POD corrections

modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm

@@ -53,13 +53,13 @@ my $reg = "Bio::EnsEMBL::Registry";
 
 =head2 new
 
-  Example      : $MergedAdaptor = new 
-               : Bio::EnsEMBL::DBSQL::MergedAdaptor(-species=> 'human', -type =>'Population', -groups => ['Sanger','Ensembl']);
   Arg [SPECIES]: (optional) string 
                   species name to get adaptors for
   Arg [TYPE]   : (optional) string 
                   type to get adaptors for
   Arg [GROUPS] : (optional) ref to list
+  Example      : $MergedAdaptor = new 
+               : Bio::EnsEMBL::DBSQL::MergedAdaptor(-species=> 'human', -type =>'Population', -groups => ['Sanger','Ensembl']);
 
   Description: Creates a new MergedAdaptor
   Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor

modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm

@@ -124,8 +124,7 @@ sub fetch_all_CoordSystems_by_feature_type {
 
   Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
   Arg [2]    : string $table
-  Example    : $max_len = 
-                $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');
+  Example    : $max_len = $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');
   Description: Returns the maximum length of features of a given type in
                a given coordinate system.
   Returntype : int or undef

modules/Bio/EnsEMBL/DensityFeature.pm

@@ -255,7 +255,7 @@ sub density_type{
  Title   : scaledvalue
  Usage   : $obj->scaledvalue($newval)
  Function:
- Returns : this objects scaled value
+ Returns : scalar - object's scaled value
  Args    : newvalue (optional)
  Status  : Stable
 
@@ -277,7 +277,7 @@ sub scaledvalue{
  Title   : url
  Usage   : $obj->url($newval)
  Function:
- Returns : this object's url
+ Returns : String containing this object's url
  Args    : newvalue (optional)
  Status  : Stable
 

modules/Bio/EnsEMBL/DensityFeatureSet.pm

@@ -150,7 +150,7 @@ sub colour{
  Title   : label
  Usage   : $obj->label($newval)
  Function: 
- Returns : value of label
+ Returns : String containing label
  Args    : newvalue (optional)
  Status  : Stable
 
@@ -170,7 +170,7 @@ sub label{
  Title   : label2
  Usage   : $obj->label2($newval)
  Function: 
- Returns : value of label2
+ Returns : String containing label2
  Args    : newvalue (optional)
  Status  : Stable
 

modules/Bio/EnsEMBL/DensityType.pm

@@ -116,8 +116,7 @@ sub new {
 
 =head2 analysis
 
-  Arg [1]    : Bio::EnsEMBL::Analysi
-  Example    : none
+  Arg [1]    : Bio::EnsEMBL::Analysis
   Description: get/set for attribute analysis
   Returntype : Bio::EnsEMBL::Analysis
   Exceptions : none
@@ -142,8 +141,7 @@ sub analysis{
 =head2 value_type
 
   Arg [1]    : string $value_type
-  Example    : none
-  Description: gettter/setter for the 
+  Description: gettter/setter for the type 
   Returntype : float
   Exceptions : none
   Caller     : general
@@ -161,7 +159,6 @@ sub value_type{
 =head2 block_size
 
   Arg [1]    : int
-  Example    : none
   Description: getter/setter for attribute block_size
   Returntype : int
   Exceptions : none

modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm

@@ -99,7 +99,6 @@ sub pair_dna_align_feature_id{
 =head2 _hit_unit
 
   Arg [1]    : none
-  Example    : none
   Description: PRIVATE implementation of abstract superclass method.  Returns
                1 as the 'unit' used for the hit sequence. 
   Returntype : int
@@ -118,7 +117,6 @@ sub _hit_unit {
 =head2 _query_unit
 
   Arg [1]    : none
-  Example    : none
   Description: PRIVATE implementation of abstract superclass method Returns
                1 as the 'unit' used for the hit sequence.
   Returntype : int

modules/Bio/EnsEMBL/DnaPepAlignFeature.pm

@@ -72,7 +72,6 @@ sub new_fast {
 =head2 _hit_unit
 
   Arg [1]    : none
-  Example    : none
   Description: PRIVATE implementation of abstract superclass method.  Returns
                1 as the 'unit' used for the hit sequence. 
   Returntype : int
@@ -91,7 +90,6 @@ sub _hit_unit {
 =head2 _query_unit
 
   Arg [1]    : none
-  Example    : none
   Description: PRIVATE implementation of abstract superclass method.  Returns
                3 as the 'unit' used for the query sequence. 
   Returntype : int

modules/Bio/EnsEMBL/Feature.pm

@@ -759,7 +759,7 @@ sub transfer {
         $clone->strand, "\n";
     }
   Description: Returns the results of 'projecting' this feature onto another
-               slcie . This is useful to see where a feature
+               slice . This is useful to see where a feature
                would lie in a coordinate system in which it
                crosses a boundary.
 
@@ -779,7 +779,7 @@ sub transfer {
                If the feature projects entirely into a gap then a reference to
                an empty list is returned.
 
-  Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
+  Returntype : listref of Bio::EnsEMBL::ProjectionSegments
                which can also be used as [$start,$end,$slice] triplets
   Exceptions : slice does not have an adaptor
   Caller     : general
@@ -853,7 +853,7 @@ sub project_to_slice {
                If the feature projects entirely into a gap then a reference to
                an empty list is returned.
 
-  Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
+  Returntype : listref of Bio::EnsEMBL::ProjectionSegments
                which can also be used as [$start,$end,$slice] triplets
   Exceptions : slice does not have an adaptor
   Caller     : general
@@ -1024,7 +1024,7 @@ sub seq_region_name {
   Example    : print $feature->seq_region_length();
   Description: Returns the length of the seq_region which this feature is on 
                Returns undef if this Feature is not on a slice.
-  Returntype : unsigned int or undef
+  Returntype : int (unsigned) or undef
   Exceptions : none
   Caller     : general
   Status     : Stable
@@ -1242,7 +1242,7 @@ sub seq {
                haplotypes will give you back the reference location, but not
                locations on the other alternate haplotypes).
 
-  Returntype : reference to list of features of the same type of this feature.
+  Returntype : listref of features of the same type of this feature.
   Exceptions : none
   Caller     : general
   Status     : Stable
@@ -1465,11 +1465,11 @@ sub species {
 ##############################################
 
 
-# contig
-#
-# This method is included for backwards compatibility.
-# Use slice() instead
-#
+=head2 contig
+
+ This method is deprecated and included for backwards compatibility only.
+ Use slice() instead
+=cut
 sub contig {
   deprecate('Use slice() instead');
   slice(@_);
@@ -1477,21 +1477,21 @@ sub contig {
 
 
 
-# sub_SeqFeature
-#
-# This method is only for genebuild backwards compatibility.
-# Avoid using it if possible
-#
+=head2 sub_SeqFeature
+
+ This method is deprecated and only for genebuild backwards compatibility.
+ Avoid using it if possible
+=cut
 sub sub_SeqFeature{
   my ($self) = @_;
   return @{$self->{'_gsf_sub_array'}} if($self->{'_gsf_sub_array'});
 }
 
-# add_sub_SeqFeature
-#
-# This method is only for genebuild backwards compatibility.
-# Avoid using it if possible
-#
+=head2 add_sub_SeqFeature
+
+ This method is deprecated and only for genebuild backwards compatibility.
+ Avoid using it if possible
+=cut
 sub add_sub_SeqFeature{
   my ($self,$feat,$expand) = @_;
   my ($p, $f, $l) = caller;
@@ -1521,11 +1521,11 @@ sub add_sub_SeqFeature{
    push(@{$self->{'_gsf_sub_array'}},$feat);
 }
 
-# flush_sub_SeqFeature
-#
-# This method is only for genebuild backwards compatibility.
-# Avoid using it isf possible
-#
+=head2 flush_sub_SeqFeature
+
+ This method is deprecated and only for genebuild backwards compatibility.
+ Avoid using it isf possible
+=cut
 sub flush_sub_SeqFeature {
   my ($self) = @_;
   $self->{'_gsf_sub_array'} = [];
@@ -1562,11 +1562,14 @@ sub _deprecated_transform {
   return $self;
 }
 
-# id
-#
-# This method is included for backwards compatibility only.
-# Use hseqname or dbID or stable_id instead
-#
+
+=head2 id
+
+This method is deprecated and only included for backwards compatibility.
+Use display_id, hseqname, dbID or stable_id instead
+
+=cut
+
 sub id {
   my $self = shift;
   deprecate("id method is not used - use display_id instead");