diff variant_effect_predictor/Bio/Search/DatabaseI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Search/DatabaseI.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,149 @@
+#-----------------------------------------------------------------
+# $Id: DatabaseI.pm,v 1.6 2002/10/22 07:38:38 lapp Exp $
+#
+# BioPerl module Bio::Search::DatabaseI
+#
+# Cared for by Steve Chervitz <[e-mail]>
+#
+# You may distribute this module under the same terms as perl itself
+#-----------------------------------------------------------------
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Search::DatabaseI - Interface for a database used in a sequence search
+
+=head1 SYNOPSIS
+
+Bio::Search::DatabaseI objects should not be instantiated since this
+module defines a pure interface.
+
+Given an object that implements the Bio::Search::DatabaseI  interface,
+you can do the following things with it:
+
+    $name = $db->name();
+
+    $date = $db->date();
+
+    $num_letters = $db->letters();
+
+    $num_entries = $db->entries();
+
+=head1 DESCRIPTION
+
+This module defines methods for an object that provides metadata
+information about a database used for sequence searching.
+
+=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://bio.perl.org/MailList.html    - 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 
+
+Steve Chervitz E<lt>[e-mail]<gt>
+
+See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
+
+=head1 COPYRIGHT
+
+Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=cut
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+
+=cut
+
+# Let the code begin...
+
+package Bio::Search::DatabaseI;
+
+use strict;
+use Bio::Root::RootI;
+use vars qw( @ISA );
+
+@ISA = qw( Bio::Root::RootI);
+
+
+=head2 name
+
+ Usage     : $name = $db->name();
+ Purpose   : Get the name of the database searched.
+ Returns   : String
+ Argument  : n/a
+
+=cut
+
+sub name {
+    my $self = shift;
+    $self->throw_not_implemented;
+}
+
+=head2 date
+
+ Usage     : $date = $db->date();
+ Purpose   : Get the creation date of the queried database.
+ Returns   : String
+ Argument  : n/a
+
+=cut
+
+sub date {
+    my $self = shift;
+    $self->throw_not_implemented;
+}
+
+
+=head2 letters
+
+ Usage     : $num_letters = $db->letters();
+ Purpose   : Get the number of letters in the queried database.
+ Returns   : Integer
+ Argument  : n/a
+
+=cut
+
+sub letters {
+    my $self = shift;
+    $self->throw_not_implemented;
+}
+
+
+=head2 entries
+
+ Usage     : $num_entries = $db->entries();
+ Purpose   : Get the number of entries in the queried database.
+ Returns   : Integer
+ Argument  : n/a
+
+=cut
+
+sub entries {
+    my $self = shift;
+    $self->throw_not_implemented;
+}
+
+1;