (optional) string $repeat_type
Limits RepeatFeatures obtained to those of specified repeat_type
Example : @rfeats = @{$rfa->fetch_all_by_Slice($slice, undef, 'LTR')};
Description: Retrieves repeat features overlapping the area designated by
the provided slice argument. Returned features will be in
in the same coordinate system as the provided slice and will
have coordinates relative to the slice start.
Returntype : reference to a list of Bio::EnsEMBL::RepeatFeatures.
Exceptions : throw on bad argument
Caller : Slice::get_all_RepeatFeatures
=cut
sub fetch_all_by_Slice_and_type {
sub fetch_all_by_Slice {
my $self = shift;
my $slice = shift;
my $type = shift;
my $logic_name = shift;
my $repeat_type = shift;
if( ! $slice || ! $slice->isa("Bio::EnsEMBL::Slice") ) {
throw( "Need slice as first argument" );
}
my $constraint = '';
if($type) {
my $constraint = "rc.repeat_type = \"$type\"";
return $self->SUPER::fetch_all_by_Slice_constraint( $slice, $constraint );
} else {
return $self->SUPER::fetch_all_by_Slice( $slice );
if($repeat_type) {
$constraint .= "rc.repeat_type =\"$repeat_type\"";
}
return $self->fetch_all_by_Slice_constraint($slice,$constraint,$logic_name);
}
......
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