Commit e15f6d4c authored by William McLaren's avatar William McLaren
Browse files

*** empty log message ***

parent d1a7d97d
......@@ -1527,9 +1527,11 @@ sub get_all_VariationFeatures{
=head2 get_all_StructuralVariations
Args : $class [optional]
Arg[1] : $source [optional]
Arg[2] : $class [optional]
Description :returns all structural variations on this slice. This function will only work
correctly if the variation database has been attached to the core database.
If $source is set, only structural variations with that source name will be returned.
If $class is set, only structural variations of that class will be returned.
ReturnType : listref of Bio::EnsEMBL::Variation::StructuralVariation
Exceptions : none
......@@ -1540,6 +1542,7 @@ sub get_all_VariationFeatures{
sub get_all_StructuralVariations{
my $self = shift;
my $source = shift;
my $sv_class = shift;
if(!$self->adaptor()) {
......@@ -1549,7 +1552,14 @@ sub get_all_StructuralVariations{
my $sv_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(-species => $self->adaptor()->db()->species, -type => "StructuralVariation");
if( $sv_adaptor ) {
if(defined $sv_class) {
if(defined $source && defined $sv_class) {
return $sv_adaptor->fetch_all_by_Slice_constraint($self, qq{ s.name = '$source' AND sv.class = '$sv_class'});
}
elsif(defined $source) {
return $sv_adaptor->fetch_all_by_Slice_constraint($self, qq{ s.name = '$source' });
}
elsif(defined $sv_class) {
return $sv_adaptor->fetch_all_by_Slice_constraint($self, qq{ sv.class = '$sv_class' });
}
else {
......
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