Bio/Restriction/Enzyme/MultiCut.pm

   1 # $Id$
   2 #------------------------------------------------------------------
   3 #
   4 # BioPerl module Bio::Restriction::Enzyme::MultiCut
   5 #
   6 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   7 #
   8 # Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #------------------------------------------------------------------
  12
  13 ## POD Documentation:
  14
  15 =head1 NAME
  16
  17 Bio::Restriction::Enzyme::MultiCut - A single restriction endonuclease
  18
  19 =head1 SYNOPSIS
  20
  21   # set up a single restriction enzyme. This contains lots of
  22   # information about the enzyme that is generally parsed from a
  23   # rebase file and can then be read back
  24
  25   use Bio::Restriction::Enzyme;
  26
  27
  28 =head1 DESCRIPTION
  29
  30 This module defines a restriction endonuclease class where one object
  31 represents one of the distinct recognition sites for that enzyme. The
  32 method L<others|others> stores references to other objects with
  33 alternative sites.
  34
  35 In this schema each object within an EnzymeCollection can be checked
  36 for matching a sequence.
  37
  38
  39 REBASE report notation C<Bsp24I (8/13)GACNNNNNNTGG(12/7)> means:
  40
  41
  42    Bsp24I
  43              5'      ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^   3'
  44              3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^        5'
  45
  46
  47
  48
  49 =head1 FEEDBACK
  50
  51 =head2 Mailing Lists
  52
  53 User feedback is an integral part of the evolution of this and other
  54 Bioperl modules. Send your comments and suggestions preferably to one
  55 of the Bioperl mailing lists. Your participation is much appreciated.
  56
  57   bioperl-l@bioperl.org                  - General discussion
  58   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  59
  60 =head2 Support
  61
  62 Please direct usage questions or support issues to the mailing list:
  63
  64 L<bioperl-l@bioperl.org>
  65
  66 rather than to the module maintainer directly. Many experienced and
  67 reponsive experts will be able look at the problem and quickly
  68 address it. Please include a thorough description of the problem
  69 with code and data examples if at all possible.
  70
  71 =head2 Reporting Bugs
  72
  73 Report bugs to the Bioperl bug tracking system to help us keep track
  74 the bugs and their resolution. Bug reports can be submitted via the
  75 web:
  76
  77   http://bugzilla.open-bio.org/
  78
  79 =head1 AUTHOR
  80
  81 Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
  82
  83 =head1 CONTRIBUTORS
  84
  85 Rob Edwards, redwards@utmem.edu
  86
  87 =head1 COPYRIGHT
  88
  89 Copyright (c) 2003 Rob Edwards.
  90
  91 Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All
  92 Rights Reserved.  This module is free software; you can redistribute
  93 it and/or modify it under the same terms as Perl itself.
  94
  95 =head1 SEE ALSO
  96
  97 L<Bio::Restriction::Enzyme>, L<Bio::Restriction::Analysis>,
  98 L<Bio::Restriction::EnzymeCollection>
  99
 100 =head1 APPENDIX
 101
 102 Methods beginning with a leading underscore are considered private and
 103 are intended for internal use by this module. They are not considered
 104 part of the public interface and are described here for documentation
 105 purposes only.
 106
 107 =cut
 108
 109 package Bio::Restriction::Enzyme::MultiCut;
 110 use strict;
 111
 112 use Data::Dumper;
 113
 114 use vars qw ();
 115 use base qw(Bio::Restriction::Enzyme);
 116
 117
 118 =head2 new
 119
 120  Title     : new
 121  Function
 122  Function  : Initializes the enzyme object
 123  Returns   : The Restriction::Enzyme::MultiCut object
 124  Argument  :
 125
 126 =cut
 127
 128 sub new {
 129     my($class, @args) = @_;
 130     my $self = $class->SUPER::new(@args);
 131
 132     my ($others) =
 133             $self->_rearrange([qw(
 134                                   OTHERS
 135                                  )], @args);
 136
 137     $others && $self->others($others);
 138     return $self;
 139 }
 140
 141 =head2 others
 142
 143  Title     : others
 144  Usage     : $re->vendor(@list_of_companies);
 145  Function  : Gets/Sets the a list of companies that you can get the enzyme from.
 146              Also sets the commercially_available boolean
 147  Arguments : A reference to an array containing the names of companies
 148              that you can get the enzyme from
 149  Returns   : A reference to an array containing the names of companies
 150              that you can get the enzyme from
 151
 152 Added for compatibility to REBASE
 153
 154 =cut
 155
 156 sub others {
 157     my $self = shift;
 158     push @{$self->{_others}}, @_ if @_;
 159     return @{$self->{'_others'}};
 160 }
 161
 162
 163 =head2 purge_others
 164
 165  Title     : purge_others
 166  Usage     : $re->purge_references();
 167  Function  : Purges the set of references for this enzyme
 168  Arguments :
 169  Returns   :
 170
 171 =cut
 172
 173 sub purge_others {
 174     my ($self) = shift;
 175     $self->{_others} = [];
 176
 177 }
 178
 179
 180 1;
 181