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1 # $Id: ExonI.pm,v 1.6 2002/10/22 07:38:41 lapp Exp $
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2 #
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3 # BioPerl module for Bio::SeqFeature::Gene::ExonI
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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::SeqFeature::Gene::ExonI - Interface for a feature representing an exon
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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 an exon. An exon in this definition is
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24 transcribed and at least for one particular transcript not spliced out
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25 of the pre-mRNA. However, it does not necessarily code for amino acid.
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26
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27 =head1 FEEDBACK
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28
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29 =head2 Mailing Lists
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30
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31 User feedback is an integral part of the evolution of this
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32 and other Bioperl modules. Send your comments and suggestions preferably
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33 to one of the Bioperl mailing lists.
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34 Your participation is much appreciated.
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35
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36 bioperl-l@bioperl.org - General discussion
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37 http://bio.perl.org/MailList.html - About the mailing lists
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38
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39 =head2 Reporting Bugs
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40
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41 Report bugs to the Bioperl bug tracking system to help us keep track
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42 the bugs and their resolution.
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43 Bug reports can be submitted via email or the web:
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44
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45 bioperl-bugs@bio.perl.org
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46 http://bugzilla.bioperl.org/
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47
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48 =head1 AUTHOR - Hilmar Lapp
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49
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50 Email hlapp@gmx.net
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51
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52 Describe contact details here
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53
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54 =head1 APPENDIX
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55
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56 The rest of the documentation details each of the object methods.
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57 Internal methods are usually preceded with a _
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58
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59 =cut
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60
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61
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62 # Let the code begin...
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63
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64
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65 package Bio::SeqFeature::Gene::ExonI;
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66 use vars qw(@ISA);
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67 use strict;
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68
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69 use Carp;
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70 use Bio::SeqFeatureI;
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71
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72 @ISA = qw(Bio::SeqFeatureI);
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73
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74
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75 =head2 is_coding
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76
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77 Title : is_coding
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78 Usage : if($exon->is_coding()) {
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79 # do something
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80 }
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81 Function: Whether or not the exon codes for amino acid.
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82 Returns : TRUE if the object represents a feature translated into protein,
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83 and FALSE otherwise.
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84 Args :
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85
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86
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87 =cut
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88
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89 sub is_coding {
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90 my ($self) = @_;
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91 $self->throw_not_implemented();
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92 }
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93
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94 =head2 cds
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95
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96 Title : cds()
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97 Usage : $cds = $exon->cds();
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98 Function: Get the coding sequence of the exon as a sequence object.
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99
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100 The returned sequence object must be in frame 0, i.e., the first
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101 base starts a codon.
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102
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103 An implementation may return undef, indicating that a coding
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104 sequence does not exist, e.g. for a UTR (untranslated region).
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105
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106 Returns : A L<Bio::PrimarySeqI> implementing object.
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107 Args :
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108
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109
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110 =cut
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111
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112 sub cds {
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113 my ($self) = @_;
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114 $self->throw_not_implemented();
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115 }
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116
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117 1;
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