branch-1-6/Bio/SeqFeature/Gene/GeneStructureI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::SeqFeature::Gene::GeneStructureI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   8 #
   9 # Copyright Hilmar Lapp
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily
  18            complex structure of a gene
  19
  20 =head1 SYNOPSIS
  21
  22   #documentation needed
  23
  24 =head1 DESCRIPTION
  25
  26 A feature representing a gene structure.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this
  33 and other Bioperl modules. Send your comments and suggestions preferably
  34 to one of the Bioperl mailing lists. Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 the bugs and their resolution.  Bug reports can be submitted via the
  54 web:
  55
  56   http://bugzilla.open-bio.org/
  57
  58 =head1 AUTHOR - Hilmar Lapp
  59
  60 Email hlapp@gmx.net
  61
  62 =head1 APPENDIX
  63
  64 The rest of the documentation details each of the object methods.
  65 Internal methods are usually preceded with a _
  66
  67 =cut
  68
  69
  70 # Let the code begin...
  71
  72
  73 package Bio::SeqFeature::Gene::GeneStructureI;
  74 use strict;
  75
  76 use Carp;
  77
  78 use base qw(Bio::SeqFeatureI);
  79
  80 =head2 transcripts
  81
  82  Title   : transcripts()
  83  Usage   : @transcripts = $gene->transcripts();
  84  Function: Get the transcript features/sites of this gene structure.
  85
  86            See Bio::SeqFeature::Gene::TranscriptI for properties of the
  87            returned objects.
  88
  89  Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects
  90            representing the promoter regions or sites.
  91  Args    :
  92
  93
  94 =cut
  95
  96 sub transcripts {
  97     my ($self) = @_;
  98     $self->throw_not_implemented();
  99 }
 100
 101 =head2 promoters
 102
 103  Title   : promoters()
 104  Usage   : @prom_sites = $gene->promoters();
 105  Function: Get the promoter features/sites of this gene structure.
 106
 107            Note that OO-modeling of regulatory elements is not stable yet.
 108            This means that this method might change or even disappear in a
 109            future release. Be aware of this if you use it.
 110
 111  Returns : An array of Bio::SeqFeatureI implementing objects representing the
 112            promoter regions or sites.
 113  Args    :
 114
 115 =cut
 116
 117 sub promoters {
 118     my ($self) = @_;
 119     $self->throw_not_implemented();
 120 }
 121
 122 =head2 exons
 123
 124  Title   : exons()
 125  Usage   : @exons = $gene->exons();
 126            @inital = $gene->exons('Initial');
 127  Function: Get all exon features or all exons of specified type of this gene
 128            structure.
 129
 130            Refer to the documentation of the class that produced this gene
 131            structure object for information about the possible types.
 132
 133            See Bio::SeqFeature::Gene::ExonI for properties of the
 134            returned objects.
 135
 136  Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
 137            representing the exon regions.
 138  Args    : An optional string specifying the type of the exon.
 139
 140 =cut
 141
 142 sub exons {
 143     my ($self, $type) = @_;
 144     $self->throw_not_implemented();
 145 }
 146
 147 =head2 introns
 148
 149  Title   : introns()
 150  Usage   : @introns = $gene->introns();
 151  Function: Get all introns of this gene structure.
 152  Returns : An array of Bio::SeqFeatureI implementing objects representing the
 153            introns.
 154  Args    :
 155
 156
 157 =cut
 158
 159 sub introns {
 160     my ($self) = @_;
 161     $self->throw_not_implemented();
 162 }
 163
 164 =head2 poly_A_sites
 165
 166  Title   : poly_A_sites()
 167  Usage   : @polyAsites = $gene->poly_A_sites();
 168  Function: Get the poly-adenylation features/sites of this gene structure.
 169  Returns : An array of Bio::SeqFeatureI implementing objects representing the
 170            poly-adenylation regions or sites.
 171  Args    :
 172
 173
 174 =cut
 175
 176 sub poly_A_sites {
 177     my ($self) = @_;
 178     $self->throw_not_implemented();
 179 }
 180
 181 =head2 utrs
 182
 183  Title   : utrs()
 184  Usage   : @utr_sites = $gene->utrs();
 185  Function: Get the UTR features/sites of this gene structure.
 186
 187            See Bio::SeqFeature::Gene::ExonI for properties of the
 188            returned objects.
 189
 190  Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
 191            representing the UTR regions or sites.
 192  Args    :
 193
 194
 195 =cut
 196
 197 sub utrs {
 198     my ($self) = @_;
 199     $self->throw_not_implemented();
 200 }
 201
 202 1;