Provided by: libbio-perl-perl_1.7.2-2_all bug


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


          # 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',
          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']);


       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.


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AUTHOR - Lincoln Stein



       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.

        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.

        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