Bio/Search/GenericDatabase.pm

   1 #-----------------------------------------------------------------
   2 # $Id$
   3 #
   4 # BioPerl module Bio::Search::GenericDatabase
   5 #
   6 # Cared for by Steve Chervitz <sac@bioperl.org>
   7 #
   8 # You may distribute this module under the same terms as perl itself
   9 #-----------------------------------------------------------------
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI
  16
  17 =head1 SYNOPSIS
  18
  19     use Bio::Search::GenericDatabase;
  20
  21     $db = Bio::Search::GenericDatabase->new( -name => 'my Blast db',
  22                                              -date => '2001-03-13',
  23                                              -length => 2352511,
  24                                              -entries => 250000 );
  25
  26     $name = $db->name();
  27     $date = $db->date();
  28     $num_letters = $db->letters();
  29     $num_entries = $db->entries();
  30
  31 =head1 DESCRIPTION
  32
  33 This module provides a basic implementation of L<Bio::Search::DatabaseI>.
  34 See documentation in that module for more information.
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules.  Send your comments and suggestions preferably to one
  42 of the Bioperl mailing lists.  Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Reporting Bugs
  48
  49 Report bugs to the Bioperl bug tracking system to help us keep track
  50 the bugs and their resolution. Bug reports can be submitted via the
  51 web:
  52
  53   http://bugzilla.open-bio.org/
  54
  55 =head1 AUTHOR
  56
  57 Steve Chervitz E<lt>sac@bioperl.orgE<gt>
  58
  59 See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
  60
  61 =head1 COPYRIGHT
  62
  63 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
  64
  65 =head1 DISCLAIMER
  66
  67 This software is provided "as is" without warranty of any kind.
  68
  69 =cut
  70
  71 =head1 APPENDIX
  72
  73
  74 The rest of the documentation details each of the object methods.
  75
  76 =cut
  77
  78 # Let the code begin...
  79
  80 package Bio::Search::GenericDatabase;
  81
  82 use strict;
  83
  84 use base qw(Bio::Root::Root Bio::Search::DatabaseI);
  85
  86 sub new {
  87     my ($class, @args) = @_;
  88     my $self = $class->SUPER::new(@args);
  89     my ($name, $date, $length, $ents) =
  90         $self->_rearrange( [qw(NAME DATE LENGTH ENTRIES)], @args);
  91
  92     $name    && $self->name($name);
  93     $date    && $self->date($date);
  94     $length  && $self->letters($length);
  95     $ents    && $self->entries($ents);
  96
  97     return $self;
  98 }
  99
 100 =head2 name
 101
 102 See L<Bio::Search::DatabaseI::name>() for documentation
 103
 104 This implementation is a combined set/get accessor.
 105
 106 =cut
 107
 108 #---------------
 109 sub name {
 110 #---------------
 111     my $self = shift;
 112     if(@_) {
 113         my $name = shift;
 114         $name =~ s/(^\s+|\s+$)//g;
 115         $self->{'_db'} = $name;
 116     }
 117     $self->{'_db'};
 118 }
 119
 120 =head2 date
 121
 122 See L<Bio::Search::DatabaseI::date>() for documentation
 123
 124 This implementation is a combined set/get accessor.
 125
 126 =cut
 127
 128 #-----------------------
 129 sub date {
 130 #-----------------------
 131     my $self = shift;
 132     if(@_) { $self->{'_dbDate'} = shift; }
 133     $self->{'_dbDate'};
 134 }
 135
 136
 137 =head2 letters
 138
 139 See L<Bio::Search::DatabaseI::letters>() for documentation
 140
 141 This implementation is a combined set/get accessor.
 142
 143 =cut
 144
 145 #----------------------
 146 sub letters {
 147 #----------------------
 148     my $self = shift;
 149     if(@_) { $self->{'_dbLetters'} = shift; }
 150     $self->{'_dbLetters'};
 151 }
 152
 153
 154 =head2 entries
 155
 156 See L<Bio::Search::DatabaseI::entries>() for documentation
 157
 158 This implementation is a combined set/get accessor.
 159
 160 =cut
 161
 162 #------------------
 163 sub entries {
 164 #------------------
 165     my $self = shift;
 166     if(@_) { $self->{'_dbEntries'} = shift; }
 167     $self->{'_dbEntries'};
 168 }
 169
 170 1;