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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::ProteinFeature
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24
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25 =head1 SYNOPSIS
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26
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27 my $feature = Bio::EnsEMBL::ProteinFeature->new(
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28 -start => $start,
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29 -end => $end,
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30 -hstart => $hit_start,
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31 -hend => $hit_end,
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32 -hseqname => $hit_name
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33 );
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34
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35 =head1 DESCRIPTION
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36
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37 ProteinFeature objects represent domains or other features of interest
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38 on a peptide sequence.
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39
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40 =head1 METHODS
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41
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42 =cut
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43
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44 package Bio::EnsEMBL::ProteinFeature;
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45
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46 use strict;
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47
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48 use Bio::EnsEMBL::FeaturePair;
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49 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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50
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51 use vars qw(@ISA);
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52 @ISA = qw(Bio::EnsEMBL::FeaturePair);
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53
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54
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55
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56 =head2 new
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57
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58 Arg [IDESC] : (optional) string An interpro description
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59 Arg [INTERPRO_AC] : (optional) string An interpro accession
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60 Arg [TRANSLATION_ID] : (optional) integer A translation dbID
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61 Arg [...] : named arguments to FeaturePair superclass
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62 Example :
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63
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64 $pf =
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65 Bio::EnsEMBL::ProteinFeature->new( -IDESC => $idesc,
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66 -INTERPRO_AC => $iac,
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67 @fp_args );
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68
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69 Description: Instantiates a Bio::EnsEMBL::ProteinFeature
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70 Returntype : Bio::EnsEMBL::FeaturePair
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71 Exceptions : none
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72 Caller : general
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73 Status : Stable
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74
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75 =cut
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76
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77 sub new {
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78 my $proto = shift;
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79
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80 my $class = ref($proto) || $proto;
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81
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82 my ( $idesc, $interpro_ac, $translation_id ) =
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83 rearrange( [ 'IDESC', 'INTERPRO_AC', 'TRANSLATION_ID' ], @_ );
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84
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85 my $self = $class->SUPER::new(@_);
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86
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87 # the strand of protein features is always 0
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88 $self->{'strand'} = 0;
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89 $self->{'idesc'} = $idesc || '';
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90 $self->{'interpro_ac'} = $interpro_ac || '';
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91 $self->{'translation_id'} = $translation_id || '';
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92
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93 return $self;
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94 }
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95
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96
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97 =head2 strand
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98
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99 Arg [1] : Ignored
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100 Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow
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101 : the strand to be set.
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102 Returntype : int
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103 Status : Stable
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104
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105 =cut
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106
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107 #do not allow the strand to be set
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108 sub strand {
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109 my $self = shift;
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110 return $self->{'strand'};
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111 }
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112
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113
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114
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115 =head2 idesc
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116
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117 Arg [1] : (optional) string The interpro description
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118 Example : print $protein_feature->idesc();
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119 Description: Getter/Setter for the interpro description of this protein
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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 idesc{
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129 my $self = shift;
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130 $self->{'idesc'} = shift if(@_);
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131 return $self->{'idesc'};
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132 }
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133
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134
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135
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136 =head2 interpro_ac
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137
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138 Arg [1] : (optional) string The interpro accession
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139 Example : print $protein_feature->interpro_ac();
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140 Description: Getter/Setter for the interpro accession of this protein
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141 feature.
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142 Returntype : string
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143 Exceptions : none
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144 Caller : general
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145 Status : Stable
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146
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147 =cut
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148
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149 sub interpro_ac{
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150 my $self = shift;
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151 $self->{'interpro_ac'} = shift if(@_);
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152 return $self->{'interpro_ac'};
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153 }
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154
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155
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156 =head2 translation_id
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157
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158 Arg [1] : (optional) integer The dbID of the translation
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159 Example : print $protein_feature->translation_id();
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160 Description: Getter/Setter for the translation dbID of this protein
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161 feature.
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162 Returntype : string
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163 Exceptions : none
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164 Caller : general
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165 Status : Stable
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166
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167 =cut
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168
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169 sub translation_id {
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170 my $self = shift;
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171 $self->{'translation_id'} = shift if (@_);
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172 return $self->{'translation_id'};
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173 }
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174
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175 1;
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