Bio::DB QueryI
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Summary
Bio::DB::QueryI - Object Interface to queryable sequence databases
Package variables
No package variables defined.
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 = 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.
Methods
countDescriptionCode
idsDescriptionCode
queryDescriptionCode
Methods description
countcode    nextTop
 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.
idscodeprevnextTop
 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
querycodeprevnextTop
 Title   : query
Usage : $query = $db->query([$query])
Function: get/set query string
Returns : string
Args : (optional) new query string
Methods code
countdescriptionprevnextTop
sub count {
  my $self = shift;
  my @ids  = $self->ids;
  scalar @ids;
}
idsdescriptionprevnextTop
sub ids {
  my $self = shift;
  $self->throw_not_implemented;
}
querydescriptionprevnextTop
sub query {
  my $self = shift;
  $self->throw_not_implemented;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Lincoln SteinTop
Email lstein@cshl.org
APPENDIXTop
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
newTop
 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.