Bio/Restriction/Enzyme/MultiCut.pm

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