diff variant_effect_predictor/Bio/EnsEMBL/Utils/BitString.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Utils/BitString.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,87 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::BitString - bitstring object implementation
+
+=head1 DESCRIPTION
+
+This is an implementation of a bitstring object, taken from Damian
+Convey's book "Object Oriented Perl".
+
+=head1 METHODS
+
+=cut
+
+
+package Bio::EnsEMBL::Utils::BitString;
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+
+sub new {
+  my $class = ref($_[0])||$_[0];
+  my $initbits = join '', map {$_?1:0} @_[1..$#_];
+  my $bs = pack 'b*', $initbits;
+  bless \$bs, $class;
+}
+
+
+sub get {
+  my ($self, $bitnum) = @_;
+  return vec($$self,$bitnum,1);
+}
+
+
+sub set {
+  my ($self, $bitnum, $newval) = @_;
+  vec($$self,$bitnum,1) = $newval?1:0;
+}
+
+
+sub bitcount {
+  8 * length ${$_[0]};
+}
+
+
+sub complement {
+  my ($self) = @_;
+  my $complement = ~$$self;
+  bless \$complement, ref($self);
+}
+
+
+sub print_me {
+  my ($self) = @_;
+  for (my $i=0; $i < $self->bitcount(); $i++)
+  {
+    print $self->get($i);
+    print ' ' unless ($i+1)%8;
+    print "\n" unless ($i+1)%64;
+  }
+  print "\n";
+}
+
+
+1;
+