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Bio::DB::QueryI(3)    User Contributed Perl Documentation   Bio::DB::QueryI(3)

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

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 = Bio::DB::GenBank->new();
	  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.

FEEDBACK
   Mailing Lists
       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/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and
       data examples if at all possible.

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

	 http://bugzilla.open-bio.org/

AUTHOR - Lincoln Stein
       Email lstein@cshl.org

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

   new
	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.

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

       Returns the number of entries that are matched by the query.

   ids
	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

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

perl v5.14.1			  2011-07-22		    Bio::DB::QueryI(3)
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