branch-1-6/Bio/Seq/RichSeqI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Seq::RichSeqI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   8 #
   9 # Copyright Ewan Birney
  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::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
  18
  19 =head1 SYNOPSIS
  20
  21     @secondary   = $richseq->get_secondary_accessions;
  22     $division    = $richseq->division;
  23     $mol         = $richseq->molecule;
  24     @dates       = $richseq->get_dates;
  25     $seq_version = $richseq->seq_version;
  26     $pid         = $richseq->pid;
  27     @keywords    = $richseq->get_keywords;
  28
  29 =head1 DESCRIPTION
  30
  31 This interface extends the Bio::SeqI interface to give additional functionality
  32 to sequences with richer data sources, in particular from database sequences
  33 (EMBL, GenBank and Swissprot).
  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   http://bugzilla.open-bio.org/
  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 methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 # Let the code begin...
  78
  79
  80 package Bio::Seq::RichSeqI;
  81 use strict;
  82
  83 use base qw(Bio::SeqI);
  84
  85
  86 =head2 get_secondary_accessions
  87
  88  Title   : get_secondary_accessions
  89  Usage   :
  90  Function: Get the secondary accessions for a sequence.
  91
  92            An implementation that allows modification of this array
  93            property should provide the methods add_secondary_accession
  94            and remove_secondary_accessions, with obvious purpose.
  95
  96  Example :
  97  Returns : an array of strings
  98  Args    : none
  99
 100
 101 =cut
 102
 103 sub get_secondary_accessions{
 104    my ($self,@args) = @_;
 105
 106    $self->throw("hit get_secondary_accessions in interface definition - error");
 107
 108 }
 109
 110
 111 =head2 division
 112
 113  Title   : division
 114  Usage   :
 115  Function: Get (and set, depending on the implementation) the divison for
 116            a sequence.
 117
 118            Examples from GenBank are PLN (plants), PRI (primates), etc.
 119  Example :
 120  Returns : a string
 121  Args    :
 122
 123
 124 =cut
 125
 126 sub division{
 127    my ($self,@args) = @_;
 128
 129    $self->throw("hit division in interface definition - error");
 130
 131 }
 132
 133
 134 =head2 molecule
 135
 136  Title   : molecule
 137  Usage   :
 138  Function: Get (and set, depending on the implementation) the molecule
 139            type for the sequence.
 140
 141            This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
 142            because it is databank-specific.
 143  Example :
 144  Returns : a string
 145  Args    :
 146
 147
 148 =cut
 149
 150 sub molecule{
 151    my ($self,@args) = @_;
 152
 153    $self->throw("hit molecule in interface definition - error");
 154 }
 155
 156 =head2 pid
 157
 158  Title   : pid
 159  Usage   :
 160  Function: Get (and set, depending on the implementation) the PID property
 161            for the sequence.
 162  Example :
 163  Returns : a string
 164  Args    :
 165
 166
 167 =cut
 168
 169 sub pid {
 170    my ($self,@args) = @_;
 171
 172    $self->throw("hit pid in interface definition - error");
 173 }
 174
 175 =head2 get_dates
 176
 177  Title   : get_dates
 178  Usage   :
 179  Function: Get (and set, depending on the implementation) the dates the
 180            databank entry specified for the sequence
 181
 182            An implementation that allows modification of this array
 183            property should provide the methods add_date and
 184            remove_dates, with obvious purpose.
 185
 186  Example :
 187  Returns : an array of strings
 188  Args    :
 189
 190
 191 =cut
 192
 193 sub get_dates{
 194    my ($self,@args) = @_;
 195
 196    $self->throw("hit get_dates in interface definition - error");
 197
 198 }
 199
 200
 201 =head2 seq_version
 202
 203  Title   : seq_version
 204  Usage   :
 205  Function: Get (and set, depending on the implementation) the version string
 206            of the sequence.
 207  Example :
 208  Returns : a string
 209  Args    :
 210
 211
 212 =cut
 213
 214 sub seq_version{
 215    my ($self,@args) = @_;
 216
 217    $self->throw("hit seq_version in interface definition - error");
 218
 219 }
 220
 221 =head2 get_keywords
 222
 223  Title   : get_keywords
 224  Usage   : $obj->get_keywords()
 225  Function: Get the keywords for this sequence object.
 226
 227            An implementation that allows modification of this array
 228            property should provide the methods add_keyword and
 229            remove_keywords, with obvious purpose.
 230
 231  Returns : an array of strings
 232  Args    :
 233
 234
 235 =cut
 236
 237 sub get_keywords {
 238    my ($self) = @_;
 239    $self->throw("hit keywords in interface definition - error");
 240 }
 241
 242 1;