diff variant_effect_predictor/Bio/EnsEMBL/Compara/MemberDomain.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Compara/MemberDomain.pm	Fri Aug 03 10:04:48 2012 -0400
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+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=head1 AUTHORSHIP
+
+Ensembl Team. Individual contributions can be found in the CVS log.
+
+=cut
+
+=head1 NAME
+
+MemberDomain - DESCRIPTION of Object
+
+=head1 DESCRIPTION
+
+A subclass of Member which extends it to store a domain (start / end)
+within the sequence
+
+=head1 INHERITANCE TREE
+
+  Bio::EnsEMBL::Compara::MemberDomain
+  +- Bio::EnsEMBL::Compara::Member
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::Compara::MemberDomain;
+
+use strict;
+use Bio::EnsEMBL::Utils::Exception;
+use Bio::EnsEMBL::Compara::Member;
+
+use base ('Bio::EnsEMBL::Compara::Member');
+
+
+##################################
+# overriden superclass methods
+##################################
+
+=head2 copy
+
+  Arg [1]     : none
+  Example     : $copy = $aligned_member->copy();
+  Description : Creates a new MemberDomain object from an existing one
+  Returntype  : Bio::EnsEMBL::Compara::MemberDomain
+  Exceptions  : none
+  Caller      : general
+  Status      : Stable
+
+=cut
+
+sub copy {
+  my $self = shift;
+  
+  my $mycopy = @_ ? shift : {};     # extending or from scratch?
+               $self->SUPER::copy($mycopy);
+  bless $mycopy, 'Bio::EnsEMBL::Compara::MemberDomain';
+
+  # The following does not Work if the initial object is only a Member
+  if (UNIVERSAL::isa($self, 'Bio::EnsEMBL::Compara::MemberDomain')) {
+    $mycopy->member_start($self->member_start);
+    $mycopy->member_end($self->member_end);
+  }
+
+  return $mycopy;
+}
+
+
+=head2 member_start
+
+  Arg [1]     : (optional) $member_start
+  Example     : $object->member_start($member_start);
+  Example     : $member_start = $object->member_start();
+  Description : Getter/setter for the member_start attribute. For non-global
+                alignments, this represent the starting point of the local
+                alignment.
+                Currently the data provided as MemberDomains (leaves of the
+                GeneTree) are obtained using global alignments and the
+                member_start is always undefined.
+  Returntype  : integer
+  Exceptions  : none
+  Caller      : general
+  Status      : Stable
+
+=cut
+
+sub member_start {
+  my $self = shift;
+  $self->{'_member_start'} = shift if(@_);
+  return $self->{'_member_start'};
+}
+
+
+=head2 member_end
+
+  Arg [1]     : (optional) $member_end
+  Example     : $object->member_end($member_end);
+  Example     : $member_end = $object->member_end();
+  Description : Getter/setter for the member_end attribute. For non-global
+                alignments, this represent the ending point of the local
+                alignment.
+                Currently the data provided as MemberDomains (leaves of the
+                GeneTree) are obtained using global alignments and the
+                member_end is always undefined.
+  Returntype  : integer
+  Exceptions  : none
+  Caller      : general
+  Status      : Stable
+
+=cut
+
+sub member_end {
+  my $self = shift;
+  $self->{'_member_end'} = shift if(@_);
+  return $self->{'_member_end'};
+}
+
+
+
+1;