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1 # $Id: Gene.pm,v 1.8 2002/10/22 07:38:48 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Tools::Prediction::Gene
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4 #
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5 # Cared for by Hilmar Lapp <hlapp@gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Tools::Prediction::Gene - a predicted gene structure feature
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16
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17 =head1 SYNOPSIS
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18
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19 See documentation of methods.
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20
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21 =head1 DESCRIPTION
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22
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23 A feature representing a predicted gene structure. This class actually
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24 inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that
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25 functionality, plus a few methods supporting predicted sequence features,
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26 like a predicted CDS and a predicted translation.
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27
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28 Exons held by an instance of this class will usually be instances of
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29 Bio::Tools::Prediction::Exon, although they do not have to be. Refer to the
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30 documentation of the class that produced the instance.
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31
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32 Normally, you will not want to create an instance of this class yourself.
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33 Instead, classes representing the results of gene structure prediction
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34 programs will do that.
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35
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36 =head1 FEEDBACK
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37
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38 =head2 Mailing Lists
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39
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40 User feedback is an integral part of the evolution of this and other
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41 Bioperl modules. Send your comments and suggestions preferably to one
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42 of the Bioperl mailing lists. Your participation is much appreciated.
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43
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44 bioperl-l@bioperl.org - General discussion
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45 http://bio.perl.org/MailList.html - About the mailing lists
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46
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47 =head2 Reporting Bugs
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48
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49 Report bugs to the Bioperl bug tracking system to help us keep track
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50 the bugs and their resolution. Bug reports can be submitted via email
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51 or the web:
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52
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53 bioperl-bugs@bio.perl.org
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54 http://bugzilla.bioperl.org/
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55
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56 =head1 AUTHOR - Hilmar Lapp
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57
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58 Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
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59
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60 Describe contact details here
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61
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62 =head1 APPENDIX
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63
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64 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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65
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66 =cut
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67
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68
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69 # Let the code begin...
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70
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71
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72 package Bio::Tools::Prediction::Gene;
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73 use vars qw(@ISA);
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74 use strict;
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75
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76 use Bio::SeqFeature::Gene::Transcript;
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77
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78
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79 @ISA = qw(Bio::SeqFeature::Gene::Transcript);
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80
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81 sub new {
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82 my($class,@args) = @_;
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83
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84 my $self = $class->SUPER::new(@args);
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85
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86 my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);
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87
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88 $primary = 'predicted_gene' unless $primary;
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89 $self->primary_tag($primary);
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90 return $self;
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91 }
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92
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93
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94 =head2 predicted_cds
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95
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96 Title : predicted_cds
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97 Usage : $predicted_cds_dna = $gene->predicted_cds();
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98 $gene->predicted_cds($predicted_cds_dna);
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99 Function: Get/Set the CDS (coding sequence) as predicted by a program.
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100
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101 This method is independent of an attached_seq. There is no
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102 guarantee whatsoever that the returned CDS has anything to do
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103 (e.g., matches) with the sequence covered by the exons as annotated
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104 through this object.
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105
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106 Example :
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107 Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
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108 defined as coding by a prediction of a program.
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109 Args : On set, a Bio::PrimarySeqI implementing object holding the DNA
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110 sequence defined as coding by a prediction of a program.
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111
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112 =cut
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113
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114 sub predicted_cds {
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115 my ($self, $cds) = @_;
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116
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117 if(defined($cds)) {
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118 $self->{'_predicted_cds'} = $cds;
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119 }
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120 return $self->{'_predicted_cds'};
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121 }
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122
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123 =head2 predicted_protein
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124
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125 Title : predicted_protein
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126 Usage : $predicted_protein_seq = $gene->predicted_protein();
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127 $gene->predicted_protein($predicted_protein_seq);
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128 Function: Get/Set the protein translation as predicted by a program.
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129
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130 This method is independent of an attached_seq. There is no
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131 guarantee whatsoever that the returned translation has anything to
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132 do with the sequence covered by the exons as annotated
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133 through this object, or the sequence returned by predicted_cds(),
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134 although it should usually be just the standard translation.
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135
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136 Example :
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137 Returns : A Bio::PrimarySeqI implementing object holding the protein
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138 translation as predicted by a program.
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139 Args : On set, a Bio::PrimarySeqI implementing object holding the protein
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140 translation as predicted by a program.
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141
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142 =cut
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143
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144 sub predicted_protein {
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145 my ($self, $aa) = @_;
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146
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147 if(defined($aa)) {
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148 $self->{'_predicted_aa'} = $aa;
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149 }
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150 return $self->{'_predicted_aa'};
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151 }
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152
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153 #
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154 # Everything else is just inherited from SeqFeature::GeneStructure.
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155 #
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156
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157 1;
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