From 3551facbc6c837dfb125f61c4f77ef77de491e48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 1 Sep 2010 14:34:49 +0000
Subject: [PATCH] Document the (optional) arguments for get_all_DBLinks() and
get_all_DBEntries(). From Michael S.
---
modules/Bio/EnsEMBL/Transcript.pm | 41 ++++++++++++++++++-------------
1 file changed, 24 insertions(+), 17 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 74ed062ac4..4cb73b0662 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -181,7 +181,9 @@ sub new {
=head2 get_all_DBLinks
- Example : my @dblinks = @{ $transcript->get_all_DBLinks };
+ Arg [1] : (optional) String, external database name
+ Arg [2] : (optional) String, external database type
+ Example : my @dblinks = @{ $transcript->get_all_DBLinks() };
Description: Retrieves _all_ related DBEntries for this transcript.
This includes all DBEntries that are associated with the
corresponding translation.
@@ -198,18 +200,21 @@ sub new {
=cut
sub get_all_DBLinks {
- my $self = shift;
- my $ex_db_exp = shift;
- my $ex_db_type = shift;
+ my ( $self, $ex_db_exp, $ex_db_type ) = @_;
my @links;
- push @links, @{$self->get_all_DBEntries($ex_db_exp, $ex_db_type)};
+ push( @links,
+ @{ $self->get_all_DBEntries( $ex_db_exp, $ex_db_type ) } );
- my $transl = $self->translation();
- push @links, @{$transl->get_all_DBEntries($ex_db_exp, $ex_db_type)} if($transl);
+ my $translation = $self->translation();
+ if ( defined($translation) ) {
+ push( @links,
+ @{$translation->get_all_DBEntries( $ex_db_exp, $ex_db_type ) }
+ );
+ }
- @links = sort {_compare_xrefs()} @links;
+ @links = sort { _compare_xrefs() } @links;
return \@links;
}
@@ -217,7 +222,9 @@ sub get_all_DBLinks {
=head2 get_all_DBEntries
- Example : my @dbentries = @{ $gene->get_all_DBEntries };
+ Arg [1] : (optional) String, external database name
+ Arg [2] : (optional) String, external database type
+ Example : my @dbentries = @{ $gene->get_all_DBEntries() };
Description: Retrieves DBEntries (xrefs) for this transcript.
This does _not_ include the corresponding translations
DBEntries (see get_all_DBLinks).
@@ -234,22 +241,22 @@ sub get_all_DBLinks {
=cut
sub get_all_DBEntries {
- my $self = shift;
- my $ex_db_exp = shift;
- my $ex_db_type = shift;
+ my ( $self, $ex_db_exp, $ex_db_type ) = @_;
my $cache_name = "dbentries";
- if(defined($ex_db_exp)){
+ if ( defined($ex_db_exp) ) {
$cache_name .= $ex_db_exp;
}
- if(defined($ex_db_type)){
+ if ( defined($ex_db_type) ) {
$cache_name .= $ex_db_type;
}
+
# if not cached, retrieve all of the xrefs for this gene
- if(!defined $self->{$cache_name} && $self->adaptor()) {
- $self->{$cache_name} =
- $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Transcript($self, $ex_db_exp, $ex_db_type);
+ if ( !defined $self->{$cache_name} && $self->adaptor() ) {
+ $self->{$cache_name} =
+ $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Transcript(
+ $self, $ex_db_exp, $ex_db_type );
}
$self->{$cache_name} ||= [];
--
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