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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 =head1 NAME
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22
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23 Bio::EnsEMBL::AssemblyExceptionFeature - A feature that represents an assembly exception
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24
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25 =head1 SYNOPSIS
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26
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27 use Bio::EnsEMBL::AssemblyExceptionFeature;
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28
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29 $feature = Bio::EnsEMBL::AssemblyExceptionFeature->new(
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30 -start => 100,
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31 -end => 220,
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32 -type => 'HAP',
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33 -slice => $slice,
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34 -adaptor => $adaptor
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35 );
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36
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37 =head1 DESCRIPTION
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38
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39 Certain features, e.g. Haplotypes and PARs, are represented as
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40 "exceptions" to the normal assembly. This class represents such
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41 features.
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42
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43 =head1 METHODS
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44
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45 =cut
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46
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47 package Bio::EnsEMBL::AssemblyExceptionFeature;
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48
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49 use strict;
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50
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51 use vars qw(@ISA);
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52
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53 use Bio::EnsEMBL::Feature;
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54 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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55 use Scalar::Util qw(weaken isweak);
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56
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57 @ISA = qw(Bio::EnsEMBL::Feature);
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58
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59
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60 =head2 new
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61
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62 Arg [TYPE] : The type (e.g. HAP for haplotype, PAR for PAR)
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63 Arg [...] : Named arguments passed to superclass
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64 Example : $feature = Bio::EnsEMBL::AssemblyExceptionFeature->new
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65 (-start => 1,
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66 -end => 100,
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67 -slice => $slice,
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68 -alternate_slice => $alt_slice,
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69 -adaptor => $adaptor,
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70 -type => 'HAP')
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71 Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses
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72 of this method are instantiated, rather than this class itself.
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73 Returntype : Bio::EnsEMBL::Feature
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74 Exceptions : Thrown on invalid -SLICE arguments
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75 Caller : general, subclass constructors
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76 Status : Stable
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77
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78 =cut
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79
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80 sub new {
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81
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82 my $caller = shift;
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83
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84 # allow this to be called as class or object method
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85 my $class = ref($caller) || $caller;
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86 my $self = $class->SUPER::new(@_);
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87
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88 my ($type, $alternate_slice) = rearrange(['TYPE', 'ALTERNATE_SLICE'],@_);
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89 $self->{'type'} = $type;
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90 $self->{'alternate_slice'} = $alternate_slice;
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91
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92 return $self;
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93 }
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94
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95 =head2 new_fast
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96
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97 Arg [1] : hashref to be blessed
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98 Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
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99 Exceptions : none
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100 Returntype : Bio::EnsEMBL::Feature
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101 Caller : general, subclass constructors
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102 Status : Stable
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103
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104 =cut
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105
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106 sub new_fast {
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107 my $class = shift;
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108 my $hashref = shift;
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109 my $self = bless $hashref, $class;
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110 weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
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111 return $self;
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112 }
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113
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114
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115 =head2 type
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116
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117 Arg [1] : (optional) string $value
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118 Example : $type = $assembly_exception_feature->type();
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119 Description: Getter/Setter for the type associated with this
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120 feature.
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121 Returntype : string
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122 Exceptions : none
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123 Caller : general
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124 Status : Stable
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125
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126 =cut
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127
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128 sub type {
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129
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130 my $self = shift;
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131
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132 $self->{'type'} = shift if(@_);
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133
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134 return $self->{'type'};
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135 }
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136
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137
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138 =head2 alternate_slice
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139
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140 Arg [1] : (optional) string $value
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141 Example : $alt_slice = $assembly_exception_feature->alternate_slice();
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142 Description: Getter/Setter for the alternate slice associated with this feature.
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143 The alternate slice represents the "other side" of the AssemblyExceptionFeature.
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144 Returntype : Bio::EnsEMBL::Slice
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145 Exceptions : none
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146 Caller : general
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147 Status : Stable
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148
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149 =cut
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150
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151 sub alternate_slice {
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152
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153 my $self = shift;
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154
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155 $self->{'alternate_slice'} = shift if(@_);
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156
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157 return $self->{'alternate_slice'};
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158 }
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159
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160
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161
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162 =head2 display_id
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163
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164 Arg [1] : none
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165 Example : print $aef->display_id();
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166 Description: This method returns a string that is considered to be
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167 the 'display' identifier. For assembly exception features
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168 this is the name of the alternate seqregion or '' if the
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169 alternate slice is not defined.
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170 Returntype : string
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171 Exceptions : none
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172 Caller : web drawing code
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173 Status : Stable
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174
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175 =cut
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176
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177 sub display_id {
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178 my $self = shift;
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179 my $slice = $self->{'alternate_slice'};
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180 return '' if(!$slice);
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181 return $slice->seq_region_name();
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182 }
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183
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184
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185
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186 1;
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