Bio/Restriction/Enzyme/MultiSite.pm

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