view variant_effect_predictor/Bio/EnsEMBL/Variation/Failable.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=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]>.

=cut

# Ensembl module for Bio::EnsEMBL::Variation::BaseStructuralVariation
#
# Copyright (c) 2011 Ensembl
#

=head1 NAME

Bio::EnsEMBL::Variation::Failable

=head1 DESCRIPTION

This object returns failed information.

=cut


use strict;
use warnings;

package Bio::EnsEMBL::Variation::Failable;


=head2 failed_description

  Arg [1]    : $failed_description (optional)
               The new value to set the failed_description attribute to. Should 
               be a reference to a list of strings, alternatively a string can
               be passed. If multiple failed descriptions are specified, they should
               be separated with semi-colons.  
  Example    : $failed_str = $sv->failed_description();
  Description: Get/Sets the failed description for this structural variant. The failed
               descriptions are lazy-loaded from the database.
  Returntype : Semi-colon separated string 
  Exceptions : Thrown on illegal argument.
  Caller     : general
  Status     : At risk

=cut

sub failed_description {
    my $self = shift;
    my $description = shift;
  
    # Update the description if necessary
    if (defined($description)) {
        
        # If the description is a string, split it by semi-colon and take the reference
        if (check_ref($description,'STRING')) {
            my @pcs = split(/;/,$description);
            $description = \@pcs;
        }
        # Throw an error if the description is not an arrayref
        assert_ref($description.'ARRAY');
        
        # Update the cached failed_description
        $self->{'failed_description'} = $description;
    }
    # Else, fetch it from the db if it's not cached
    elsif (!defined($self->{'failed_description'})) {
        $self->{'failed_description'} = $self->get_all_failed_descriptions();
    }
    
    # Return a semi-colon separated string of descriptions
    return join(";",@{$self->{'failed_description'}});
}


=head2 get_all_failed_descriptions

  Example    :  
                if ($sv->is_failed()) {
                    my $descriptions = $sv->get_all_failed_descriptions();
                    print "Structural variant " . $sv->variation_name() . " has been flagged as failed because '";
                    print join("' and '",@{$descriptions}) . "'\n";
                }
                
  Description: Gets all failed descriptions associated with this Structural variant.
  Returntype : Reference to a list of strings 
  Exceptions : Thrown if an adaptor is not attached to this object.
  Caller     : general
  Status     : At risk

=cut

sub get_all_failed_descriptions {
  my $self = shift;
  
    # If the failed descriptions haven't been cached yet, load them from db
    unless (defined($self->{'failed_description'})) {
        
        # Check that this allele has an adaptor attached
        unless (defined($self->adaptor())) {
            throw('An adaptor must be attached to the ' . ref($self)  . ' object');
        }
    
        $self->{'failed_description'} = $self->adaptor->get_all_failed_descriptions($self);
    }
    
    return $self->{'failed_description'};
}


=head2 is_failed

  Example    : print "Structural variant '" . $sv->variation_name() . "' has " . ($sv->is_failed() ? "" : "not ") . "been flagged as failed\n";
  Description: Gets the failed attribute for this structural variant. The failed attribute
               is lazy-loaded from the database.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : At risk

=cut

sub is_failed {
  my $self = shift;
  
  return (length($self->failed_description()) > 0);
}
1;