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1 # POD documentation - main docs before the code
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2
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3 # $Id: Failover.pm,v 1.5.2.1 2003/06/25 13:44:18 heikki Exp $
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4
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5
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6 =head1 NAME
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7
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8 Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs
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9
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10 =head1 SYNOPSIS
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11
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12 $failover = Bio::DB::Failover->new();
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13
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14 $failover->add_database($db);
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15
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16 # fail over Bio::DB::RandomAccessI.pm
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17
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18 # this will check each database in priority, returning when
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19 # the first one succeeds
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20
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21 $seq = $failover->get_Seq_by_id($id);
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22
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23 =head1 DESCRIPTION
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24
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25 This module provides fail over access to a set of Bio::DB::RandomAccessI objects
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26
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27
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28 =head1 CONTACT
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29
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30 Ewan Birney originally wrote this class.
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31
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32 =head2 Reporting Bugs
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33
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34 Report bugs to the Bioperl bug tracking system to help us keep track
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35 the bugs and their resolution. Bug reports can be submitted via email
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36 or the web:
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37
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38 bioperl-bugs@bio.perl.org
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39 http://bugzilla.bioperl.org/
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40
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41 =head1 APPENDIX
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42
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43 The rest of the documentation details each of the object
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44 methods. Internal methods are usually preceded with a _
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45
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46 =cut
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47
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48
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49 # Let the code begin...
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50
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51 package Bio::DB::Failover;
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52
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53 use vars qw(@ISA);
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54 use strict;
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55
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56 use Bio::Root::Root;
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57 use Bio::DB::RandomAccessI;
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58 @ISA = qw(Bio::Root::Root Bio::DB::RandomAccessI );
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59
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60 sub new {
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61 my ($class,@args) = @_;
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62
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63 my $self = $class->SUPER::new(@args);
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64
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65 $self->{'_database'} = [];
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66 return $self;
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67 }
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68
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69 =head2 add_database
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70
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71 Title : add_database
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72 Usage : add_database(%db)
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73 Function: Adds a database to the
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74 Returns : count of number of databases
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75 Args : hash of db resource name to Bio::DB::SeqI object
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76
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77 =cut
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78
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79 sub add_database {
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80 my ($self,@db) = @_;
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81 foreach my $db ( @db ) {
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82 if( !ref $db || !$db->isa('Bio::DB::RandomAccessI') ) {
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83 $self->throw("Database objects $db is a not a Bio::DB::RandomAccessI");
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84 next;
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85 }
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86
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87 push(@{$self->{'_database'}},$db);
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88 }
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89 }
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90
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91
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92 =head2 get_Seq_by_id
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93
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94 Title : get_Seq_by_id
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95 Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
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96 Function: Gets a Bio::Seq object by its name
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97 Returns : a Bio::Seq object
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98 Args : the id (as a string) of a sequence
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99 Throws : "id does not exist" exception
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100
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101
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102 =cut
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103
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104 sub get_Seq_by_id {
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105 my ($self,$id) = @_;
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106
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107 if( !defined $id ) {
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108 $self->throw("no id is given!");
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109 }
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110
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111 foreach my $db ( @{$self->{'_database'}} ) {
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112 my $seq;
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113
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114 eval {
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115 $seq = $db->get_Seq_by_id($id);
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116 };
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117 if( defined $seq ) {
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118 return $seq;
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119 }
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120 }
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121
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122 return undef;
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123 }
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124
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125 =head2 get_Seq_by_acc
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126
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127 Title : get_Seq_by_acc
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128 Usage : $seq = $db->get_Seq_by_acc('X77802');
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129 Function: Gets a Bio::Seq object by accession number
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130 Returns : A Bio::Seq object
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131 Args : accession number (as a string)
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132 Throws : "acc does not exist" exception
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133
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134
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135 =cut
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136
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137 sub get_Seq_by_acc {
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138 my ($self,$id) = @_;
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139
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140 if( !defined $id ) {
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141 $self->throw("no id is given!");
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142 }
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143
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144 foreach my $db ( @{$self->{'_database'}} ) {
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145 my $seq;
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146 eval {
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147 $seq = $db->get_Seq_by_acc($id);
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148 };
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149 if( defined $seq ) {
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150 return $seq;
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151 }
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152 }
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153 return undef;
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154 }
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155
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156
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157 ## End of Package
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158
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159 1;
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160
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161 __END__
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162
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