Bio/Search/GenericDatabase.pm

   1 #-----------------------------------------------------------------
   2 #
   3 # BioPerl module Bio::Search::GenericDatabase
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Steve Chervitz <sac@bioperl.org>
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10 #-----------------------------------------------------------------
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Search::GenericDatabase;
  21
  22     $db = Bio::Search::GenericDatabase->new( -name => 'my Blast db',
  23                                              -date => '2001-03-13',
  24                                              -length => 2352511,
  25                                              -entries => 250000 );
  26
  27     $name = $db->name();
  28     $date = $db->date();
  29     $num_letters = $db->letters();
  30     $num_entries = $db->entries();
  31
  32 =head1 DESCRIPTION
  33
  34 This module provides a basic implementation of L<Bio::Search::DatabaseI>.
  35 See documentation in that module for more information.
  36
  37 =head1 FEEDBACK
  38
  39 =head2 Mailing Lists
  40
  41 User feedback is an integral part of the evolution of this and other
  42 Bioperl modules.  Send your comments and suggestions preferably to one
  43 of the Bioperl mailing lists.  Your participation is much appreciated.
  44
  45   bioperl-l@bioperl.org                  - General discussion
  46   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  47
  48 =head2 Support
  49
  50 Please direct usage questions or support issues to the mailing list:
  51
  52 I<bioperl-l@bioperl.org>
  53
  54 rather than to the module maintainer directly. Many experienced and
  55 reponsive experts will be able look at the problem and quickly
  56 address it. Please include a thorough description of the problem
  57 with code and data examples if at all possible.
  58
  59 =head2 Reporting Bugs
  60
  61 Report bugs to the Bioperl bug tracking system to help us keep track
  62 the bugs and their resolution. Bug reports can be submitted via the
  63 web:
  64
  65   https://github.com/bioperl/bioperl-live/issues
  66
  67 =head1 AUTHOR
  68
  69 Steve Chervitz E<lt>sac@bioperl.orgE<gt>
  70
  71 See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
  72
  73 =head1 COPYRIGHT
  74
  75 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
  76
  77 =head1 DISCLAIMER
  78
  79 This software is provided "as is" without warranty of any kind.
  80
  81 =cut
  82
  83 =head1 APPENDIX
  84
  85
  86 The rest of the documentation details each of the object methods.
  87
  88 =cut
  89
  90 # Let the code begin...
  91
  92 package Bio::Search::GenericDatabase;
  93
  94 use strict;
  95
  96 use base qw(Bio::Root::Root Bio::Search::DatabaseI);
  97
  98 sub new {
  99     my ($class, @args) = @_;
 100     my $self = $class->SUPER::new(@args);
 101     my ($name, $date, $length, $ents) =
 102         $self->_rearrange( [qw(NAME DATE LENGTH ENTRIES)], @args);
 103
 104     $name    && $self->name($name);
 105     $date    && $self->date($date);
 106     $length  && $self->letters($length);
 107     $ents    && $self->entries($ents);
 108
 109     return $self;
 110 }
 111
 112 =head2 name
 113
 114 See L<Bio::Search::DatabaseI::name>() for documentation
 115
 116 This implementation is a combined set/get accessor.
 117
 118 =cut
 119
 120 #---------------
 121 sub name {
 122 #---------------
 123     my $self = shift;
 124     if(@_) {
 125         my $name = shift;
 126         $name =~ s/(^\s+|\s+$)//g;
 127         $self->{'_db'} = $name;
 128     }
 129     $self->{'_db'};
 130 }
 131
 132 =head2 date
 133
 134 See L<Bio::Search::DatabaseI::date>() for documentation
 135
 136 This implementation is a combined set/get accessor.
 137
 138 =cut
 139
 140 #-----------------------
 141 sub date {
 142 #-----------------------
 143     my $self = shift;
 144     if(@_) { $self->{'_dbDate'} = shift; }
 145     $self->{'_dbDate'};
 146 }
 147
 148
 149 =head2 letters
 150
 151 See L<Bio::Search::DatabaseI::letters>() for documentation
 152
 153 This implementation is a combined set/get accessor.
 154
 155 =cut
 156
 157 #----------------------
 158 sub letters {
 159 #----------------------
 160     my $self = shift;
 161     if(@_) { $self->{'_dbLetters'} = shift; }
 162     $self->{'_dbLetters'};
 163 }
 164
 165
 166 =head2 entries
 167
 168 See L<Bio::Search::DatabaseI::entries>() for documentation
 169
 170 This implementation is a combined set/get accessor.
 171
 172 =cut
 173
 174 #------------------
 175 sub entries {
 176 #------------------
 177     my $self = shift;
 178     if(@_) { $self->{'_dbEntries'} = shift; }
 179     $self->{'_dbEntries'};
 180 }
 181
 182 1;