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1 # $Id: QueryI.pm,v 1.1 2002/11/20 08:39:03 lstein Exp $
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2 #
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3 # BioPerl module for Bio::DB::QueryI.pm
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4 #
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5 # Cared for by Lincoln Stein <lstein@cshl.org>
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6 #
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7 # Copyright Lincoln Stein
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8 #
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9 # You may distribute this module under the same terms as perl itself
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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
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14 =head1 NAME
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15
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16 Bio::DB::QueryI - Object Interface to queryable sequence databases
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17
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18 =head1 SYNOPSIS
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19
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20 # using Bio::DB::Query::GenBank as an example
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21 my $query_string = 'Oryza[Organism] AND EST[Keyword]';
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22 my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide',
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23 -query=>$query_string);
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24 my $count = $query->count;
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25 my @ids = $query->ids;
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26
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27 # get a genbank database handle
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28 $gb = new Bio::DB::GenBank;
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29 my $stream = $db->get_Stream_by_query($query);
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30 while (my $seq = $stream->next_seq) {
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31 ...
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32 }
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33
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34 # initialize the list yourself
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35 my $query = Bio::DB::Query::GenBank->new(-ids=>['X1012','CA12345']);
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36
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37 =head1 DESCRIPTION
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38
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39 This interface provides facilities for managing sequence queries such
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40 as those offered by Entrez. A query object is created by calling
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41 new() with a database-specific argument list. From the query object
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42 you can either obtain the list of IDs returned by the query, or a
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43 count of entries that would be returned. You can pass the query
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44 object to a Bio::DB::RandomAccessI object to return the entries
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45 themselves as a list or a stream.
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46
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47 =head1 FEEDBACK
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48
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49 =head2 Mailing Lists
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50
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51 User feedback is an integral part of the
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52 evolution of this and other Bioperl modules. Send
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53 your comments and suggestions preferably to one
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54 of the Bioperl mailing lists. Your participation
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55 is much appreciated.
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56
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57 bioperl-l@bioperl.org - General discussion
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58 http://bioperl.org/MailList.shtml - About the mailing lists
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59
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60 =head2 Reporting Bugs
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61
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62 Report bugs to the Bioperl bug tracking system to
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63 help us keep track the bugs and their resolution.
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64 Bug reports can be submitted via email or the
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65 web:
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66
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67 bioperl-bugs@bio.perl.org
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68 http://bugzilla.bioperl.org/
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69
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70 =head1 AUTHOR - Lincoln Stein
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71
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72 Email lstein@cshl.org
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73
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74 =head1 APPENDIX
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75
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76 The rest of the documentation details each of the
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77 object methods. Internal methods are usually
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78 preceded with a _
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79
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80 =cut
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81
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82 # Let the code begin...
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83
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84 package Bio::DB::QueryI;
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85 use strict;
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86 use Bio::Root::RootI;
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87
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88 use vars qw(@ISA $VERSION);
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89
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90 @ISA = qw(Bio::Root::RootI);
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91 $VERSION = '0.1';
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92
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93 =head2 new
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94
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95 Title : new
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96 Usage : $db = Bio::DB::QueryI->new(@args);
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97 Function: constructor
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98 Returns : QueryI object
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99 Args : -query a query string
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100 -ids a list of ids as an arrayref
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101
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102 Create new QueryI object. You may initialize with either a query
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103 string or with a list of ids. If both ids and a query are provided,
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104 the former takes precedence.
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105
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106 Subclasses may recognize additional arguments.
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107
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108 =cut
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109
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110 =head2 count
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111
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112 Title : count
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113 Usage : $count = $db->count;
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114 Function: return count of number of entries retrieved by query
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115 Returns : integer
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116 Args : none
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117
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118 Returns the number of entries that are matched by the query.
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119
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120 =cut
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121
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122 sub count {
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123 my $self = shift;
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124 my @ids = $self->ids;
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125 scalar @ids;
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126 }
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127
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128 =head2 ids
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129
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130 Title : ids
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131 Usage : @ids = $db->ids([@ids])
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132 Function: get/set matching ids
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133 Returns : array of sequence ids
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134 Args : (optional) array ref with new set of ids
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135
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136 =cut
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137
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138 sub ids {
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139 my $self = shift;
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140 $self->throw_not_implemented;
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141 }
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142
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143 =head2 query
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144
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145 Title : query
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146 Usage : $query = $db->query([$query])
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147 Function: get/set query string
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148 Returns : string
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149 Args : (optional) new query string
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150
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151 =cut
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152
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153 sub query {
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154 my $self = shift;
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155 $self->throw_not_implemented;
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156 }
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157
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158 1;
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