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 = $db->entries();
  30
  31 =head1 DESCRIPTION
  32
  33 This module provides a basic implementation of B<Bio::Search::DatabaseI>.
  34 See documentation in that module for more information.
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules.  Send your comments and suggestions preferably to one
  42 of the Bioperl mailing lists.  Your participation is much appreciated.
  43
  44     bioperl-l@bioperl.org                - General discussion
  45     http://bio.perl.org/MailList.html    - About the mailing lists
  46
  47 =head2 Reporting Bugs
  48
  49 Report bugs to the Bioperl bug tracking system to help us keep track
  50 the bugs and their resolution. Bug reports can be submitted via email
  51 or the web:
  52
  53     bioperl-bugs@bio.perl.org
  54     http://bugzilla.bioperl.org/
  55
  56 =head1 AUTHOR
  57
  58 Steve Chervitz E<lt>sac@bioperl.orgE<gt>
  59
  60 See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
  61
  62 =head1 COPYRIGHT
  63
  64 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
  65
  66 =head1 DISCLAIMER
  67
  68 This software is provided "as is" without warranty of any kind.
  69
  70 =cut
  71
  72 =head1 APPENDIX
  73
  74
  75 The rest of the documentation details each of the object methods.
  76
  77 =cut
  78
  79 # Let the code begin...
  80
  81 package Bio::Search::GenericDatabase;
  82
  83 use strict;
  84 use Bio::Search::DatabaseI;
  85 use Bio::Root::Root;
  86 use vars qw( @ISA );
  87
  88 @ISA = qw( Bio::Root::Root Bio::Search::DatabaseI);
  89
  90 sub new {
  91     my ($class, @args) = @_;
  92     my $self = $class->SUPER::new(@args);
  93     my ($name, $date, $length, $ents) =
  94         $self->_rearrange( [qw(NAME DATE LENGTH ENTRIES)], @args);
  95
  96     $name    && $self->name($name);
  97     $date    && $self->date($date);
  98     $length  && $self->letters($length);
  99     $ents    && $self->entries($ents);
 100
 101     return $self;
 102 }
 103
 104 =head2 name
 105
 106 See L<Bio::Search::DatabaseI::name>() for documentation
 107
 108 This implementation is a combined set/get accessor.
 109
 110 =cut
 111
 112 #---------------
 113 sub name {
 114 #---------------
 115     my $self = shift;
 116     if(@_) {
 117         my $name = shift;
 118         $name =~ s/(^\s+|\s+$)//g;
 119         $self->{'_db'} = $name;
 120     }
 121     $self->{'_db'};
 122 }
 123
 124 =head2 date
 125
 126 See L<Bio::Search::DatabaseI::date>() for documentation
 127
 128 This implementation is a combined set/get accessor.
 129
 130 =cut
 131
 132 #-----------------------
 133 sub date {
 134 #-----------------------
 135     my $self = shift;
 136     if(@_) { $self->{'_dbDate'} = shift; }
 137     $self->{'_dbDate'};
 138 }
 139
 140
 141 =head2 letters
 142
 143 See L<Bio::Search::DatabaseI::letters>() for documentation
 144
 145 This implementation is a combined set/get accessor.
 146
 147 =cut
 148
 149 #----------------------
 150 sub letters {
 151 #----------------------
 152     my $self = shift;
 153     if(@_) { $self->{'_dbLetters'} = shift; }
 154     $self->{'_dbLetters'};
 155 }
 156
 157
 158 =head2 entries
 159
 160 See L<Bio::Search::DatabaseI::entries>() for documentation
 161
 162 This implementation is a combined set/get accessor.
 163
 164 =cut
 165
 166 #------------------
 167 sub entries {
 168 #------------------
 169     my $self = shift;
 170     if(@_) { $self->{'_dbEntries'} = shift; }
 171     $self->{'_dbEntries'};
 172 }
 173
 174 1;