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.\" ========================================================================
.\"
.IX Title "Bio::DB::QueryI 3pm"
.TH Bio::DB::QueryI 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::DB::QueryI \- Object Interface to queryable sequence databases
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&   # using Bio::DB::Query::GenBank as an example
\&   my $query_string = \*(AqOryza[Organism] AND EST[Keyword]\*(Aq;
\&   my $query = Bio::DB::Query::GenBank\->new(\-db=>\*(Aqnucleotide\*(Aq,
\&                                            \-query=>$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=>[\*(AqX1012\*(Aq,\*(AqCA12345\*(Aq]);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This interface provides facilities for managing sequence queries such
as those offered by Entrez.  A query object is created by calling
\&\fBnew()\fR 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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Lincoln Stein"
.IX Header "AUTHOR - Lincoln Stein"
Email lstein@cshl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 6
\& 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
.Ve
.PP
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.
.PP
Subclasses may recognize additional arguments.
.SS "count"
.IX Subsection "count"
.Vb 5
\& Title   : count
\& Usage   : $count = $db\->count;
\& Function: return count of number of entries retrieved by query
\& Returns : integer
\& Args    : none
.Ve
.PP
Returns the number of entries that are matched by the query.
.SS "ids"
.IX Subsection "ids"
.Vb 5
\& 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
.Ve
.SS "query"
.IX Subsection "query"
.Vb 5
\& Title   : query
\& Usage   : $query = $db\->query([$query])
\& Function: get/set query string
\& Returns : string
\& Args    : (optional) new query string
.Ve