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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 # Ensembl module for Bio::EnsEMBL::Variation::BaseStructuralVariation
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22 #
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23 # Copyright (c) 2011 Ensembl
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24 #
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25
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26 =head1 NAME
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27
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28 Bio::EnsEMBL::Variation::Failable
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29
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30 =head1 DESCRIPTION
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31
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32 This object returns failed information.
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33
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34 =cut
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35
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36
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37 use strict;
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38 use warnings;
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39
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40 package Bio::EnsEMBL::Variation::Failable;
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41
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42
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43 =head2 failed_description
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44
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45 Arg [1] : $failed_description (optional)
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46 The new value to set the failed_description attribute to. Should
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47 be a reference to a list of strings, alternatively a string can
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48 be passed. If multiple failed descriptions are specified, they should
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49 be separated with semi-colons.
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50 Example : $failed_str = $sv->failed_description();
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51 Description: Get/Sets the failed description for this structural variant. The failed
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52 descriptions are lazy-loaded from the database.
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53 Returntype : Semi-colon separated string
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54 Exceptions : Thrown on illegal argument.
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55 Caller : general
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56 Status : At risk
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57
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58 =cut
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59
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60 sub failed_description {
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61 my $self = shift;
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62 my $description = shift;
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63
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64 # Update the description if necessary
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65 if (defined($description)) {
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66
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67 # If the description is a string, split it by semi-colon and take the reference
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68 if (check_ref($description,'STRING')) {
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69 my @pcs = split(/;/,$description);
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70 $description = \@pcs;
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71 }
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72 # Throw an error if the description is not an arrayref
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73 assert_ref($description.'ARRAY');
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74
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75 # Update the cached failed_description
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76 $self->{'failed_description'} = $description;
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77 }
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78 # Else, fetch it from the db if it's not cached
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79 elsif (!defined($self->{'failed_description'})) {
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80 $self->{'failed_description'} = $self->get_all_failed_descriptions();
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81 }
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82
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83 # Return a semi-colon separated string of descriptions
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84 return join(";",@{$self->{'failed_description'}});
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85 }
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86
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87
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88 =head2 get_all_failed_descriptions
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89
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90 Example :
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91 if ($sv->is_failed()) {
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92 my $descriptions = $sv->get_all_failed_descriptions();
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93 print "Structural variant " . $sv->variation_name() . " has been flagged as failed because '";
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94 print join("' and '",@{$descriptions}) . "'\n";
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95 }
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96
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97 Description: Gets all failed descriptions associated with this Structural variant.
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98 Returntype : Reference to a list of strings
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99 Exceptions : Thrown if an adaptor is not attached to this object.
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100 Caller : general
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101 Status : At risk
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102
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103 =cut
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104
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105 sub get_all_failed_descriptions {
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106 my $self = shift;
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107
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108 # If the failed descriptions haven't been cached yet, load them from db
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109 unless (defined($self->{'failed_description'})) {
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110
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111 # Check that this allele has an adaptor attached
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112 unless (defined($self->adaptor())) {
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113 throw('An adaptor must be attached to the ' . ref($self) . ' object');
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114 }
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115
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116 $self->{'failed_description'} = $self->adaptor->get_all_failed_descriptions($self);
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117 }
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118
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119 return $self->{'failed_description'};
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120 }
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121
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122
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123 =head2 is_failed
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124
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125 Example : print "Structural variant '" . $sv->variation_name() . "' has " . ($sv->is_failed() ? "" : "not ") . "been flagged as failed\n";
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126 Description: Gets the failed attribute for this structural variant. The failed attribute
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127 is lazy-loaded from the database.
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128 Returntype : int
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129 Exceptions : none
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130 Caller : general
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131 Status : At risk
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132
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133 =cut
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134
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135 sub is_failed {
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136 my $self = shift;
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137
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138 return (length($self->failed_description()) > 0);
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139 }
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140 1;
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