diff variant_effect_predictor/Bio/DB/QueryI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/QueryI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,158 @@
+# $Id: QueryI.pm,v 1.1 2002/11/20 08:39:03 lstein Exp $
+#
+# BioPerl module for Bio::DB::QueryI.pm
+#
+# Cared for by Lincoln Stein <[e-mail]>
+#
+# Copyright Lincoln Stein
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation - main docs before the code
+#
+
+=head1 NAME
+
+Bio::DB::QueryI - Object Interface to queryable sequence databases
+
+=head1 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']);
+
+=head1 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.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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 email or the
+web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Lincoln Stein
+
+Email [e-mail]
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the
+object methods. Internal methods are usually
+preceded with a _
+
+=cut
+
+# Let the code begin...
+
+package Bio::DB::QueryI;
+use strict;
+use Bio::Root::RootI;
+
+use vars qw(@ISA $VERSION);
+
+@ISA = qw(Bio::Root::RootI);
+$VERSION = '0.1';
+
+=head2 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.
+
+=cut
+
+=head2 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.
+
+=cut
+
+sub count   {
+  my $self = shift;
+  my @ids  = $self->ids;
+  scalar @ids;
+}
+
+=head2 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
+
+=cut
+
+sub ids     {
+  my $self = shift;
+  $self->throw_not_implemented;
+}
+
+=head2 query
+
+ Title   : query
+ Usage   : $query = $db->query([$query])
+ Function: get/set query string
+ Returns : string
+ Args    : (optional) new query string
+
+=cut
+
+sub query   {
+  my $self = shift;
+  $self->throw_not_implemented;
+}
+
+1;