Deprecating a number of calls. Instead we want more API compatible calls

modules/Bio/EnsEMBL/AltAlleleGroup.pm

@@ -459,7 +459,7 @@ sub get_all_Genes {
 }
 
 
-=head2 get_all_Gene_ids
+=head2 get_all_Genes_types
 
   Arg[1]      : Boolean - Do not include representative gene in list of ids.
   Description : Fetches all the Gene objects within the allele group and their
@@ -516,4 +516,4 @@ sub get_all_members {
 }
 
 
-1;
+1;
\ No newline at end of file

modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm

@@ -32,16 +32,16 @@ Alternative allele groupings
   my $aag_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor("Human","core","AltAlleleGroup");
   
   # For a known Gene, find the reference alternative allele
-  my $aag = $aag_adaptor->fetch_Group_by_dbID($gene->dbID);
+  my $aag = $aag_adaptor->fetch_by_gene_id($gene->dbID);
   my $reference_gene = $aag->get_ref_Gene;
   
   # Get a list of AltAlleleGroups
-  my $list = $aag_adaptor->fetch_all_Groups_by_type('IS_REPRESENTATIVE');
-  $list = $aag_adaptor->fetch_all_Groups();
+  my $list = $aag_adaptor->fetch_all_('IS_REPRESENTATIVE');
+  $list = $aag_adaptor->fetch_all();
   
   my $dbID = $aag_adaptor->store($aag);
   
-  $aag = $aag_adaptor->fetch_Group_by_id($dbID);
+  $aag = $aag_adaptor->fetch_by_dbID($dbID);
   $aag_adaptor->remove($aag);
 
 =head1 DESCRIPTION
@@ -59,23 +59,41 @@ use warnings;
 use base qw/Bio::EnsEMBL::DBSQL::BaseAdaptor/;
 
 use Bio::EnsEMBL::AltAlleleGroup;
-use Bio::EnsEMBL::Utils::Exception qw/throw/;
+use Bio::EnsEMBL::Utils::Exception qw/throw deprecate/;
 use Bio::EnsEMBL::Utils::Scalar qw/assert_ref/;
 use DBI qw( :sql_types );
 
 =head2 fetch_all_Groups
 
   Arg[1]      : (optional) String - type of group
+  Description : DEPRECATED. Please use fetch_all()
+  Returntype  : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+sub fetch_all_Groups {
+    my ($self, $type) = @_;
+    deprecate('Please use fetch_all()');
+    return $self->fetch_all($type);
+}
+
+=head2 fetch_all
+
+  Arg[1]      : (optional) String - type of group
+                Restrict group fetches to just one type. Technically it selects 
+                out mixed-annotation groups where a single member contains that type.
   Description : Fetches all the alt-allele groups, creates objects to represent
-                them and returns them in a list
+                them and returns them in a list. Specifying a group type 
+                identifies all groups containing a member of this type. It 
+                does not filter out the other members
+                
                 Multispecies support is triggered by the is_multispecies flag
                 and species_id of the DBAdaptor.
-                Specifying a group type identifies all groups containing a
-                member of this type. It does not filter out the other members
-  Returntype  : Listref of Bio::EnsEMBL::AltAlleleGroup
+  Returntype  : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
+
 =cut
 
-sub fetch_all_Groups {
+sub fetch_all {
     my $self = shift;
     my $type = shift;
 
@@ -103,16 +121,18 @@ sub fetch_all_Groups {
                 WHERE c.species_id = ? AND b.attrib = ?
             );
         }
-        $get_all_sql = q(
-            SELECT DISTINCT alt_allele_group_id FROM alt_allele a
-            JOIN (gene g, seq_region s, coord_system c)
-            ON (
-                c.coord_system_id = s.coord_system_id 
-                AND s.seq_region_id = g.seq_region_id
-                AND g.gene_id = a.gene_id
-            )
-            WHERE c.species_id = ? 
-        );
+        else {
+            $get_all_sql = q(
+                SELECT DISTINCT alt_allele_group_id FROM alt_allele a
+                JOIN (gene g, seq_region s, coord_system c)
+                ON (
+                    c.coord_system_id = s.coord_system_id 
+                    AND s.seq_region_id = g.seq_region_id
+                    AND g.gene_id = a.gene_id
+                )
+                WHERE c.species_id = ? 
+            );
+        }
     } else {
         if ($type) {
             $get_all_sql = q(SELECT DISTINCT alt_allele_group_id 
@@ -144,7 +164,7 @@ sub fetch_all_Groups {
     $sth->bind_col(1, \$group_id );
     
     while ( $sth->fetch() ) {
-        my $aag = $self->fetch_Group_by_id($group_id);
+        my $aag = $self->fetch_by_dbID($group_id);
         push @group_list, $aag;
     }
     $sth->finish;
@@ -154,22 +174,34 @@ sub fetch_all_Groups {
 =head2 fetch_all_Groups_by_type
 
   Arg[1]      : String - type of group
-  Description : Convenience method for restricting group fetches to just one
-                type. Technically it selects out mixed-annotation groups where 
-                a single member contains that type.       
-  Returntype  : Listref of Bio::EnsEMBL::AltAlleleGroup
+  Description : DEPRECATED. Please use fetch_all()
+  Returntype  : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
+
 =cut
 
 sub fetch_all_Groups_by_type {
-    my $self = shift;
-    my $type = shift; # refers to alt_allele_attrib type
-    
-    my $group_list = $self->fetch_all_Groups($type);
+    my ($self, $type) = @_;
+    deprecate('Please use fetch_all()');
+    my $group_list = $self->fetch_all($type);
     return $group_list;
 }
 
 =head2 fetch_Group_by_id
 
+  Arg[1]      : AltAlleleGroup dbID.
+  Description : DEPRECATED. Please use fetch_by_dbID
+  Returntype  : Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+sub fetch_Group_by_id {
+    my ($self, $group_id) = @_;
+    deprecate('Please use fetch_by_dbID()');
+    return $self->fetch_by_dbID($group_id);
+}
+
+=head2 fetch_by_dbID
+
   Arg[1]      : AltAlleleGroup dbID.
   Description : Creates and returns an AltAlleleGroup for the given group id
                 
@@ -177,7 +209,7 @@ sub fetch_all_Groups_by_type {
 
 =cut
 
-sub fetch_Group_by_id {
+sub fetch_by_dbID {
     my $self = shift;
     my $group_id = shift;
     
@@ -225,10 +257,33 @@ sub fetch_Group_by_id {
     return;
 }
 
+=head2 fetch_Group_by_Gene_dbID
+
+  Arg[1]      : Integer Gene ID of the member to query by
+  Description : DEPRECATED. Please use fetch_by_gene_id 
+  Returntype  : Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+
 sub fetch_Group_by_Gene_dbID {
-    my $self = shift;
-    my $gene_id = shift;
-    
+    my ($self, $gene_id) = @_;
+    deprecate('Please use fetch_by_gene_id()');
+    return $self->fetch_by_gene_id($gene_id);
+}
+
+=head2 fetch_by_gene_id
+
+  Arg[1]      : Integer Gene ID of the member to query by
+  Description : Creates and returns an AltAlleleGroup which contains
+                the specified gene member                
+  Returntype  : Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+sub fetch_by_gene_id {
+    my ($self, $gene_id) = @_;
+
     my $gene_id_sql = q(
         SELECT alt_allele_group_id FROM alt_allele
         WHERE gene_id = ?
@@ -242,14 +297,14 @@ sub fetch_Group_by_Gene_dbID {
     $sth->fetch;
     $sth->finish;
     if (!$@ && $group_id) {
-        return $self->fetch_Group_by_id($group_id);
+        return $self->fetch_by_dbID($group_id);
     }
     return;
 }
 
 =head2 store
 
-  Arg[0]     : Bio::EnsEMBL::AltAlleleGroup
+  Arg[1]     : Bio::EnsEMBL::AltAlleleGroup
   Description: Used for persisting new groups to the database.
                It updates the dbID of the object handed to it to match the
                database.
@@ -373,4 +428,4 @@ sub _tables {
     return (['alt_allele', 'a'], ['alt_allele_group', 'g'], ['alt_allele_attrib', 'b']);
 }
 
-1;
+1;
\ No newline at end of file

modules/t/altAlleleGroup.t

@@ -86,7 +86,7 @@ ok($db, 'DB was retrieved');
 my $aaga = $db->get_adaptor('AltAlleleGroup');
 # Test data consists of a single group, of type AUTOMATIC, with a reference Allele and 3 others
 
-my $group_list = $aaga->fetch_all_Groups;
+my $group_list = $aaga->fetch_all;
 my $aag = $group_list->[0];
 is($aag->rep_Gene_id, 18256,"Check for correct selection of allele");
 
@@ -101,26 +101,26 @@ $gene = $gene_list->[0];
 is (ref($gene),'Bio::EnsEMBL::Gene',"Returned object type from get_all_Genes");
 ok ($gene->dbID == 18256,"Ensure Gene objects acquire correct information");
 
-# test fetch_all_Groups_by_type
-$group_list = $aaga->fetch_all_Groups_by_type('UNLIKELY STRING');
+# test fetch_all
+$group_list = $aaga->fetch_all('UNLIKELY STRING');
 ok(scalar(@{$group_list}) == 0,"Try outlandish typed group lookup");
-$group_list = $aaga->fetch_all_Groups_by_type('HAS_CODING_POTENTIAL');
+$group_list = $aaga->fetch_all('HAS_CODING_POTENTIAL');
 ok(scalar(@$group_list) == 1,"Try known group type lookup");
 
 # fetch_Group_by_id
 $aag = $group_list->[0];
 my $group_id = $aag->dbID;
-my $new_aag = $aaga->fetch_Group_by_id($group_id);
+my $new_aag = $aaga->fetch_by_dbID($group_id);
 
 is_deeply($aag, $new_aag, "Compare previously fetched group with group found by using the dbID");
 
-$aag = $aaga->fetch_Group_by_id(undef);
+$aag = $aaga->fetch_by_dbID(undef);
 
 ok(!defined($aag), "See what happens if no argument is given");
 
 # fetch_Group_by_Gene_dbID
-$aag = $aaga->fetch_all_Groups->[0];
-$new_aag = $aaga->fetch_Group_by_Gene_dbID(18257);
+$aag = $aaga->fetch_all->[0];
+$new_aag = $aaga->fetch_by_gene_id(18257);
 is_deeply($new_aag,$aag,"Check single gene ID returns entire group correctly");
 
 # check store method
@@ -128,7 +128,7 @@ my $dbID = $aaga->store($group);
 ok($dbID, 'A dbID was returned from the store method');
 
 {
-    my $aag2 = $aaga->fetch_Group_by_id($dbID);
+    my $aag2 = $aaga->fetch_by_dbID($dbID);
     is_deeply($aag2->get_all_members,$group->get_all_members,"Compare stored with original");
     $group->add_member(4, {});
     my $update_dbID = $aaga->update($group);
@@ -137,11 +137,11 @@ ok($dbID, 'A dbID was returned from the store method');
 
 $group->remove_member(4);
 $aaga->remove($group);
-ok(! defined $aaga->fetch_Group_by_id($dbID), 'Using a deleted ID means no group returned');
+ok(! defined $aaga->fetch_by_dbID($dbID), 'Using a deleted ID means no group returned');
 my $new_dbID = $aaga->store($group);
 
 cmp_ok($new_dbID, '!=', $dbID, 'Should have been assgined a new ID');
-my $aag2 = $aaga->fetch_Group_by_id($new_dbID);
+my $aag2 = $aaga->fetch_by_dbID($new_dbID);
 my $gene_ids = $aag2->get_all_Gene_ids();
 eq_or_diff($gene_ids,[1,2,3], "Update and re-retrieve the same AltAlleleGroup") or diag explain $gene_ids;
 
@@ -149,7 +149,7 @@ eq_or_diff($gene_ids,[1,2,3], "Update and re-retrieve the same AltAlleleGroup")
 # Proper test data is hard to fabricate and no samples exist.
 
 $aaga->db->is_multispecies(1);
-$group_list = $aaga->fetch_all_Groups;
+$group_list = $aaga->fetch_all;
 $aag = $group_list->[0];
 
 ok(scalar(@$group_list) == 1, "Pretend multi-species fetch returns same groups as normal.");