PODs

modules/Bio/EnsEMBL/Container.pm

@@ -9,13 +9,13 @@ $container = new Bio::EnsEMBL::Container($obj);
 This object is a hack necessary to work around perls circular reference 
 memory leak problems.  Its sole purpose is to channel calls to the 
 object which is held onto by the container and to invoke the objects deleteObj
-method to breaks all circular memory references at the correct time. 
+method to breaks all circular memory references at the correct time.
+
+Eventually this problem may be solved through the use of WeakRef instead. 
 
 =head1 CONTACT
 
-Arne Stabenau - stabenau@ebi.ac.uk
-Graham McVicker - mcvicker@ebi.ac.uk
-Ewan Birney - birney@ebi.ac.uk 
+Post questions to the EnsEMBL developer mailing list: <ensembl-dev@ebi.ac.uk>
 
 =head1 APPENDIX
 

modules/Bio/EnsEMBL/DBEntry.pm

@@ -11,23 +11,24 @@
 
 =pod 
 
-=head1 NAME
+=head1 NAME 
 
-Bio::EnsEMBL::DBEntry - Module to collect information about an
- external reference
+Bio::EnsEMBL::DBEntry - Module to collect information about an external reference
 
 =head1 SYNOPSIS
 
 =head1 DESCRIPTION
 
+This module stores information about external references to EnsEMBL objects
+
 =head1 CONTACT
 
-  Arne Stabenau <stabenau@ebi.ac.uk>
-  Ewan Birney <birney@ebi.ac.uk>
+Post questions to the EnsEMBL developer mailing list: <ensembl-dev@ebi.ac.uk> 
 
 =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
 
@@ -45,6 +46,19 @@ use strict;
 @ISA = qw( Bio::EnsEMBL::Root Bio::Annotation::DBLink );
 
 
+=head2 new_fast
+
+  Arg [1]    : hash reference $hashref
+  Example    : none
+  Description: A very quick constructor that requires internal knowledge of
+               the class. This is used in speed critical sections of the code
+               where many objects need to be created quickly.
+  Returntype : Bio::EnsEMBL::DBEntry
+  Exceptions : none
+  Caller     : ?
+
+=cut
+
 sub new_fast {
   my $class = shift;
   my $hashref = shift;
@@ -52,6 +66,24 @@ sub new_fast {
   return bless $hashref, $class;
 }
 
+
+
+=head2 new
+
+  Args [...] : list of named parameters 
+  Example    : my $dbentry = new Bio::EnsEMBL::DBEntry(-adaptor => $adaptor,
+						       -primary_id => $pid,
+						       -version => $version,
+						       -dbname  => $dbname,
+						       -release => $release,
+						       -display_id => $did);
+  Description: Creates a new DBEntry object
+  Returntype : Bio::EnsEMBL::DBEntry
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::DBEntryAdaptor
+
+=cut
+
 sub new {
   my ($class, @args) = @_;
 
@@ -81,6 +113,7 @@ sub new {
 }
 
 
+
 =head2 primary_id
 
   Arg [1]    : string $primary_id
@@ -93,7 +126,6 @@ sub new {
 
 =cut
 
-
 sub primary_id {
   my ( $self, $arg ) = @_;
   if( defined $arg ) {
@@ -103,6 +135,7 @@ sub primary_id {
 }
 
 
+
 =head2 display_id
 
   Arg [1]    : string $display_id
@@ -116,8 +149,6 @@ sub primary_id {
 
 =cut
 
-
-
 sub display_id{
    my ( $self, $arg ) = @_;
    if( defined $arg ) {
@@ -128,6 +159,7 @@ sub display_id{
 }
 
 
+
 =head2 dbname
 
   Arg [1]    : string $dbname
@@ -139,7 +171,6 @@ sub display_id{
 
 =cut
 
-
 sub dbname {
   my ( $self, $arg ) = @_;
   if( defined $arg ) {
@@ -149,6 +180,7 @@ sub dbname {
 }
 
 
+
 =head2 database
 
   Args       : none
@@ -161,13 +193,13 @@ sub dbname {
 
 =cut
 
-
 sub database {
   my $self = shift;
   return $self->dbname();
 }
 
 
+
 =head2 optional_id
 
   Args       : none
@@ -180,14 +212,13 @@ sub database {
 
 =cut
 
-
-
 sub optional_id {
   my $self = shift;
   return $self->display_id;
 }
 
 
+
 =head2 release
 
   Arg [1]    : string $release
@@ -199,8 +230,6 @@ sub optional_id {
 
 =cut
 
-
-
 sub release {
   my ( $self, $arg ) = @_;
   if( defined $arg ) {
@@ -210,6 +239,20 @@ sub release {
 }
 
 
+
+=head2 adaptor
+
+  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBEntryAdaptor $arg
+  Example    : $adaptor = $dbentry->adaptor;
+  Description: Getter/Setter for the adaptor used by this object for database 
+               interaction. This attribute is set by the adaptor when this
+               object is stored in the database or retrieved from the database.
+  Returntype : Bio::EnsEMBL::DBSQL::DBEntryAdaptor
+  Exceptions : none
+  Caller     : general
+
+=cut
+
 sub adaptor {
   my ( $self, $arg ) = @_;
   if( defined $arg ) {
@@ -219,6 +262,20 @@ sub adaptor {
 }
 
 
+
+=head2 dbID
+
+  Arg [1]    : (optional) int 
+  Example    : $dbID = $dbentry->dbID;
+  Description: Getter/Setter for this objects unique database identifier. This
+               attribute is set the adaptor when this object is store in the
+               database or retrieved from the database.
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+
+=cut
+
 sub dbID {
   my ( $self, $arg ) = @_;
   if( defined $arg ) {