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Summary

Bio::DB::QueryI - Object Interface to queryable sequence databases

Package variables

Included modules

Inherit

Bio::Root::RootI

Synopsis

   # using Bio::DB::Query::GenBank as an example
   my $query_string = 'Oryza[Organism] AND EST[Keyword]';
   my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide',
                                            -query=>$query_string);
   my $count = $query->count;
   my @ids   = $query->ids;

   # get a genbank database handle
   $gb = new Bio::DB::GenBank;
   my $stream = $db->get_Stream_by_query($query);
   while (my $seq = $stream->next_seq) {
      ...
   }

   # initialize the list yourself
   my $query = Bio::DB::Query::GenBank->new(-ids=>['X1012','CA12345']);

Description

This interface provides facilities for managing sequence queries such
as those offered by Entrez. A query object is created by calling
new() with a database-specific argument list. From the query object
you can either obtain the list of IDs returned by the query, or a
count of entries that would be returned. You can pass the query
object to a Bio::DB::RandomAccessI object to return the entries
themselves as a list or a stream.

Methods

Methods description

 Title   : count
 Usage   : $count = $db->count;
 Function: return count of number of entries retrieved by query
 Returns : integer
 Args    : none

 Title   : ids
 Usage   : @ids = $db->ids([@ids])
 Function: get/set matching ids
 Returns : array of sequence ids
 Args    : (optional) array ref with new set of ids

 Title   : query
 Usage   : $query = $db->query([$query])
 Function: get/set query string
 Returns : string
 Args    : (optional) new query string

Methods code

sub count {

  my $self = shift;
  my @ids  = $self->ids;
  scalar @ids;

}

sub ids {

  my $self = shift;
  $self->throw_not_implemented;

}

sub query {

  my $self = shift;
  $self->throw_not_implemented;
}

1;

}

General documentation

User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to
help us keep track the bugs and their resolution.
Bug reports can be submitted via email or the
web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email lstein@cshl.org

The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _

 Title   : new
 Usage   : $db = Bio::DB::QueryI->new(@args);
 Function: constructor
 Returns : QueryI object
 Args    : -query       a query string
           -ids         a list of ids as an arrayref

Create new QueryI object. You may initialize with either a query
string or with a list of ids. If both ids and a query are provided,
the former takes precedence.
Subclasses may recognize additional arguments.