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1 #-----------------------------------------------------------------
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2 # $Id: GenericDatabase.pm,v 1.5 2002/10/22 07:38:38 lapp Exp $
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3 #
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4 # BioPerl module Bio::Search::GenericDatabase
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5 #
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6 # Cared for by Steve Chervitz <sac@bioperl.org>
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7 #
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8 # You may distribute this module under the same terms as perl itself
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9 #-----------------------------------------------------------------
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Search::GenericDatabase;
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20
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21 $db = Bio::Search::GenericDatabase->new( -name => 'my Blast db',
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22 -date => '2001-03-13',
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23 -length => 2352511,
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24 -entries => 250000 );
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25
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26 $name = $db->name();
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27 $date = $db->date();
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28 $num_letters = $db->letters();
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29 $num_entries = $db->entries();
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30
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31 =head1 DESCRIPTION
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32
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33 This module provides a basic implementation of B<Bio::Search::DatabaseI>.
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34 See documentation in that module for more information.
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35
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36 =head1 FEEDBACK
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37
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38 =head2 Mailing Lists
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39
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40 User feedback is an integral part of the evolution of this and other
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41 Bioperl modules. Send your comments and suggestions preferably to one
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42 of the Bioperl mailing lists. Your participation is much appreciated.
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43
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44 bioperl-l@bioperl.org - General discussion
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45 http://bio.perl.org/MailList.html - About the mailing lists
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46
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47 =head2 Reporting Bugs
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48
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49 Report bugs to the Bioperl bug tracking system to help us keep track
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50 the bugs and their resolution. Bug reports can be submitted via email
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51 or the web:
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52
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53 bioperl-bugs@bio.perl.org
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54 http://bugzilla.bioperl.org/
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55
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56 =head1 AUTHOR
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57
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58 Steve Chervitz E<lt>sac@bioperl.orgE<gt>
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59
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60 See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
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61
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62 =head1 COPYRIGHT
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63
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64 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
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65
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66 =head1 DISCLAIMER
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67
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68 This software is provided "as is" without warranty of any kind.
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69
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70 =cut
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71
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72 =head1 APPENDIX
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73
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74
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75 The rest of the documentation details each of the object methods.
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76
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77 =cut
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78
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79 # Let the code begin...
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80
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81 package Bio::Search::GenericDatabase;
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82
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83 use strict;
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84 use Bio::Search::DatabaseI;
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85 use Bio::Root::Root;
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86 use vars qw( @ISA );
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87
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88 @ISA = qw( Bio::Root::Root Bio::Search::DatabaseI);
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89
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90 sub new {
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91 my ($class, @args) = @_;
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92 my $self = $class->SUPER::new(@args);
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93 my ($name, $date, $length, $ents) =
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94 $self->_rearrange( [qw(NAME DATE LENGTH ENTRIES)], @args);
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95
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96 $name && $self->name($name);
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97 $date && $self->date($date);
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98 $length && $self->letters($length);
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99 $ents && $self->entries($ents);
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100
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101 return $self;
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102 }
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103
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104 =head2 name
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105
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106 See L<Bio::Search::DatabaseI::name>() for documentation
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107
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108 This implementation is a combined set/get accessor.
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109
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110 =cut
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111
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112 #---------------
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113 sub name {
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114 #---------------
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115 my $self = shift;
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116 if(@_) {
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117 my $name = shift;
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118 $name =~ s/(^\s+|\s+$)//g;
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119 $self->{'_db'} = $name;
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120 }
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121 $self->{'_db'};
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122 }
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123
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124 =head2 date
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125
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126 See L<Bio::Search::DatabaseI::date>() for documentation
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127
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128 This implementation is a combined set/get accessor.
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129
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130 =cut
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131
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132 #-----------------------
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133 sub date {
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134 #-----------------------
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135 my $self = shift;
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136 if(@_) { $self->{'_dbDate'} = shift; }
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137 $self->{'_dbDate'};
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138 }
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139
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140
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141 =head2 letters
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142
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143 See L<Bio::Search::DatabaseI::letters>() for documentation
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144
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145 This implementation is a combined set/get accessor.
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146
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147 =cut
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148
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149 #----------------------
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150 sub letters {
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151 #----------------------
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152 my $self = shift;
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153 if(@_) { $self->{'_dbLetters'} = shift; }
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154 $self->{'_dbLetters'};
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155 }
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156
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157
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158 =head2 entries
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159
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160 See L<Bio::Search::DatabaseI::entries>() for documentation
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161
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162 This implementation is a combined set/get accessor.
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163
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164 =cut
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165
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166 #------------------
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167 sub entries {
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168 #------------------
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169 my $self = shift;
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170 if(@_) { $self->{'_dbEntries'} = shift; }
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171 $self->{'_dbEntries'};
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172 }
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173
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174 1;
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