diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 425a1d683e932340e2e119491f71593441719183..b1a2e309df3f784d32ac570102240ea367284dcb 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 d78ef198423e6f0b078d9e7103ad2a1c780a0e09..c5c30a477c3fe7f8ac97972a067a7c24507bb384 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 9a1f6c8dada3f90989d73116869d6bc29d33ac4c..722699032ccfd5b2cbd708655004cd0553cb9a67 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 2f395532de92139a4f113f750e84a0e5ab8a2441..2613bc3f2da771fd9011e4db63ce2e5266b1ed81 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) ) {