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Commit b47157ec authored by Kieron Taylor's avatar Kieron Taylor :angry:
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Clean up tabs and returned undef.

parent 987b7857
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......@@ -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};
......
......@@ -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;
......
......@@ -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;
}
......
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