lib/Bio/BioEntry.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::BioEntry
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Hilmar Lapp <hlapp at 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::BioEntry - DESCRIPTION of Object
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Describe the object here
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to
  33 the Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via
  53 the web:
  54
  55   http://redmine.open-bio.org/projects/bioperl/
  56
  57 =head1 AUTHOR - Hilmar Lapp
  58
  59 Email hlapp at gmx.net
  60
  61 Describe contact details here
  62
  63 =head1 CONTRIBUTORS
  64
  65 Additional contributors names and emails here
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74
  75 # Let the code begin...
  76
  77
  78 package Bio::BioEntry;
  79 use vars qw(@ISA);
  80 use strict;
  81
  82 # Object preamble - inherits from Bio::Root::Root
  83
  84 use Bio::Root::Root;
  85 use Bio::IdentifiableI;
  86 use Bio::DescribableI;
  87
  88 @ISA = qw(Bio::Root::Root Bio::IdentifiableI Bio::DescribableI);
  89
  90 =head2 new
  91
  92  Title   : new
  93  Usage   : my $obj = Bio::BioEntry->new();
  94  Function: Builds a new Bio::BioEntry object
  95  Returns : an instance of Bio::BioEntry
  96  Args    :
  97
  98
  99 =cut
 100
 101 sub new {
 102   my($class,@args) = @_;
 103
 104   my $self = $class->SUPER::new(@args);
 105   my ($objid, $ns, $auth, $v, $display_id, $desc) =
 106       $self->_rearrange([qw(OBJECT_ID
 107                             NAMESPACE
 108                             AUTHORITY
 109                             VERSION
 110                             DISPLAY_ID
 111                             DESCRIPTION)
 112                          ],
 113                         @args);
 114
 115   $self->object_id($objid) if $objid;
 116   $self->namespace($ns) if $ns;
 117   $self->authority($auth) if $auth;
 118   $self->version($v) if $v;
 119   $self->display_name($display_id) if $display_id;
 120   $self->description($desc) if $desc;
 121
 122   return $self;
 123 }
 124
 125 =head1 Methods for Bio::IdentifiableI compliance
 126
 127 =head2 object_id
 128
 129  Title   : object_id
 130  Usage   : $string    = $obj->object_id()
 131  Function: a string which represents the stable primary identifier
 132            in this namespace of this object. For DNA sequences this
 133            is its accession_number, similarly for protein sequences
 134
 135            This is aliased to accession_number().
 136  Returns : A scalar
 137
 138
 139 =cut
 140
 141 sub object_id {
 142     my ($self, $value) = @_;
 143
 144     if( defined $value) {
 145         $self->{'object_id'} = $value;
 146     }
 147     return $self->{'object_id'};
 148 }
 149
 150 =head2 version
 151
 152  Title   : version
 153  Usage   : $version    = $obj->version()
 154  Function: a number which differentiates between versions of
 155            the same object. Higher numbers are considered to be
 156            later and more relevant, but a single object described
 157            the same identifier should represent the same concept
 158
 159  Returns : A number
 160
 161 =cut
 162
 163 sub version{
 164     my ($self,$value) = @_;
 165     if( defined $value) {
 166         $self->{'_version'} = $value;
 167     }
 168     return $self->{'_version'};
 169 }
 170
 171
 172 =head2 authority
 173
 174  Title   : authority
 175  Usage   : $authority    = $obj->authority()
 176  Function: a string which represents the organisation which
 177            granted the namespace, written as the DNS name for
 178            organisation (eg, wormbase.org)
 179
 180  Returns : A scalar
 181
 182 =cut
 183
 184 sub authority {
 185     my ($obj,$value) = @_;
 186     if( defined $value) {
 187         $obj->{'authority'} = $value;
 188     }
 189     return $obj->{'authority'};
 190 }
 191
 192 =head2 namespace
 193
 194  Title   : namespace
 195  Usage   : $string    = $obj->namespace()
 196  Function: A string representing the name space this identifier
 197            is valid in, often the database name or the name
 198            describing the collection
 199
 200  Returns : A scalar
 201
 202
 203 =cut
 204
 205 sub namespace{
 206     my ($self,$value) = @_;
 207     if( defined $value) {
 208         $self->{'namespace'} = $value;
 209     }
 210     return $self->{'namespace'} || "";
 211 }
 212
 213 =head1 Methods for Bio::DescribableI compliance
 214
 215 =head2 display_name
 216
 217  Title   : display_name
 218  Usage   : $string    = $obj->display_name()
 219  Function: A string which is what should be displayed to the user
 220            the string should have no spaces (ideally, though a cautious
 221            user of this interface would not assumme this) and should be
 222            less than thirty characters (though again, double checking
 223            this is a good idea)
 224
 225            This is aliased to display_id().
 226  Returns : A scalar
 227
 228 =cut
 229
 230 sub display_name {
 231     my ($self,$value) = @_;
 232     if( defined $value) {
 233         $self->{'_display_name'} = $value;
 234     }
 235     return $self->{'_display_name'};
 236 }
 237
 238 =head2 description
 239
 240  Title   : description
 241  Usage   : $string    = $obj->description()
 242  Function: A text string suitable for displaying to the user a
 243            description. This string is likely to have spaces, but
 244            should not have any newlines or formatting - just plain
 245            text. The string should not be greater than 255 characters
 246            and clients can feel justified at truncating strings at 255
 247            characters for the purposes of display
 248
 249            This is aliased to desc().
 250  Returns : A scalar
 251
 252 =cut
 253
 254 sub description {
 255     my ($self,$value) = @_;
 256
 257     if( defined $value) {
 258         $self->{'_description'} = $value;
 259     }
 260     return $self->{'_description'};
 261 }
 262
 263
 264 1;