Bio/SeqFeature/Gene/GeneStructureI.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Gene::GeneStructureI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   7 #
   8 # Copyright Hilmar Lapp
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily
  17            complex structure of a gene
  18
  19 =head1 SYNOPSIS
  20
  21   #documentation needed
  22
  23 =head1 DESCRIPTION
  24
  25 A feature representing a gene structure.
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this
  32 and other Bioperl modules. Send your comments and suggestions preferably
  33 to one of the Bioperl mailing lists. Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 the bugs and their resolution.  Bug reports can be submitted via the
  53 web:
  54
  55   https://github.com/bioperl/bioperl-live/issues
  56
  57 =head1 AUTHOR - Hilmar Lapp
  58
  59 Email hlapp@gmx.net
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object methods.
  64 Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68
  69 # Let the code begin...
  70
  71
  72 package Bio::SeqFeature::Gene::GeneStructureI;
  73 use strict;
  74
  75 use Carp;
  76
  77 use base qw(Bio::SeqFeatureI);
  78
  79 =head2 transcripts
  80
  81  Title   : transcripts()
  82  Usage   : @transcripts = $gene->transcripts();
  83  Function: Get the transcript features/sites of this gene structure.
  84
  85            See Bio::SeqFeature::Gene::TranscriptI for properties of the
  86            returned objects.
  87
  88  Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects
  89            representing the promoter regions or sites.
  90  Args    :
  91
  92
  93 =cut
  94
  95 sub transcripts {
  96     my ($self) = @_;
  97     $self->throw_not_implemented();
  98 }
  99
 100 =head2 promoters
 101
 102  Title   : promoters()
 103  Usage   : @prom_sites = $gene->promoters();
 104  Function: Get the promoter features/sites of this gene structure.
 105
 106            Note that OO-modeling of regulatory elements is not stable yet.
 107            This means that this method might change or even disappear in a
 108            future release. Be aware of this if you use it.
 109
 110  Returns : An array of Bio::SeqFeatureI implementing objects representing the
 111            promoter regions or sites.
 112  Args    :
 113
 114 =cut
 115
 116 sub promoters {
 117     my ($self) = @_;
 118     $self->throw_not_implemented();
 119 }
 120
 121 =head2 exons
 122
 123  Title   : exons()
 124  Usage   : @exons = $gene->exons();
 125            @inital = $gene->exons('Initial');
 126  Function: Get all exon features or all exons of specified type of this gene
 127            structure.
 128
 129            Refer to the documentation of the class that produced this gene
 130            structure object for information about the possible types.
 131
 132            See Bio::SeqFeature::Gene::ExonI for properties of the
 133            returned objects.
 134
 135  Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
 136            representing the exon regions.
 137  Args    : An optional string specifying the type of the exon.
 138
 139 =cut
 140
 141 sub exons {
 142     my ($self, $type) = @_;
 143     $self->throw_not_implemented();
 144 }
 145
 146 =head2 introns
 147
 148  Title   : introns()
 149  Usage   : @introns = $gene->introns();
 150  Function: Get all introns of this gene structure.
 151  Returns : An array of Bio::SeqFeatureI implementing objects representing the
 152            introns.
 153  Args    :
 154
 155
 156 =cut
 157
 158 sub introns {
 159     my ($self) = @_;
 160     $self->throw_not_implemented();
 161 }
 162
 163 =head2 poly_A_sites
 164
 165  Title   : poly_A_sites()
 166  Usage   : @polyAsites = $gene->poly_A_sites();
 167  Function: Get the poly-adenylation features/sites of this gene structure.
 168  Returns : An array of Bio::SeqFeatureI implementing objects representing the
 169            poly-adenylation regions or sites.
 170  Args    :
 171
 172
 173 =cut
 174
 175 sub poly_A_sites {
 176     my ($self) = @_;
 177     $self->throw_not_implemented();
 178 }
 179
 180 =head2 utrs
 181
 182  Title   : utrs()
 183  Usage   : @utr_sites = $gene->utrs();
 184  Function: Get the UTR features/sites of this gene structure.
 185
 186            See Bio::SeqFeature::Gene::ExonI for properties of the
 187            returned objects.
 188
 189  Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
 190            representing the UTR regions or sites.
 191  Args    :
 192
 193
 194 =cut
 195
 196 sub utrs {
 197     my ($self) = @_;
 198     $self->throw_not_implemented();
 199 }
 200
 201 1;