Commit 415106bd authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Merge in documentation change for, and formatting of, the length()

method from HEAD on the release 60 brnch.
parent d06c6ec3
......@@ -307,32 +307,34 @@ sub move {
Arg [1] : none
Example : $length = $feat->length();
Description: Returns the length of this feature
Returntype : int
Exceptions : none
Returntype : Integer
Exceptions : Throws if end < start and the feature is not on a
circular slice
Caller : general
Status : Stable
=cut
sub length {
my $self = shift;
my ($self) = @_;
if ( $self->{'end'} < $self->{'start'} ) {
# if circular, we can work out the length of an origin-spanning gene using the size of the underlying region
if($self->slice() && $self->slice()->is_circular()) {
my $len = $self->slice()->seq_region_length() - ($self->{'start'} - $self->{'end'}) + 1;
return $len;
} else {
throw "Cannot determine length of non-circular feature where start>end";
}
# if circular, we can work out the length of an origin-spanning
# feature using the size of the underlying region.
if ( $self->slice() && $self->slice()->is_circular() ) {
my $len =
$self->slice()->seq_region_length() -
( $self->{'start'} - $self->{'end'} ) + 1;
return $len;
} else {
throw( "Cannot determine length of non-circular feature "
. "where start > end" );
}
}
return $self->{'end'} - $self->{'start'} + 1;
}
=head2 analysis
Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis
......
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