Created; API support for motifs that are common between regulatory features.

modules/Bio/EnsEMBL/RegulatoryMotif.pm

+use strict;
+
+package Bio::EnsEMBL::RegulatoryMotif;
+
+use Bio::EnsEMBL::Storable;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Storable);
+
+
+=head2 new
+
+  Arg [NAME] : string (optional)
+               The name of this regulatory motif
+  Arg [TYPE]: string (optional)
+               The type of repeat consensus
+  Arg [...]: Named arguments to superclass constructor
+             (see Bio::EnsEMBL::Storable)
+  Example    : $rc = Bio::EnsEMBL::RegulatoryMotif->new
+                       (-NAME    => 'SomeMotifName'
+                        -TYPE    => 'promoter',
+                        -DBID    => 1023,
+                        -ADAPTOR => $rc_adaptor);
+  Description: Creates a new Bio::EnsEMBL::RegulatoryMotif object
+  Returntype : Bio::EnsEMBL::RegulatoryMotif
+  Exceptions : none
+  Caller     : RegulatoryMotif
+
+=cut
+
+sub new {
+  my $caller = shift;
+
+  my $class = ref($caller) || $caller;
+
+  my $self = $class->SUPER::new(@_);
+
+  my ($name, $type ) =
+    rearrange(['NAME', 'TYPE'], @_);
+
+  $self->{'name'} = $name;
+  $self->{'type'} = $type;
+
+  return $self;
+}
+
+
+sub new_fast {
+  my $class = shift;
+  my $hashref = shift;
+  return bless $hashref, $class;
+}
+
+
+=head2 name
+
+  Arg [1]    : string $name (optional)
+  Example    : $name = $regulatory_motif->name()
+  Description: Getter/Setter for the name of this regulatory motif
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub name {
+  my $self = shift;
+  $self->{'name'} = shift if(@_);
+  return $self->{'name'};
+}
+
+
+=head2 type
+
+  Arg [1]    : string $type
+  Example    : $type = $regulatory_motif->type()
+  Description: Getter/Setter for the length of this regulatory motif
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub type {
+  my $self = shift;
+  $self->{'type'} = shift if(@_);
+  return $self->{'type'};
+}
+
+1;
+
+__END__
+
+=head1 NAME - Bio::EnsEMBL::RegulatoryMotif
+
+=head1 DESCRIPTION
+
+This object represents an entry in the
+regulatory_motif table.
+
+=head1 AUTHOR
+
+Glenn Proctor< email> glenn@ebi.ac.uk
+