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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Search/GenericDatabase.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,174 @@
+#-----------------------------------------------------------------
+# $Id: GenericDatabase.pm,v 1.5 2002/10/22 07:38:38 lapp Exp $
+#
+# BioPerl module Bio::Search::GenericDatabase
+#
+# 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::GenericDatabase - Generic implementation of Bio::Search::DatabaseI
+
+=head1 SYNOPSIS
+
+    use Bio::Search::GenericDatabase;
+
+    $db = Bio::Search::GenericDatabase->new( -name => 'my Blast db',
+					     -date => '2001-03-13',
+					     -length => 2352511,
+					     -entries => 250000 );
+
+    $name = $db->name();
+    $date = $db->date();
+    $num_letters = $db->letters();
+    $num_entries = $db->entries();
+
+=head1 DESCRIPTION
+
+This module provides a basic implementation of B<Bio::Search::DatabaseI>.
+See documentation in that module for more information.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists 
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules.  Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+    [e-mail]                - General discussion
+    http://bio.perl.org/MailList.html    - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution. Bug reports can be submitted via email
+or the web:
+
+    [e-mail]                   
+    http://bugzilla.bioperl.org/           
+
+=head1 AUTHOR 
+
+Steve Chervitz E<lt>[e-mail]<gt>
+
+See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
+
+=head1 COPYRIGHT
+
+Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=cut
+
+=head1 APPENDIX
+
+
+The rest of the documentation details each of the object methods.
+
+=cut
+
+# Let the code begin...
+
+package Bio::Search::GenericDatabase;
+
+use strict;
+use Bio::Search::DatabaseI;
+use Bio::Root::Root;
+use vars qw( @ISA );
+
+@ISA = qw( Bio::Root::Root Bio::Search::DatabaseI);
+
+sub new {
+    my ($class, @args) = @_; 
+    my $self = $class->SUPER::new(@args);
+    my ($name, $date, $length, $ents) = 
+        $self->_rearrange( [qw(NAME DATE LENGTH ENTRIES)], @args);
+
+    $name    && $self->name($name);
+    $date    && $self->date($date);
+    $length  && $self->letters($length);
+    $ents    && $self->entries($ents);
+
+    return $self;
+}
+
+=head2 name
+
+See L<Bio::Search::DatabaseI::name>() for documentation
+
+This implementation is a combined set/get accessor.
+
+=cut
+
+#---------------
+sub name {
+#---------------
+    my $self = shift;
+    if(@_) { 
+        my $name = shift;
+        $name =~ s/(^\s+|\s+$)//g;
+        $self->{'_db'} = $name;
+    }
+    $self->{'_db'};
+}
+
+=head2 date
+
+See L<Bio::Search::DatabaseI::date>() for documentation
+
+This implementation is a combined set/get accessor.
+
+=cut
+
+#-----------------------
+sub date {
+#-----------------------
+    my $self = shift;
+    if(@_) { $self->{'_dbDate'} = shift; }
+    $self->{'_dbDate'};
+}
+
+
+=head2 letters
+
+See L<Bio::Search::DatabaseI::letters>() for documentation
+
+This implementation is a combined set/get accessor.
+
+=cut
+
+#----------------------
+sub letters {
+#----------------------
+    my $self = shift;
+    if(@_) { $self->{'_dbLetters'} = shift; }
+    $self->{'_dbLetters'};
+}
+
+
+=head2 entries
+
+See L<Bio::Search::DatabaseI::entries>() for documentation
+
+This implementation is a combined set/get accessor.
+
+=cut
+
+#------------------
+sub entries {
+#------------------
+    my $self = shift;
+    if(@_) { $self->{'_dbEntries'} = shift; }
+    $self->{'_dbEntries'};
+}
+
+1;