Correct documentation.

modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm

@@ -87,7 +87,7 @@ sub new {
 =head2 fetch_all
 
   Args       : none
-  Example    : my @analysis = $analysis_adaptor->fetch_all()
+  Example    : my @analysis = @{$analysis_adaptor->fetch_all()};
   Description: fetches all of the Analysis objects from the database and caches
                them internally.
   Returntype : listref of Bio::EnsEMBL::Analysis retrieved from the database

modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm

@@ -55,8 +55,9 @@ use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
                A lower bound for the hcoverage of feats to obtain.
   Arg [3]    : (optional) string $logic_name
                The logic name of the type of features to obtain.
-  Example    : @feats =
-                $adaptor->fetch_all_by_Slice_and_hcoverage( $slice, 50.0 );
+  Example    : @feats = @{
+                $adaptor->fetch_all_by_Slice_and_hcoverage( $slice,
+                  50.0 ) };
   Description: Returns a listref of features created from the
                database which are on the Slice $slice and with a
                hcoverage greater than $hcoverage.  If logic name
@@ -92,8 +93,9 @@ sub fetch_all_by_Slice_and_hcoverage {
                should be restricted.
   Arg [3]    : (optional) string $logic_name
                The logic name of the type of features to obtain.
-  Example    : @feats =
-                $adaptor->fetch_all_by_Slice_and_external_db( $slice, 'EMBL' );
+  Example    : @feats = @{
+                  $adaptor->fetch_all_by_Slice_and_external_db( $slice,
+                    'EMBL' ) };
   Description: Returns a listref of features created from the
                database which are on the Slice $slice and associated
                with external DB $external_db_name.  If logic name
@@ -151,7 +153,8 @@ sub fetch_all_by_Slice_and_external_db {
                to obtain.
   Arg [3]    : (optional) string $logic_name
                The logic name of the type of features to obtain.
-  Example    : @feats = $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 );
+  Example    : @feats =
+                 @{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };
   Description: Returns a listref of features created from the
                database which are on the Slice $slice and with a
                percentage identity greater than $pid.  If logic name
@@ -197,7 +200,8 @@ sub fetch_all_by_Slice_and_pid {
                The analysis logic name of the type of features to
                obtain.
   Example    : @feats =
-                $adaptor->fetch_all_by_hit_name( $name, $logic_name );
+                 @{ $adaptor->fetch_all_by_hit_name( $name,
+                   $logic_name ); }
   Description: Returns a listref of features created from the
                database which correspond to the given hit_name.  If
                logic name is defined, only features with an analysis
@@ -244,7 +248,8 @@ sub fetch_all_by_hit_name {
                The analysis logic name of the type of features to
                obtain.
   Example    : @feats =
-                $adaptor->fetch_all_by_hit_name( $name, $logic_name );
+                  @{ $adaptor->fetch_all_by_hit_name( $name,
+                    $logic_name ) };
   Description: Returns a listref of features created from the
                database which start with the given hit_name.  If
                logic name is defined, only features with an analysis

modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm

@@ -89,7 +89,7 @@ sub get_schema_version {
 
   Arg [1]    : string $key
                the key to obtain values from the meta table with
-  Example    : my @values = $meta_container->list_value_by_key($key);
+  Example    : my @values = @{ $meta_container->list_value_by_key($key) };
   Description: gets a value for a key. Can be anything 
   Returntype : listref of strings 
   Exceptions : none

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -359,7 +359,7 @@ sub fetch_by_exon_stable_id {
 
   Arg [1]    : String $domain
                The domain to fetch genes from
-  Example    : my @genes = $gene_adaptor->fetch_all_by_domain($domain);
+  Example    : my @genes = @{ $gene_adaptor->fetch_all_by_domain($domain) };
   Description: Retrieves a listref of genes whose translation contain interpro
                domain $domain. The genes are returned in their native coord
                system (i.e. the coord_system they are stored in). If the coord
@@ -1343,7 +1343,9 @@ sub remove {
 
   Arg [1]    : String $gene_stable_id
                The stable ID of the gene to obtain
-  Example    : @i = $gene_adaptor->get_Interpro_by_geneid($gene->stable_id()); 
+  Example    : @i = @{
+                  $gene_adaptor->get_Interpro_by_geneid(
+                    $gene->stable_id() ) };
   Description: Gets interpro accession numbers by gene stable id. A hack really
                - we should have a much more structured system than this.
   Returntype : listref of strings (Interpro_acc:description)

modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm

@@ -61,7 +61,8 @@ use vars qw(@ISA);
   Arg [1]    : int $transl
                the internal id of the translation corresponding to protein 
                whose features are desired 
-  Example    : @prot_feats = $prot_feat_adaptor->fetch_by_translation_id(1234);
+  Example    : @prot_feats =
+                  @{ $prot_feat_adaptor->fetch_by_translation_id(1234) };
   Description: Gets all protein features present on a peptide using the
                translations internal identifier.  This method will return
                an unsorted list of all protein_feature types.  The feature

modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm

@@ -338,8 +338,11 @@ sub get {
   Arg[1]      : String $dbtype - db type ('source' or 'target')
   Arg[2]      : String $class - key identifying a gene type (see class_key())
   Arg[3]      : String $subclass - status identifier (e.g. 'mapped', 'lost')
-  Example     : my @mapped_stable_ids = $analyser->get_all_by_subclass('source',
-                  'KNOWN-ensembl-protein_coding', 'mapped');
+  Example     : my @mapped_stable_ids = @{
+                  $analyser->get_all_by_subclass(
+                    'source', 'KNOWN-ensembl-protein_coding',
+                    'mapped'
+                  ) };
   Description : Gets a list of stable Id for a given subclass.
   Return type : Arrayref of String (stable Ids)
   Exceptions  : thrown on missing arguments
@@ -365,8 +368,9 @@ sub get_all_by_subclass {
 
   Arg[1]      : String $dbtype - db type ('source' or 'target')
   Arg[2]      : String $class - key identifying a gene type (see class_key())
-  Example     : my @stable_ids = $analyser->get_all_by_class('source',
-                  'KNOWN-ensembl-protein_coding');
+  Example     : my @stable_ids = @{
+                  $analyser->get_all_by_class( 'source',
+                    'KNOWN-ensembl-protein_coding' ) };
   Description : Gets a list of stable Id for a given class.
   Return type : Arrayref of String (stable Ids)
   Exceptions  : thrown on missing arguments

modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm

@@ -379,7 +379,7 @@ sub get_score {
 =head2 get_targets_for_source
 
   Arg[1]      : Int $source - source object's internal Id ("dbID")
-  Example     : my @targets = $gene_scores->get_targets_for_source(1234);
+  Example     : my @targets = @{ $gene_scores->get_targets_for_source(1234) };
   Description : Returns a list of all targets which have a score against a given
                 source object.
   Return type : Arrayref of Int (target objects' internal Ids)
@@ -401,7 +401,7 @@ sub get_targets_for_source {
 =head2 get_Entries_for_source
 
   Arg[1]      : Int $source - source object's internal Id ("dbID")
-  Example     : my @entries = $gene_scores->get_Entries_for_source(1234);
+  Example     : my @entries = @{ $gene_scores->get_Entries_for_source(1234) };
   Description : Returns a list of all Entries in the scoring matrix for a given
                 source object.
   Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry objects
@@ -424,7 +424,7 @@ sub get_Entries_for_source {
 =head2 get_sources_for_target
 
   Arg[1]      : Int $target - target object's internal Id ("dbID")
-  Example     : my @sources = $gene_scores->get_sources_for_target(5678);
+  Example     : my @sources = @{ $gene_scores->get_sources_for_target(5678) };
   Description : Returns a list of all sources which have a score against a given
                 target object.
   Return type : Arrayref of Int (source objects' internal Ids)
@@ -446,7 +446,7 @@ sub get_sources_for_target {
 =head2 get_Entries_for_target
 
   Arg[1]      : Int $target - target object's internal Id ("dbID")
-  Example     : my @entries = $gene_scores->get_Entries_for_target(5678);
+  Example     : my @entries = @{ $gene_scores->get_Entries_for_target(5678) };
   Description : Returns a list of all Entries in the scoring matrix for a given
                 target object.
   Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry objects