Initial implementation of support for regions of the genome which were...

Initial implementation of support for regions of the genome which were searched for regulatory features.

modules/Bio/EnsEMBL/RegulatorySearchRegion.pm

+#
+# Ensembl module for Bio::EnsEMBL::RegulatorySearchRegion
+#
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::RegulatorySearchRegion - A feature representing a part of the genome that was searched for regulatory features.
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::RegulatorySearchRegion;
+
+$region  = Bio::EnsEMBL::RegulatorySearchRegion->new(-start            	  => 100,
+                                                     -end              	  => 220,
+                                                     -strand           	  => -1,
+                                                     -slice            	  => $slice,
+                                                     -analysis         	  => $analysis,
+                                                     -ensembl_object_type => "Gene",
+                                                     -ensembl_object_id   => 12340,
+                                                     -dbID                => 1230,
+                                                     -adaptor             => $adaptor);
+
+=head1 DESCRIPTION
+
+A feature representing a part of the genome that was searched for regulatory features.
+
+=head1 AUTHOR - Glenn Proctor
+
+This module is part of the Ensembl project http://www.ensembl.org
+
+=head1 CONTACT
+
+Post comments/questions to the ensembl development list: ensembl-dev@ebi.ac.uk
+
+=head1 METHODS
+
+=cut
+
+use strict;
+
+package Bio::EnsEMBL::RegulatorySearchRegion;
+
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+
+@ISA = qw(Bio::EnsEMBL::Feature);
+
+
+=head2 new
+
+  Arg [...]  : Named arguments passed to superclass
+  Example    : $feature = Bio::EnsEMBL::RegulatoryFeatureSearchRegion->new
+                                               (-name                => 'CisRed_search_1',
+						-start               => 100,
+                                                -end                 => 220,
+                                                -strand              => -1,
+                                                -slice               => $slice,
+                                                -analysis            => $analysis,
+                                                -ensembl_object_type => "Gene",
+                                                -ensembl_object_id   => 12340,
+                                                -dbID                => 1230,
+                                                -adaptor             => $adaptor);
+  Description: Constructs a new Bio::EnsEMBL::RegulatorySearchRegion.
+  Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
+  Caller     : general, subclass constructors
+  Status     : At Risk
+             : under development
+
+=cut
+
+sub new {
+  my $caller = shift;
+
+  #allow this to be called as class or object method
+  my $class = ref($caller) || $caller;
+  my $self = $class->SUPER::new(@_);
+
+  my ($name, $factor, $ensembl_object_type, $ensembl_object_id) = rearrange(['NAME', 'ENSEMBL_OBJECT_TYPE', 'ENSEMBL_OBJECT_ID'],@_);
+
+  $self->{'name'} = $name;
+  $self->{'ensembl_object_type'} = $ensembl_object_type;
+  $self->{'ensembl_object_id'} = $ensembl_object_id;
+
+  return $self;
+}
+
+
+sub new_fast {
+  my $class = shift;
+  my $hashref = shift;
+  return bless $hashref, $class;
+}
+
+=head2 name
+
+  Arg [1]    : none
+  Example    : print $rsr->name();
+  Description: Getter/setter for this search region's name.
+  Returntype : string
+  Exceptions : none
+  Caller     : web drawing code
+  Status     : At Risk
+             : under development
+
+=cut
+
+sub name {
+  my $self = shift;
+  $self->{'name'} = shift if(@_);
+  return $self->{'name'};
+}
+
+=head2 ensembl_object_type
+
+  Arg [1]    : none
+  Example    : print $rsr->ensembl_object_type();
+  Description: Getter/setter for this search region's ensembl_object_type.
+  Returntype : string
+  Exceptions : none
+  Caller     : web drawing code
+  Status     : At Risk
+             : under development
+
+=cut
+
+sub ensembl_object_type {
+  my $self = shift;
+  $self->{'ensembl_object_type'} = shift if(@_);
+  return $self->{'ensembl_object_type'};
+}
+
+=head2 ensembl_object_id
+
+  Arg [1]    : none
+  Example    : print $rsr->ensembl_object_id();
+  Description: Getter/setter for this search region's ensembl_object_id.
+  Returntype : string
+  Exceptions : none
+  Caller     : web drawing code
+  Status     : At Risk
+             : under development
+
+=cut
+
+sub ensembl_object_id {
+  my $self = shift;
+  $self->{'ensembl_object_id'} = shift if(@_);
+  return $self->{'ensembl_object_id'};
+}
+
+1;