From 5cebf8d439ed8d667a80dc3f2e5f643a5b8525a1 Mon Sep 17 00:00:00 2001
From: William McLaren <wm2@ebi.ac.uk>
Date: Mon, 19 Oct 2009 13:14:07 +0000
Subject: [PATCH] Added get_all_StructuralVariationFeatures method
---
modules/Bio/EnsEMBL/Slice.pm | 38 ++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 8659500266..7d7695c437 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -1525,6 +1525,44 @@ sub get_all_VariationFeatures{
}
}
+=head2 get_all_StructuralVariationFeatures
+
+ Args : $class [optional]
+ Description :returns all structural variation features on this slice. This function will only work
+ correctly if the variation database has been attached to the core database.
+ If $class is set, only structural variations of that class will be returned.
+ ReturnType : listref of Bio::EnsEMBL::Variation::StructuralVariationFeature
+ Exceptions : none
+ Caller : contigview, snpview
+ Status : At Risk
+
+=cut
+
+sub get_all_StructuralVariationFeatures{
+ my $self = shift;
+ my $sv_class = shift;
+
+ if(!$self->adaptor()) {
+ warning('Cannot get structural variation features without attached adaptor');
+ return [];
+ }
+
+ my $svf_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(-species => $self->adaptor()->db()->species, -type => "StructuralVariationFeature");
+ if( $svf_adaptor ) {
+ if(defined $sv_class) {
+ return $svf_adaptor->fetch_all_by_Slice_constraint($self, qq{ svf.class = '$sv_class' });
+ }
+ else {
+ return $svf_adaptor->fetch_all_by_Slice($self);
+ }
+ }
+ else {
+ warning("Variation database must be attached to core database to " .
+ "retrieve variation information" );
+ return [];
+ }
+}
+
=head2 get_all_IndividualSlice
--
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