Clean up tabs and returned undef.

modules/Bio/EnsEMBL/Analysis.pm

@@ -73,7 +73,7 @@ use Bio::EnsEMBL::Storable;
 use Bio::EnsEMBL::Utils::Exception qw(throw);
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
 
-@ISA = qw(Bio::EnsEMBL::Storable);
+use base 'Bio::EnsEMBL::Storable';
 
 
 =head2 new
@@ -112,26 +112,26 @@ sub new {
       $parameters, $created, $logic_name, $description, $display_label,
       $displayable, $web_data) =
 
-	  rearrange([qw(ID
-	  			ADAPTOR
-				DB
-				DB_VERSION
-				DB_FILE
-				PROGRAM
-				PROGRAM_VERSION
-				PROGRAM_FILE
-				GFF_SOURCE
-				GFF_FEATURE
-				MODULE
-				MODULE_VERSION
-				PARAMETERS
-				CREATED
-				LOGIC_NAME
-			        DESCRIPTION
-                                DISPLAY_LABEL
-			        DISPLAYABLE
-                                WEB_DATA
-				)],@args);
+  rearrange([qw(ID
+    ADAPTOR
+    DB
+    DB_VERSION
+    DB_FILE
+    PROGRAM
+    PROGRAM_VERSION
+    PROGRAM_FILE
+    GFF_SOURCE
+    GFF_FEATURE
+    MODULE
+    MODULE_VERSION
+    PARAMETERS
+    CREATED
+    LOGIC_NAME
+    DESCRIPTION
+    DISPLAY_LABEL
+    DISPLAYABLE
+    WEB_DATA
+  )],@args);
 
   $displayable ||= 0;
 
@@ -173,7 +173,7 @@ sub db {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_db} = $arg;
+      $self->{_db} = $arg;
     }
 
     return $self->{_db};
@@ -195,7 +195,7 @@ sub db_version {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_db_version} = $arg;
+      $self->{_db_version} = $arg;
     }
 
     return $self->{_db_version};
@@ -217,7 +217,7 @@ sub db_file {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_db_file} = $arg;
+      $self->{_db_file} = $arg;
     }
 
     return $self->{_db_file};
@@ -240,7 +240,7 @@ sub program {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_program} = $arg;
+      $self->{_program} = $arg;
     }
 
     return $self->{_program};
@@ -262,7 +262,7 @@ sub program_version {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_program_version} = $arg;
+      $self->{_program_version} = $arg;
     }
 
     return $self->{_program_version};
@@ -284,7 +284,7 @@ sub program_file {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_program_file} = $arg;
+      $self->{_program_file} = $arg;
     }
 
     return $self->{_program_file};
@@ -307,7 +307,7 @@ sub module {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_module} = $arg;
+      $self->{_module} = $arg;
     }
 
     return $self->{_module};
@@ -329,7 +329,7 @@ sub module_version {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_module_version} = $arg;
+      $self->{_module_version} = $arg;
     }
 
     return $self->{_module_version};
@@ -351,7 +351,7 @@ sub gff_source {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_gff_source} = $arg;
+      $self->{_gff_source} = $arg;
     }
 
     return $self->{_gff_source};
@@ -373,7 +373,7 @@ sub gff_feature {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_gff_feature} = $arg;
+      $self->{_gff_feature} = $arg;
     }
 
     return $self->{_gff_feature};
@@ -396,7 +396,7 @@ sub parameters {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_parameters} = $arg;
+      $self->{_parameters} = $arg;
     }
 
     return $self->{_parameters};
@@ -418,7 +418,7 @@ sub created {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_created} = $arg;
+      $self->{_created} = $arg;
     }
 
     return $self->{_created};
@@ -481,7 +481,7 @@ sub description {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_description} = $arg;
+      $self->{_description} = $arg;
     }
 
     return $self->{_description};
@@ -503,7 +503,7 @@ sub display_label {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_display_label} = $arg;
+      $self->{_display_label} = $arg;
     }
 
     return $self->{_display_label};
@@ -524,7 +524,7 @@ sub displayable {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_displayable} = $arg;
+      $self->{_displayable} = $arg;
     }
 
     return $self->{_displayable};
@@ -546,7 +546,7 @@ sub web_data {
     my ($self,$arg) = @_;
 
     if (defined($arg)) {
-	$self->{_web_data} = $arg;
+      $self->{_web_data} = $arg;
     }
 
     return $self->{_web_data};

modules/Bio/EnsEMBL/BaseAlignFeature.pm

@@ -385,7 +385,7 @@ sub transform {
     my @segments = @{ $self->project(@_) };
 
     if ( !@segments ) {
-      return undef;
+      return;
     }
 
     my @ungapped;
@@ -396,7 +396,7 @@ sub transform {
       } else {
         warning( "Failed to transform alignment feature; "
             . "ungapped component could not be transformed" );
-        return undef;
+        return;
       }
     }
 
@@ -404,7 +404,7 @@ sub transform {
 
     if ($@) {
       warning($@);
-      return undef;
+      return;
     }
   } ## end if ( !defined($new_feature...))
 
@@ -604,7 +604,7 @@ sub _parse_features {
 
   my $hstrand     = $f[0]->hstrand;
   my $slice       = $f[0]->slice();
-  my $hslice       = $f[0]->hslice();
+  my $hslice      = $f[0]->hslice();
   my $name        = $slice ? $slice->name() : undef;
   my $hname       = $f[0]->hseqname;
   my $score       = $f[0]->score;

modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm

@@ -242,7 +242,7 @@ sub fetch_by_dbID {
   $sth->execute();
   my $rowHashRef = $sth->fetchrow_hashref;
   if( ! defined $rowHashRef ) {
-    return undef;
+    return;
   }
 
   my $anal = $self->_objFromHashref( $rowHashRef );
@@ -306,7 +306,7 @@ WHERE  LOWER(logic_name) = ?)
   $sth->execute();
   my $rowHashRef = $sth->fetchrow_hashref();
 
-  if ( !defined($rowHashRef) ) { return undef }
+  if ( !defined($rowHashRef) ) { return }
 
   $analysis = $self->_objFromHashref($rowHashRef);
 
@@ -499,7 +499,7 @@ sub update {
   }
 
   if(!$a->is_stored($self->db())) {
-    return undef;
+    return;
   }
 
   my $sth = $self->prepare
@@ -590,7 +590,7 @@ sub remove {
   }
 
   if(!$analysis->is_stored($self->db())) {
-    return undef;
+    return;
   }
 
   my $sth = $self->prepare("DELETE FROM analysis WHERE analysis_id = ?");
@@ -655,7 +655,7 @@ sub exists {
   }
 
   #no analysis like this one exists in the database
-  return undef;
+  return;
 }