Merge 76e007f into 4596b19

modules/Bio/EnsEMBL/Variation/Variation.pm

@@ -403,11 +403,8 @@ sub get_VariationFeature_by_dbID{
 
   Arg [1]    : (optional) string $source - the source of the synonyms to
                return.
-  Arg [2]    : (optional) integer $include_source - include the source of the synonyms in
-               the output.
   Example    : @dbsnp_syns = @{$v->get_all_synonyms('dbSNP')};
                @all_syns = @{$v->get_all_synonyms()};
-               @all_syns_with_source = @{$v->get_all_synonyms('', 1)};
   Description: Retrieves synonyms for this Variation. If a source argument
                is provided all synonyms from that source are returned,
                otherwise all synonyms are returned.
@@ -421,7 +418,6 @@ sub get_VariationFeature_by_dbID{
 sub get_all_synonyms {
     my $self = shift;
     my $source = shift;
-    my $include_source = shift;
 
     if ($source) {
         $source = [$source];
@@ -431,21 +427,13 @@ sub get_all_synonyms {
     }
 
     my @synonyms;
-
-    if(!$include_source) {
-      map {push(@synonyms,keys(%{$self->{synonyms}{$_}}))} @{$source};
-    }
-    else {
-      foreach my $source (keys %{$self->{'synonyms'}}) {
-        my @list_synonyms = keys %{$self->{'synonyms'}->{$source}};
-        push(@synonyms, $source . ': ' . join(',', @list_synonyms));
-      }
-    }
+    map {push(@synonyms,keys(%{$self->{synonyms}{$_}}))} @{$source};
 
     return \@synonyms;
 }
 
 
+
 =head2 get_all_synonym_sources
 
   Arg [1]    : none

modules/t/variation.t

@@ -138,14 +138,6 @@ ok($sources[0] eq 'TSC' &&
 my @dbsnp_syns = @{$v->get_all_synonyms('dbSNP')};
 ok(@{$v->get_all_synonyms()} == 4, "count synonyms");
 
-# test variation synonyms - get_all_synonyms() returns the source name and the variation synonyms
-my $var_syn_1 = $variation_adaptor->fetch_by_name('rs2299222');
-my $variation_synonyms_1 = $var_syn_1->get_all_synonyms('',1);
-ok(@$variation_synonyms_1[0] eq 'Archive dbSNP: rs60739517,rs17765152', 'get_all_synonyms include source - valid (source Archive dbSNP)');
-
-my $var_syn_3 = $variation_adaptor->fetch_by_name('rs117161559');
-my $variation_synonyms_3 = $var_syn_3->get_all_synonyms('',1);
-ok(@$variation_synonyms_3 == 0, 'get_all_synonyms include source - no variant synonyms');
 
 
 # test add_Allele, get_all_Alleles