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
  83 use strict;
  84
  85 use base qw(Bio::SeqI);
  86
  87
  88 =head2 get_secondary_accessions
  89
  90  Title   : get_secondary_accessions
  91  Usage   :
  92  Function: Get the secondary accessions for a sequence.
  93
  94            An implementation that allows modification of this array
  95            property should provide the methods add_secondary_accession
  96            and remove_secondary_accessions, with obvious purpose.
  97
  98  Example :
  99  Returns : an array of strings
 100  Args    : none
 101
 102
 103 =cut
 104
 105 sub get_secondary_accessions{
 106    my ($self,@args) = @_;
 107
 108    $self->throw("hit get_secondary_accessions in interface definition - error");
 109
 110 }
 111
 112
 113 =head2 division
 114
 115  Title   : division
 116  Usage   :
 117  Function: Get (and set, depending on the implementation) the division for
 118            a sequence.
 119
 120            Examples from GenBank are PLN (plants), PRI (primates), etc.
 121  Example :
 122  Returns : a string
 123  Args    :
 124
 125
 126 =cut
 127
 128 sub division{
 129    my ($self,@args) = @_;
 130
 131    $self->throw("hit division in interface definition - error");
 132
 133 }
 134
 135
 136 =head2 molecule
 137
 138  Title   : molecule
 139  Usage   :
 140  Function: Get (and set, depending on the implementation) the molecule
 141            type for the sequence.
 142
 143            This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
 144            because it is databank-specific.
 145  Example :
 146  Returns : a string
 147  Args    :
 148
 149
 150 =cut
 151
 152 sub molecule{
 153    my ($self,@args) = @_;
 154
 155    $self->throw("hit molecule in interface definition - error");
 156 }
 157
 158 =head2 pid
 159
 160  Title   : pid
 161  Usage   :
 162  Function: Get (and set, depending on the implementation) the PID property
 163            for the sequence.
 164  Example :
 165  Returns : a string
 166  Args    :
 167
 168
 169 =cut
 170
 171 sub pid {
 172    my ($self,@args) = @_;
 173
 174    $self->throw("hit pid in interface definition - error");
 175 }
 176
 177 =head2 get_dates
 178
 179  Title   : get_dates
 180  Usage   :
 181  Function: Get (and set, depending on the implementation) the dates the
 182            databank entry specified for the sequence
 183
 184            An implementation that allows modification of this array
 185            property should provide the methods add_date and
 186            remove_dates, with obvious purpose.
 187
 188  Example :
 189  Returns : an array of strings
 190  Args    :
 191
 192
 193 =cut
 194
 195 sub get_dates{
 196    my ($self,@args) = @_;
 197
 198    $self->throw("hit get_dates in interface definition - error");
 199
 200 }
 201
 202
 203 =head2 seq_version
 204
 205  Title   : seq_version
 206  Usage   :
 207  Function: Get (and set, depending on the implementation) the version string
 208            of the sequence.
 209  Example :
 210  Returns : a string
 211  Args    :
 212  Note    : this differs from Bio::PrimarySeq version() in that this explicitly
 213            refers to the sequence record version one would find in a typical
 214            sequence file.  It is up to the implementation whether this is set
 215            separately or falls back to the more generic Bio::Seq::version()
 216
 217 =cut
 218
 219 sub seq_version{
 220    my ($self,@args) = @_;
 221
 222    $self->throw("hit seq_version in interface definition - error");
 223
 224 }
 225
 226 =head2 get_keywords
 227
 228  Title   : get_keywords
 229  Usage   : $obj->get_keywords()
 230  Function: Get the keywords for this sequence object.
 231
 232            An implementation that allows modification of this array
 233            property should provide the methods add_keyword and
 234            remove_keywords, with obvious purpose.
 235
 236  Returns : an array of strings
 237  Args    :
 238
 239
 240 =cut
 241
 242 sub get_keywords {
 243    my ($self) = @_;
 244    $self->throw("hit keywords in interface definition - error");
 245 }
 246
 247 1;