=head1 LICENSE

 Copyright (c) 1999-2013 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/legal/code_licence.html

=head1 CONTACT

 Please email comments or questions to the public Ensembl
 developers list at <dev@ensembl.org>.

 Questions may also be sent to the Ensembl help desk at
 <helpdesk@ensembl.org>.

=cut

# Ensembl module for Bio::EnsEMBL::Variation::StructuralVariation
#
# Copyright (c) 2004 Ensembl
#


=head1 NAME

Bio::EnsEMBL::Variation::StructuralVariation - Ensembl representation of a structural variation.

=head1 SYNOPSIS
    # A Study object
    $study = $study_adaptor->fetch_by_name('estd59');
    
    # Structural variation representing a CNV
    $sv = Bio::EnsEMBL::Variation::StructuralVariation->new
       (-variation_name => 'esv234231',
        -class_so_term => 'structural_variant',
        -source => 'DGVa',
        -source_description => 'Database of Genomic Variants Archive',
        -is_evidence => 0,
        -is_somatic => 0);

    ...

    print $sv->variation_name(), ":", $sv->var_class();

=head1 DESCRIPTION

This is a class representing a structural variation from the
ensembl-variation database. A structural variant may have a copy number variation, a tandem duplication, 
an inversion of the sequence or others structural variations. 

The position of a StructuralVariation object on the Genome is represented
by the <Bio::EnsEMBL::Variation::StructuralVariationFeature> class.

=head1 METHODS

=cut

use strict;
use warnings;

package Bio::EnsEMBL::Variation::StructuralVariation;

use Bio::EnsEMBL::Variation::BaseStructuralVariation;
use Bio::EnsEMBL::Utils::Exception qw(deprecate);

our @ISA = ('Bio::EnsEMBL::Variation::BaseStructuralVariation');


sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;
  
  my $self = Bio::EnsEMBL::Variation::BaseStructuralVariation->new(@_);
  return(bless($self, $class));
}

=head2 get_all_SupportingStructuralVariants

  Example     : $sv->get_all_SupportingStructuralVariants();
  Description : Retrieves all SupportingStructuralVariation associated with this structural variation.
                Return empty list if there are none.
  Returntype  : reference to list of Bio::EnsEMBL::Variation::SupportingStructuralVariation objects
  Exceptions  : None
  Caller      : general
  Status      : Stable

=cut

sub get_all_SupportingStructuralVariants {
  my $self = shift;
  
  if (defined ($self->{'adaptor'})){
    my $ssv_adaptor = $self->{'adaptor'}->db()->get_SupportingStructuralVariationAdaptor();
    return $ssv_adaptor->fetch_all_by_StructuralVariation($self);
  }
  warn("No variation database attached");
  return [];
}



=head2 get_all_supporting_evidence_classes

  Example     : $sv->get_all_supporting_evidence_classes
  Description : Retrieves the classes (SO term) of the supporting evidence associated with this structural variation.
                Return empty list if there are none.
  Returntype  : reference to list of string
  Exceptions  : None
  Caller      : general
  Status      : Stable

=cut

sub get_all_supporting_evidence_classes {
  my $self = shift;
	deprecate('Use the method "_get_all_supporting_evidence_classes" in the StructuralVariationFeature object.');
}


=head2 summary_as_hash

  Example       : $sv_summary = $sv->summary_as_hash();
  Description   : Retrieves a textual summary of this StructuralVariation object.
  Returns       : hashref of descriptive strings

=cut

sub summary_as_hash {
  my $self = shift;
  my %summary;
  $summary{'display_id'} = $self->display_id;
  $summary{'study_name'} = $self->study_name;
  $summary{'study_description'} = $self->study_description;
  $summary{'class'} = $self->var_class;
  return \%summary;

}

1;