From 2151b2cc10c1b98d9a1effbdea8c3ecb549ed67d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 24 Oct 2011 13:19:07 +0000
Subject: [PATCH] In equals(): Reorder so that the defined() test is first.
Reformat.
---
modules/Bio/EnsEMBL/Exon.pm | 13 ++++++------
modules/Bio/EnsEMBL/Feature.pm | 33 ++++++++++++-------------------
modules/Bio/EnsEMBL/Gene.pm | 17 +++++++---------
modules/Bio/EnsEMBL/Transcript.pm | 17 ++++++++--------
4 files changed, 36 insertions(+), 44 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 425a1d683e..b1a2e309df 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -848,8 +848,8 @@ sub slice {
sub equals {
my ( $self, $exon ) = @_;
+ if ( !defined($exon) ) { return 0 }
if ( $self eq $exon ) { return 1 }
- if ( ! defined $exon ) { return 0 }
assert_ref( $exon, 'Bio::EnsEMBL::Exon' );
@@ -862,15 +862,16 @@ sub equals {
{
if ( $self->stable_id() eq $exon->stable_id() ) {
return 1;
- } else {
+ }
+ else {
return 0;
}
}
- if ( $self->start() == $exon->start()
- && $self->end() == $exon->end()
- && $self->strand() == $exon->strand()
- && $self->phase() == $exon->phase() )
+ if ( $self->start() == $exon->start() &&
+ $self->end() == $exon->end() &&
+ $self->strand() == $exon->strand() &&
+ $self->phase() == $exon->phase() )
{
return 1;
}
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index d78ef19842..c5c30a477c 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -438,12 +438,8 @@ sub equals {
my ( $self, $feature ) = @_;
# If the features are the same object, they are equal.
- if ( $self eq $feature ) {
- return 1;
- }
- if ( ! defined $feature ) {
- return 0;
- }
+ if ( !defined($feature) ) { return 0 }
+ if ( $self eq $feature ) { return 1 }
assert_ref( $feature, 'Bio::EnsEMBL::Feature' );
@@ -454,12 +450,10 @@ sub equals {
# If the features has the same dbID, they are equal.
if ( defined( $self->dbID() ) && defined( $feature->dbID() ) ) {
- if ( $self->dbID() == $feature->dbID() ) {
- return 1;
- } else {
- return 0;
- }
+ if ( $self->dbID() == $feature->dbID() ) { return 1 }
+ else { return 0 }
}
+
# We now know that one of the features do not have a dbID.
# If the features have the same start, end, strand and seq_region_id,
@@ -468,19 +462,18 @@ sub equals {
( defined( $self->analysis() ) && defined( $feature->analysis() ) )
&& ( defined( $self->slice() ) && defined( $feature->slice() ) ) )
{
- if ( ( $self->start() == $feature->start() )
- && ( $self->end() == $feature->end() )
- && ( $self->strand() == $feature->strand() )
- && ( $self->slice()->get_seq_region_id() ==
- $feature->slice()->get_seq_region_id() )
- && ( $self->analysis()->dbID() == $feature->analysis()->dbID() )
- )
+ if ( ( $self->start() == $feature->start() ) &&
+ ( $self->end() == $feature->end() ) &&
+ ( $self->strand() == $feature->strand() ) &&
+ ( $self->slice()->get_seq_region_id() ==
+ $feature->slice()->get_seq_region_id() ) &&
+ ( $self->analysis()->dbID() == $feature->analysis()->dbID() ) )
{
return 1;
- } else {
- return 0;
}
+ else { return 0 }
}
+
# We now know that one of the features does not have either analysis
# or slice.
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 9a1f6c8dad..722699032c 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -389,8 +389,8 @@ sub description {
sub equals {
my ( $self, $gene ) = @_;
+ if ( !defined($gene) ) { return 0 }
if ( $self eq $gene ) { return 1 }
- if ( ! defined $gene ) { return 0 }
assert_ref( $gene, 'Bio::EnsEMBL::Gene' );
@@ -405,20 +405,17 @@ sub equals {
if ( defined( $self->stable_id() ) && defined( $gene->stable_id() ) )
{
- if ( $self->stable_id() eq $gene->stable_id() ) {
- return 1;
- } else {
- return 0;
- }
+ if ( $self->stable_id() eq $gene->stable_id() ) { return 1 }
+ else { return 0 }
}
my @self_transcripts = sort {
- $a->start() <=> $b->start()
- || $a->length() <=> $b->length()
+ $a->start() <=> $b->start() ||
+ $a->length() <=> $b->length()
} @{ $self->get_all_Transcripts() };
my @gene_transcripts = sort {
- $a->start() <=> $b->start()
- || $a->length() <=> $b->length()
+ $a->start() <=> $b->start() ||
+ $a->length() <=> $b->length()
} @{ $gene->get_all_Transcripts() };
if ( scalar(@self_transcripts) != scalar(@gene_transcripts) ) {
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 2f395532de..2613bc3f2d 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -2091,7 +2091,7 @@ sub swap_exons {
sub equals {
my ( $self, $transcript ) = @_;
- if ( ! defined $transcript ) { return 0 }
+ if ( !defined($transcript) ) { return 0 }
if ( $self eq $transcript ) { return 1 }
assert_ref( $transcript, 'Bio::EnsEMBL::Transcript' );
@@ -2105,23 +2105,24 @@ sub equals {
return 0;
}
- if ( defined( $self->stable_id() )
- && defined( $transcript->stable_id() ) )
+ if ( defined( $self->stable_id() ) &&
+ defined( $transcript->stable_id() ) )
{
if ( $self->stable_id() eq $transcript->stable_id() ) {
return 1;
- } else {
+ }
+ else {
return 0;
}
}
my @self_exons = sort {
- $a->start() <=> $b->start()
- || $a->length() <=> $b->length()
+ $a->start() <=> $b->start() ||
+ $a->length() <=> $b->length()
} @{ $self->get_all_Exons() };
my @transcript_exons = sort {
- $a->start() <=> $b->start()
- || $a->length() <=> $b->length()
+ $a->start() <=> $b->start() ||
+ $a->length() <=> $b->length()
} @{ $transcript->get_all_Exons() };
if ( scalar(@self_exons) != scalar(@transcript_exons) ) {
--
GitLab