lib/Bio/Seq/RichSeqI.pm

   1 #
   2 # BioPerl module for Bio::Seq::RichSeqI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   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::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
  17
  18 =head1 SYNOPSIS
  19
  20     @secondary   = $richseq->get_secondary_accessions;
  21     $division    = $richseq->division;
  22     $mol         = $richseq->molecule;
  23     @dates       = $richseq->get_dates;
  24     $seq_version = $richseq->seq_version;
  25     $pid         = $richseq->pid;
  26     @keywords    = $richseq->get_keywords;
  27
  28 =head1 DESCRIPTION
  29
  30 This interface extends the L<Bio::SeqI> interface to give additional
  31 functionality to sequences with richer data sources, in particular from database
  32 sequences (EMBL, GenBank and Swissprot). For a general implementation, please
  33 see the documentation for L<Bio::Seq::RichSeq>.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this
  40 and other Bioperl modules. Send your comments and suggestions preferably
  41  to one of the Bioperl mailing lists.
  42 Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Support
  48
  49 Please direct usage questions or support issues to the mailing list:
  50
  51 I<bioperl-l@bioperl.org>
  52
  53 rather than to the module maintainer directly. Many experienced and
  54 reponsive experts will be able look at the problem and quickly
  55 address it. Please include a thorough description of the problem
  56 with code and data examples if at all possible.
  57
  58 =head2 Reporting Bugs
  59
  60 Report bugs to the Bioperl bug tracking system to help us keep track
  61 the bugs and their resolution.  Bug reports can be submitted via the
  62 web:
  63
  64   https://github.com/bioperl/bioperl-live/issues
  65
  66 =head1 AUTHOR - Ewan Birney
  67
  68 Email birney@ebi.ac.uk
  69
  70 =head1 APPENDIX
  71
  72 The rest of the documentation details each of the object methods. Internal
  73 methods are usually preceded with a _
  74
  75 =cut
  76
  77
  78 # Let the code begin...
  79
  80
  81 package Bio::Seq::RichSeqI;
  82 use strict;
  83
  84 use base qw(Bio::SeqI);
  85
  86
  87 =head2 get_secondary_accessions
  88
  89  Title   : get_secondary_accessions
  90  Usage   :
  91  Function: Get the secondary accessions for a sequence.
  92
  93            An implementation that allows modification of this array
  94            property should provide the methods add_secondary_accession
  95            and remove_secondary_accessions, with obvious purpose.
  96
  97  Example :
  98  Returns : an array of strings
  99  Args    : none
 100
 101
 102 =cut
 103
 104 sub get_secondary_accessions{
 105    my ($self,@args) = @_;
 106
 107    $self->throw("hit get_secondary_accessions in interface definition - error");
 108
 109 }
 110
 111
 112 =head2 division
 113
 114  Title   : division
 115  Usage   :
 116  Function: Get (and set, depending on the implementation) the division for
 117            a sequence.
 118
 119            Examples from GenBank are PLN (plants), PRI (primates), etc.
 120  Example :
 121  Returns : a string
 122  Args    :
 123
 124
 125 =cut
 126
 127 sub division{
 128    my ($self,@args) = @_;
 129
 130    $self->throw("hit division in interface definition - error");
 131
 132 }
 133
 134
 135 =head2 molecule
 136
 137  Title   : molecule
 138  Usage   :
 139  Function: Get (and set, depending on the implementation) the molecule
 140            type for the sequence.
 141
 142            This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
 143            because it is databank-specific.
 144  Example :
 145  Returns : a string
 146  Args    :
 147
 148
 149 =cut
 150
 151 sub molecule{
 152    my ($self,@args) = @_;
 153
 154    $self->throw("hit molecule in interface definition - error");
 155 }
 156
 157 =head2 pid
 158
 159  Title   : pid
 160  Usage   :
 161  Function: Get (and set, depending on the implementation) the PID property
 162            for the sequence.
 163  Example :
 164  Returns : a string
 165  Args    :
 166
 167
 168 =cut
 169
 170 sub pid {
 171    my ($self,@args) = @_;
 172
 173    $self->throw("hit pid in interface definition - error");
 174 }
 175
 176 =head2 get_dates
 177
 178  Title   : get_dates
 179  Usage   :
 180  Function: Get (and set, depending on the implementation) the dates the
 181            databank entry specified for the sequence
 182
 183            An implementation that allows modification of this array
 184            property should provide the methods add_date and
 185            remove_dates, with obvious purpose.
 186
 187  Example :
 188  Returns : an array of strings
 189  Args    :
 190
 191
 192 =cut
 193
 194 sub get_dates{
 195    my ($self,@args) = @_;
 196
 197    $self->throw("hit get_dates in interface definition - error");
 198
 199 }
 200
 201
 202 =head2 seq_version
 203
 204  Title   : seq_version
 205  Usage   :
 206  Function: Get (and set, depending on the implementation) the version string
 207            of the sequence.
 208  Example :
 209  Returns : a string
 210  Args    :
 211  Note    : this differs from Bio::PrimarySeq version() in that this explicitly
 212            refers to the sequence record version one would find in a typical
 213            sequence file.  It is up to the implementation whether this is set
 214            separately or falls back to the more generic Bio::Seq::version()
 215
 216 =cut
 217
 218 sub seq_version{
 219    my ($self,@args) = @_;
 220
 221    $self->throw("hit seq_version in interface definition - error");
 222
 223 }
 224
 225 =head2 get_keywords
 226
 227  Title   : get_keywords
 228  Usage   : $obj->get_keywords()
 229  Function: Get the keywords for this sequence object.
 230
 231            An implementation that allows modification of this array
 232            property should provide the methods add_keyword and
 233            remove_keywords, with obvious purpose.
 234
 235  Returns : an array of strings
 236  Args    :
 237
 238
 239 =cut
 240
 241 sub get_keywords {
 242    my ($self) = @_;
 243    $self->throw("hit keywords in interface definition - error");
 244 }
 245
 246 1;