lists -> listrefs

modules/Bio/EnsEMBL/Analysis.pm

@@ -44,7 +44,8 @@ Describe contact details here
 
 =head1 APPENDIX
 
-The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+The rest of the documentation details each of the object methods. 
+Internal methods are usually preceded with a _
 
 =cut
 

modules/Bio/EnsEMBL/BaseAlignFeature.pm

@@ -192,62 +192,6 @@ sub ungapped_features {
 
 
 
-=head2 transform
-
-  Arg [1]    : Bio::EnsEMBL::Slice $slice
-  Example    : none
-  Description: if argument is given, transforms this feature into the slice
-               coordinate system, invalidating this one.
-               if no argument is given, transforms this feature into raw contig
-               coordinates, invalidating this one.
-               The process can produce more than one feature so we return an array. 
-  Returntype : list of Bio::EnsEMBL::BaseAlignFeature
-  Exceptions : none
-  Caller     : general
-
-=cut
-
-
-sub transform{
-  my ($self, $slice) = @_;
-  #print "transforming ".$self." to ".$slice." coords\n";
-  if( ! defined $slice ) {
-    #Since slice arg is not defined -  we want raw contig coords
-    if(( defined  $self->contig ) && 
-       ( $self->contig->isa( "Bio::EnsEMBL::RawContig" )) ) {
-   #   print STDERR "BaseAlignFeature::transform, you are already apparently in rawcontig coords so why try to transform to them\n";
-      #we are already in rawcontig coords, nothing needs to be done
-      return $self;
-    } else {
-      #transform to raw_contig coords from Slice coords
-      my @array =  $self->_transform_to_rawcontig();
-    #  print "transform to  rawcontig has returned ".@array." features\n";
-    #  foreach my $a(@array){
-#	print "feature is ".$a."\n";
-#      }
-      return @array;
-    }
-  }
-
-  if( defined $self->contig ) {  
-    if($self->contig->isa( "Bio::EnsEMBL::RawContig" ))  {
-      #transform to slice coords from raw contig coords
-      return $self->_transform_to_slice( $slice );
-    } elsif($self->contig->isa( "Bio::EnsEMBL::Slice" )) {
-      #transform to slice coords from other slice coords
-      return $self->_transform_between_slices( $slice );
-    } else {
-      #Unknown contig type - throw an exception
-      return $self->throw("Exon's 'contig' is of unknown type " 
-		   . $self->contig() . " - cannot transform to Slice coords");
-    }
-  } else {
-    #Can't convert to slice coords without a contig to work with
-    return $self->throw("Exon's contig is not defined - cannot transform to " .
-			"Slice coords");
-  }
-}
-
 =head2 dbID
 
   Arg [1]    : int $dbID
@@ -803,7 +747,7 @@ sub _parse_features {
 
 
 
-sub _transform_to_rawcontig{
+sub _transform_to_RawContig{
   my ($self) = @_;
   #print STDERR "transforming to raw contig coord\n\n";
   if(!$self->contig){
@@ -820,7 +764,7 @@ sub _transform_to_rawcontig{
   my %rc_features;
 
   foreach my $f(@features){
-    my @new_features = $self->_transform_feature_to_rawcontig($f);
+    my @new_features = $self->_transform_feature_to_RawContig($f);
     push(@mapped_features, @new_features);
   }
 
@@ -850,14 +794,6 @@ sub _transform_to_rawcontig{
 
 
 
-sub _transform_between_slices {
-  my ( $self, $to_slice ) = @_;
-}
-
-
-
-
-
 =head2 _hit_unit
 
   Args       : none
@@ -893,7 +829,7 @@ sub _query_unit {
 }
 
 
-sub _transform_feature_to_rawcontig{
+sub _transform_feature_to_RawContig{
   my($self, $feature) =  @_;
 
   my $verbose = 0;

modules/Bio/EnsEMBL/Clone.pm

@@ -137,7 +137,7 @@ sub get_all_Genes {
   Example    : none
   Description: get RawContig objects from this Clone (either manually added
                or from the database).
-  Returntype : list of Bio::EnsEMBL::RawContig
+  Returntype : listref of Bio::EnsEMBL::RawContig
   Exceptions : none
   Caller     : general
 
@@ -153,11 +153,11 @@ sub get_all_Contigs {
   #from the database
   unless ($c_list = $self->{'_contig_list'}) {
     my $ra = $self->adaptor->db->get_RawContigAdaptor;
-    $c_list = $ra->fetch_by_clone($self);
+    $c_list = $ra->fetch_by_Clone($self);
     $self->{'_contig_list'} = $c_list;
   }
 
-  return @$c_list;
+  return $c_list;
 }
 
 
@@ -230,10 +230,11 @@ sub get_rawcontig_by_position {
         $self->throw("get_rawcontig_by_position error: Position must be > 0");
     }
     
-    my @contigs =  $self->get_all_Contigs();
-    @contigs = sort { $b->embl_offset <=> $a->embl_offset } @contigs;
+    my $contigs =  $self->get_all_Contigs();
+    my @sorted_contigs = 
+      sort { $b->embl_offset <=> $a->embl_offset } @$contigs;
     
-    foreach my $c ( @contigs ) {
+    foreach my $c ( @sorted_contigs ) {
         if ($pos > $c->embl_offset) {
              return $c;
         } 

modules/Bio/EnsEMBL/DBEntry.pm

@@ -295,17 +295,17 @@ sub add_synonym {
 =head2 get_synonyms
 
   Args       : none
-  Example    : none
+  Example    : @synonyms = @{$db_entry->get_all_synonyms()};
   Description: get a list of synonym added to this object
-  Returntype : list of string 
+  Returntype : list reference of strings 
   Exceptions : none
   Caller     : general
 
 =cut
 
-sub get_synonyms {
+sub get_all_synonyms {
   my $self = shift;
-  return @{$self->{_synonyms}};
+  return $self->{_synonyms};
 }
 
 
@@ -367,4 +367,24 @@ sub comment {
     }
 }
 
+
+
+=head2 get_synonyms
+
+  Arg [1]    : none
+  Example    : none
+  Description: DEPRECATED use get_all_synonyms instead
+  Returntype : none
+  Exceptions : none
+  Caller     : none
+
+=cut
+
+sub get_synonyms {
+  my $self = shift;
+
+  $self->warn("get_synonyms has been rename get_all_synonyms\n" . caller);
+  return $self->get_all_synonyms;
+}
+
 1;

modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm

@@ -84,7 +84,7 @@ sub new {
   Example    : my @analysis = $analysis_adaptor->fetch_all()
   Description: fetches all of the Analysis objects from the database and caches
                them internally.
-  Returntype : list of Bio::EnsEMBL::Analysis retrieved from the database
+  Returntype : listref of Bio::EnsEMBL::Analysis retrieved from the database
   Exceptions : none
   Caller     : AnalysisAdaptor::new
 
@@ -114,7 +114,7 @@ sub fetch_all {
     $self->{_logic_name_cache}->{$analysis->logic_name()} = $analysis;
   }
 
-  return values %{$self->{_cache}};
+  return \{values %{$self->{_cache}}};
 }
 
 

modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm

@@ -67,7 +67,7 @@ use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
                are on the contig defined by $cid and with a percentage id 
                greater than $pid.  If logic name is defined, only features
                with an analysis of type $logic_name will be returned. 
-  Returntype : list of Bio::EnsEMBL::*AlignFeature in contig coordinates
+  Returntype : listref of Bio::EnsEMBL::*AlignFeature in contig coordinates
   Exceptions : thrown if $pid is not defined
   Caller     : general
 
@@ -82,10 +82,7 @@ sub fetch_by_Contig_and_pid {
     $constraint = "perc_ident > $pid";
   }
 
-  my @features = 
-    $self->fetch_by_Contig_constraint($contig, $constraint, $logic_name);
-  
-  return @features;
+  return $self->fetch_by_Contig_constraint($contig, $constraint, $logic_name);
 }
 
 
@@ -102,7 +99,7 @@ sub fetch_by_Contig_and_pid {
                are on the Slice $slice and with a percentage id 
                greater than $pid.  If logic name is defined, only features
                with an analysis of type $logic_name will be returned. 
-  Returntype : list of Bio::EnsEMBL::*AlignFeature in Slice coordinates
+  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures in Slice coordinates
   Exceptions : thrown if pid is not defined
   Caller     : general
 

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -192,7 +192,7 @@ sub fetch_by_Contig_constraint {
     $constraint = "contig_id = $cid";
   }
 
-  return @{$self->generic_fetch($constraint, $logic_name)};
+  return $self->generic_fetch($constraint, $logic_name);
 }
 
 

modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm

@@ -154,7 +154,7 @@ sub fetch_by_chr_name{
   Args       : none
   Example    : @chromosomes = $chromosome_adaptor->fetch_all(); 
   Description: Retrieves every chromosome object from the database.
-  Returntype : list of Bio::EnsEMBL::Chromosome
+  Returntype : listref of Bio::EnsEMBL::Chromosome
   Exceptions : none
   Caller     : general
 
@@ -189,7 +189,7 @@ sub fetch_all {
     push @chrs, $chr;
   }
 
-  return @chrs;
+  return \@chrs;
 }
 
 
@@ -230,6 +230,9 @@ sub get_dbID_by_chr_name {
 }    
 
 
+
+
+
 =head2 get_landmark_MarkerFeatures
 
   Arg [1]    : none

modules/Bio/EnsEMBL/DBSQL/CloneAdaptor.pm

@@ -223,7 +223,7 @@ sub fetch_by_dbID {
   Arg [1]    : none
   Example    : @clones = $clone_adaptor->fetch_all();
   Description: Retrieves every clone from the database.  
-  Returntype : Bio::EnsEMBL::Clone
+  Returntype : listref of Bio::EnsEMBL::Clone
   Exceptions : none
   Caller     : none
 
@@ -253,7 +253,7 @@ sub fetch_all {
 					  $created, $modified);
   }
 
-  return @clones;
+  return \@clones;
 }
 
 
@@ -264,7 +264,7 @@ sub fetch_all {
                the EMBL accession of the clone versions to retrieve
   Example    : @vers = $clone->list_embl_version_by_accession($accession) 
   Description: Returns a list of versions for a given EMBL accession
-  Returntype : list of ints
+  Returntype : listref of ints
   Exceptions : thrown if $id arg is not defined or if no clone with accession
                $id exists in the database
   Caller     : general
@@ -291,7 +291,7 @@ sub list_embl_version_by_accession {
 
     $self->throw("no clone $id") unless scalar @vers > 0;
     
-    return @vers;
+    return \@vers;
 }
 
 
@@ -364,9 +364,9 @@ sub delete_by_dbID {
                retrieved
   Example    : my @genes = $clone_adaptor->get_all_Genes('AC011082');
   Description: Retrieves a list of Gene objects which are present on a clone.
-               It might be better to have this on the gene adaptor but 
+               It would be better to have this on the gene adaptor but 
                for now it will stay here.
-  Returntype : list of Bio::EnsEMBL::Genes
+  Returntype : listref of Bio::EnsEMBL::Genes
   Exceptions : thrown if $clone_id is not defined
   Caller     : Clone::get_all_Genes
 
@@ -400,7 +400,7 @@ sub get_all_Genes {
             $got{$gene_id} = 1;
         }
     }
-    return @genes;
+    return \@genes;
 }
 
 

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -303,14 +303,15 @@ sub store {
 
 
 
-=head2 fetch_by_gene
+=head2 fetch_by_Gene
 
-  Arg [1]    : 
-  Example    : 
-  Description: 
-  Returntype : 
-  Exceptions : 
-  Caller     : 
+  Arg [1]    : Bio::EnsEMBL::Gene $gene 
+               The gene to retrienve DBEntries for
+  Example    : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($gene)};
+  Description: This should be changed, it modifies the gene passed in
+  Returntype : listref of Bio::EnsEMBL::DBEntries
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::Gene
 
 =cut
 
@@ -324,49 +325,49 @@ sub fetch_by_Gene {
   $sth1->execute( $gene->dbID );
 
   while (my $transid = $sth1->fetchrow) {
-
-    my @translation_xrefs = $self->_fetch_by_EnsObject_type( $transid, 'Translation' );
-    foreach my $translink(@translation_xrefs) {
+    my $translation_xrefs = 
+      $self->_fetch_by_object_type( $transid, 'Translation' );
+    foreach my $translink(@$translation_xrefs) {
       $gene->add_DBLink($translink);
     }
   }
-  my @genelinks = $self->_fetch_by_EnsObject_type( $gene->stable_id, 'Gene' );
-  foreach my $genelink ( @genelinks ) {
+  my $genelinks = $self->_fetch_by_object_type( $gene->stable_id, 'Gene' );
+  foreach my $genelink ( @$genelinks ) {
     $gene->add_DBLink( $genelink );
   }
 }
 
 
 
-=head2 fetch_by_rawContig
+=head2 fetch_by_RawContig
 
-  Arg [1]    : 
-  Example    : 
-  Description: 
-  Returntype : 
-  Exceptions : 
-  Caller     : 
+  Arg [1]    : Bio::EnsEMBL::RawContig $contig
+  Example    : @db_entries = @{$db_entry_adaptor->fetch_by_RawContig($contig)}
+  Description: Retrieves a list of RawContigs for this object
+  Returntype : listref of Bio::EnsEMBL::DBEntries
+  Exceptions : none
+  Caller     : general
 
 =cut
 
-sub fetch_by_rawContig {
-  my ( $self, $rawContigId ) = @_;
-  return $self->_fetch_by_EnsObject_type( $rawContigId, 'RawContig' );
+sub fetch_by_RawContig {
+  my ( $self, $contig ) = @_;
+  return $self->_fetch_by_object_type( $rawContigId, 'RawContig' );
 }
 
 
-=head2 fetch_by_transcript
+=head2 fetch_by_Transcript
 
-  Arg [1]    : 
+  Arg [1]    : Bio::EnsEMBL::Transcript
   Example    : 
-  Description: 
+  Description: This should be changed, it modifies the transcipt passed in
   Returntype : 
   Exceptions : 
   Caller     : 
 
 =cut
 
-sub fetch_by_transcript {
+sub fetch_by_Transcript {
   my ( $self, $trans ) = @_;
 
   my $query1 = "SELECT t.translation_id 
@@ -383,34 +384,35 @@ sub fetch_by_transcript {
   #
   
   while (my $transid = $sth1->fetchrow) {
-      my @translation_xrefs = $self->_fetch_by_EnsObject_type( $transid, 'Translation' );
-      foreach my $translink(@translation_xrefs) {
+    my $translation_xrefs = $self->_fetch_by_object_type( $transid, 
+							  'Translation' );
+    foreach my $translink(@$translation_xrefs) {
       $trans->add_DBLink($translink);
     }
   }
-
-
 }
 
 
-=head2 fetch_by_translation
+=head2 fetch_by_Translation
 
-  Arg [1]    : 
-  Example    : 
-  Description: 
-  Returntype : 
-  Exceptions : 
-  Caller     : 
+  Arg [1]    : Bio::EnsEMBL::Translation $trans
+               The translation to fetch database entries for
+  Example    : @db_entries = @{$db_entry_adptr->fetch_by_Translation($trans)};
+  Description: Retrieves external database entries for an EnsEMBL translation
+  Returntype : listref of dbEntries to obtain
+  Exceptions : none
+  Caller     : general
 
 =cut
 
-sub fetch_by_translation {
-  my ( $self, $trslId ) = @_;
-  return $self->_fetch_by_EnsObject_type( $trslId, 'Translation' );
+sub fetch_by_Translation {
+  my ( $self, $trans ) = @_;
+  return $self->_fetch_by_object_type( $trans->dbID(), 'Translation' );
 }
 
 
-=head2 fetch_by_EnsObject_type
+
+=head2 fetch_by_object_type
 
   Arg [1]    : 
   Example    : 
@@ -421,15 +423,19 @@ sub fetch_by_translation {
 
 =cut
 
-sub _fetch_by_EnsObject_type {
+sub _fetch_by_object_type {
   my ( $self, $ensObj, $ensType ) = @_;
   my @out;
   
   my $sth = $self->prepare("
-    SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,
-          xref.version, xref.description,
-          exDB.db_name, exDB.release, oxr.object_xref_id, es.synonym, idt.query_identity, idt.target_identity
-    FROM xref, external_db exDB, object_xref oxr LEFT JOIN external_synonym es on es.xref_id = xref.xref_id 
+    SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
+           xref.description,
+           exDB.db_name, exDB.release, 
+           oxr.object_xref_id, 
+           es.synonym, 
+           idt.query_identity, idt.target_identity
+    FROM   xref xref, external_db exDB, object_xref oxr 
+    LEFT JOIN external_synonym es on es.xref_id = xref.xref_id 
     LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
     WHERE  xref.xref_id = oxr.xref_id
       AND  xref.external_db_id = exDB.external_db_id 
@@ -443,9 +449,9 @@ sub _fetch_by_EnsObject_type {
   my %seen;
   
   while ( my $arrRef = $sth->fetchrow_arrayref() ) {
-    my ( $refID, $dbprimaryId, $displayid, $version, $desc, $dbname, $release, $objid, 
-         $synonym, $queryid, $targetid ) =
-      @$arrRef;
+    my ( $refID, $dbprimaryId, $displayid, $version, 
+	 $desc, $dbname, $release, $objid, 
+         $synonym, $queryid, $targetid ) = @$arrRef;
     
     my $exDB;
     
@@ -493,7 +499,7 @@ sub _fetch_by_EnsObject_type {
     #}
   }                                     # while <a row from database>
   
-  return @out;
+  return \out;
 }
 
 
@@ -718,20 +724,78 @@ sub create_tables {
 }
 
 
-1;
 
+=head2 fetch_by_translation
 
-__END__
+  Arg [1]    : none
+  Example    : none
+  Description: DEPRECATED use fetch_by_Translation instead
+  Returntype : none
+  Exceptions : none
+  Caller     : none
+
+=cut
+
+sub fetch_by_translation {
+  my ($self, $trans_id) = @_;
 
+  $self->warn("fetch_by_translation has been renamed fetch_by_Translation");
+  my $trans = $self->db->get_TranslationAdaptor->fetch_by_dbID($trans_id);
 
-# remove the tables from database
-sub delete_tables {
+  return $self->fetch_by_Translation($trans);
 }
 
-# check if tables exist
-sub exists_tables {
+
+
+=head2 fetch_by_rawContig
+
+  Arg [1]    : none
+  Example    : none
+  Description: DEPRECATED use Bio::EnsEMBL::fetch_by_rawContig instead
+  Returntype : none
+  Exceptions : none
+  Caller     : none
+
+=cut
+
+sub fetch_by_rawContig {
+  my ( $self, $rawContigId ) = @_;
+  
+  $self->warn("fetch_by_rawContig has been renamed fetch_by_RawContig");
+  my $contig = 
+    $self->db->get_RawContigAdaptor->fetch_by_dbID($rawContigID);
+
+  return $self->fetch_by_RawContig( $contig );
 }
 
+
+
+=head2 fetch_by_transcript
+
+  Arg [1]    : none
+  Example    : none
+  Description: DEPRECATED fetch_by_Transcript instead
+  Returntype : none
+  Exceptions : none
+  Caller     : none
+
+=cut
+
+sub fetch_by_transcript {
+  my ( $self, $trans ) = @_;
+
+  $self->warn("fetch_by_transcript has been renamed fetch_by_Transcript");
+
+  return $self->fetch_by_Transcript($trans);
+}
+
+
+1;
+
+
+__END__
+
+
 Objectxref
 =============
 ensembl_id varchar, later int

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -121,26 +121,26 @@ sub fetch_by_stable_id {
 
 
 
-=head2 fetch_by_geneId