From 9f6ad393af6578f13dd71abfc78599b68012235e Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 11 Nov 2013 17:32:30 +0000
Subject: [PATCH] new method store_multiple_mapping_path same as
store_mapping_path, but for multiple mappings a multiple mapping is needed
when a single component can be mapped to multiple assembled regions this uses
the '#' operator instead of the '|' for the mapping key
---
.../Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm | 78 +++++++++++++++++++
1 file changed, 78 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
index ccbb593f4a..e68eed6e5f 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
@@ -938,6 +938,84 @@ sub store_mapping_path{
return [@retlist];
}
+
+=head2 store_multiple_mapping_path
+
+ Arg [1] : Bio::EnsEMBL::CoordSystem $cs1
+ Arg [2] : Bio::EnsEMBL::CoordSystem $cs2
+ Arg [3..n] : Bio::EnsEMBL::CoordSystem $cs3..$csN
+ Example : my $pathref = $csa->store_multiple_mapping_path($cs1,$cs2);
+ Description: Given two or more coordinate systems this will store
+ multiple mapping paths between them in the database.
+
+ Works similarly to the store_mapping_path method
+ But will presume every coord system can be mapped in multiple
+ ways to the other coord systems
+ This is represented by the use of '#' instead of '|'
+ in the mapping key
+
+ Returntype : reference to a list of lists of new meta_value mapping strings
+ created for assembly.mapping
+ Exceptions : CoordSystems with no rank/duplicated rank
+ Caller : general
+ Status : Experimental
+
+=cut
+
+sub store_multiple_mapping_path{
+ my $self = shift;
+ my @csystems = @_;
+
+ # Validate and sort the args
+ my %seen_ranks;
+ @csystems >= 2 or throw('Need two or more CoordSystems');
+ my $validate = sub{
+ ref($_[0]) && $_[0]->isa('Bio::EnsEMBL::CoordSystem') or
+ throw('CoordSystem argument expected.');
+ my $rank = $_[0]->rank ||
+ throw('CoordSystem has no rank: '.$_[0]->name);
+ $seen_ranks{$rank} &&
+ throw('CoordSystem '.$_[0]->name." shares rank $rank with ".
+ $seen_ranks{$rank}->name);
+ $seen_ranks{$rank} = $_[0];
+ };
+ @csystems = map{&{$validate}($_)} @csystems;
+ my ($key, @keys);
+ foreach my $cs (@csystems) {
+ $key = $cs->name();
+ if ($cs->version()) {
+ $key .= ":" . $cs->version();
+ }
+ push @keys, $key;
+ }
+ # For each pair in the sorted list, store in the DB
+ my $meta = $self->db->get_MetaContainer;
+ my @retlist;
+ for( my $i=1; $i<@keys; $i++ ){
+ for( my $j=0; $j<(@keys-$i); $j++ ){
+ my $mapping = join( "#", @keys );
+
+ my $mapping_key = join( "#", @keys );
+ # Skip existing
+ next if $self->{'_mapping_paths'}->{$mapping_key};
+
+ # Update the database
+ $meta->store_key_value('assembly.mapping',$mapping);
+ push @retlist, $mapping;
+ }
+ }
+
+ if( @retlist ){
+ # Update mapping path cache
+ $self->_cache_mapping_paths;
+ }
+
+ # Return the mappings that we have just created
+ return [@retlist];
+}
+
+
+
=head2 fetch_by_attrib
Arg [1] : string attrib
--
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