diff --git a/modules/Bio/EnsEMBL/Biotype.pm b/modules/Bio/EnsEMBL/Biotype.pm
index ffe530d8433475a637781bfbaf5fd81d0fad2dde..11b7c5e104d6c903c03414791de8ec2994894b66 100644
--- a/modules/Bio/EnsEMBL/Biotype.pm
+++ b/modules/Bio/EnsEMBL/Biotype.pm
@@ -90,9 +90,6 @@ use base qw(Bio::EnsEMBL::Storable);
Description: Creates a new biotype object
Returntype : Bio::EnsEMBL::Biotype
Exceptions : none
- Caller : general
- Status : Stable
-
=cut
@@ -126,8 +123,6 @@ sub new {
Description: Getter/Setter for the name of this biotype.
Returntype : string
Exceptions : none
- Caller : general
- Status : Stable
=cut
@@ -146,6 +141,8 @@ sub name {
Arg [1] : (optional) string $biotype_group
Example : $biotype_group = $biotype->biotype_group();
Description: Getter/Setter for the biotype_group of this biotype.
+ Biotype groups are used internally at ensembl pipelines
+ and consist on few defined categories.
Returntype : string
Exceptions : none
Caller : general
@@ -167,14 +164,10 @@ sub biotype_group {
Arg [1] : (optional) string $so_acc
Example : $feat->so_acc();
- Description: Getter/Setter for the so_acc of this biotype.
- It must be a Sequence Ontology like accession (SO:\d*)
- -1 is the reverse (negative) so_acc and 1 is the forward
- (positive) so_acc. No other values are permitted.
+ Description: Getter/Setter for the Sequence Ontology accession of this biotype.
+ It must be a SO like accession.
Returntype : string
Exceptions : thrown if an invalid so_acc argument is passed
- Caller : general
- Status : Stable
=cut
@@ -197,10 +190,10 @@ sub so_acc {
Arg [1] : (optional) string $object_type
Example : $object_type = $biotype->object_type();
Description: Getter/Setter for the object_type of this biotype.
+ Biotypes can be assigned to either genes or transcripts,
+ object_type refers to which of them.
Returntype : string
- Exceptions : none
- Caller : general
- Status : Stable
+ Exceptions : thrown if an invalid object_type argument is passed (not gene or transcript)
=cut
@@ -208,31 +201,16 @@ sub object_type {
my ( $self, $value ) = @_;
if ( defined($value) ) {
+ $value = lc $value;
+ throw("object_type must be gene or transcript. Got '$value'.")
+ unless ( $value eq 'gene' || $value eq 'transcript' );
+
$self->{'object_type'} = $value;
}
return $self->{'object_type'};
}
-=head2 as_hash
-
- Example : $biotype_hash = $biotype->as_hash();
- Description : Retrieves this Biotype as a hash.
- Returns : hashref of descriptive strings
- Status : Intended for internal use
-=cut
-
-sub as_hash {
- my ( $self ) = @_;
-
- return {
- name => $self->name,
- biotype_group => $self->biotype_group,
- so_acc => $self->so_acc,
- object_type => $self->object_type,
- };
-}
-
use overload '""' => \&as_string;
@@ -245,7 +223,7 @@ use overload '""' => \&as_string;
If Biotype object is called this is what is returned to maintain compatibility
with legacy biotype() methods in Gene and Transcript objects.
Returns : string for the biotype.
- Status : Intended for internal use
+
=cut
sub as_string {
diff --git a/modules/Bio/EnsEMBL/DBSQL/BiotypeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BiotypeAdaptor.pm
index 6fc73229e2c3d53268617eb7b895e733aef99f74..97ebb4144a1761734d3643d4839d2b64bedeaf9b 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BiotypeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BiotypeAdaptor.pm
@@ -30,19 +30,20 @@ limitations under the License.
=head1 NAME
-Bio::EnsEMBL::DBSQL::BiotypeAdaptor - Encapsulates all generic access
-to database meta information
+ Bio::EnsEMBL::DBSQL::BiotypeAdaptor - An adaptor which performs database
+ interaction relating to the storage and retrieval of Biotypes
=head1 SYNOPSIS
- my $meta_container = $db_adaptor->get_MetaContainer();
-
- my @mapping_info =
- @{ $meta_container->list_value_by_key('assembly.mapping') };
+ my $biotype = $db_adaptor->fetch_by_name_object_type('protein_coding', 'gene');
=head1 DESCRIPTION
- An object that encapsulates access to db meta data
+ This adaptor provides a means to retrieve and store information related
+ to Biotypes. Primarily this involves the retrieval or storage of
+ Bio::EnsEMBL::Biotype objects from a database.
+
+ See Bio::EnsEMBL::Biotype for details of the Biotype class.
=head1 METHODS
@@ -66,8 +67,6 @@ use base qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
Returns the names, aliases of the tables to use for queries.
Returntype : list of listrefs of strings
Exceptions : none
- Caller : internal
- Status : Stable
=cut
@@ -85,8 +84,6 @@ sub _tables {
Returns a list of columns to use for queries.
Returntype : list of strings
Exceptions : none
- Caller : internal
- Status : Stable
=cut
@@ -102,10 +99,8 @@ sub _columns {
Example : none
Description: PROTECTED implementation of abstract superclass method.
responsible for the creation of ProteinFeatures
- Returntype : listref of Bio::EnsEMBL::Biotype
+ Returntype : listref of Bio::EnsEMBL::Biotype objects
Exceptions : none
- Caller : internal
- Status : At Risk
=cut
@@ -149,8 +144,6 @@ sub _objs_from_sth {
created with the provided name and object_type to be returned.
Returntype : Bio::EnsEMBL::Biotype
Exceptions : none
- Caller : general
- Status : Stable
=cut
@@ -179,10 +172,8 @@ sub fetch_by_name_object_type {
The object_type of the biotypes to retrieve (gene or transcript).
Example : $biotypes = $biotype_adaptor->fetch_all_by_object_type('gene');
Description: Retrieves an array reference of biotype objects from the database.
- Returntype : listref of Bio::EnsEMBL::Biotype objects or undef
+ Returntype : listref of Bio::EnsEMBL::Biotype objects or empty list
Exceptions : none
- Caller : general
- Status : Stable
=cut