From dc9cd2aba56f7186e4c8bc53858fc4d464eacef0 Mon Sep 17 00:00:00 2001
From: Tiago Grego <tgrego@ebi.ac.uk>
Date: Fri, 23 Feb 2018 14:21:42 +0000
Subject: [PATCH] updated Biotype.pm, percritic -3 OK
---
modules/Bio/EnsEMBL/Biotype.pm | 40 +++++++++++++++++++---------------
1 file changed, 23 insertions(+), 17 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Biotype.pm b/modules/Bio/EnsEMBL/Biotype.pm
index 6477ecd9a4..636b6430c0 100644
--- a/modules/Bio/EnsEMBL/Biotype.pm
+++ b/modules/Bio/EnsEMBL/Biotype.pm
@@ -101,14 +101,14 @@ use parent qw(Bio::EnsEMBL::Storable);
=cut
sub new {
- my $caller = shift;
+ my ( $caller, @args ) = @_;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new();
my($dbID, $name, $object_type, $biotype_group, $so_acc, $description, $db_type, $attrib_type_id) =
- rearrange([qw(BIOTYPE_ID NAME OBJECT_TYPE BIOTYPE_GROUP SO_ACC DESCRIPTION DB_TYPE ATTRIB_TYPE_ID)], @_);
+ rearrange([qw(BIOTYPE_ID NAME OBJECT_TYPE BIOTYPE_GROUP SO_ACC DESCRIPTION DB_TYPE ATTRIB_TYPE_ID)], @args);
$self->{'dbID'} = $dbID;
$self->{'name'} = $name;
@@ -136,7 +136,10 @@ sub new_fast {
my ( $class, $hashref ) = @_;
my $self = bless $hashref, $class;
- weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
+
+ if ( !isweak($self->{adaptor}) ) {
+ weaken($self->{adaptor})
+ }
return $self;
}
@@ -153,10 +156,10 @@ sub new_fast {
=cut
sub name {
- my ( $self, $value ) = @_;
+ my ( $self, $name ) = @_;
- if ( defined($value) ) {
- $self->{'name'} = $value;
+ if ( defined($name) ) {
+ $self->{'name'} = $name;
}
return $self->{'name'};
@@ -177,10 +180,10 @@ sub name {
=cut
sub biotype_group {
- my ( $self, $value ) = @_;
+ my ( $self, $biotype_group ) = @_;
- if ( defined($value) ) {
- $self->{'biotype_group'} = $value;
+ if ( defined($biotype_group) ) {
+ $self->{'biotype_group'} = $biotype_group;
}
return $self->{'biotype_group'};
@@ -202,8 +205,9 @@ sub so_acc {
if ( defined($so_acc) ) {
# throw an error if setting something that does not look like an SO acc
- throw("so_acc must be a Sequence Ontology accession. '$so_acc' does not look like one.")
- unless ( $so_acc =~ m/\ASO:\d+\z/ );
+ unless ( $so_acc =~ m/\ASO:\d+\z/x ) {
+ throw("so_acc must be a Sequence Ontology accession. '$so_acc' does not look like one.")
+ }
$self->{'so_acc'} = $so_acc;
}
@@ -224,14 +228,16 @@ sub so_acc {
=cut
sub object_type {
- my ( $self, $value ) = @_;
+ my ( $self, $object_type ) = @_;
- if ( defined($value) ) {
- $value = lc $value;
- throw("object_type must be gene or transcript. Got '$value'.")
- unless ( $value eq 'gene' || $value eq 'transcript' );
+ if ( defined($object_type) ) {
+ $object_type = lc $object_type;
+ # throw an error if setting something that does not look like an SO acc
+ unless ( $object_type eq 'gene' || $object_type eq 'transcript' ) {
+ throw("object_type must be gene or transcript. Got '$object_type'.")
+ }
- $self->{'object_type'} = $value;
+ $self->{'object_type'} = $object_type;
}
return $self->{'object_type'};
--
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