NAME

       Bio::Restriction::EnzymeCollection - Set of restriction endonucleases

SYNOPSIS

         use Bio::Restriction::EnzymeCollection;

         # Create a collection with the default enzymes.
         my $default_collection = Bio::Restriction::EnzymeCollection->new();

         # Or create a collection from a REBASE 'withrefm' file obtained from
         # ftp://ftp.neb.com/pub/rebase/. (See Bio::Restriction::IO for more
         # information.)
         my $rebase = Bio::Restriction::IO->new(
             -file   => 'withrefm.610',
             -format => 'withrefm' );
         my $rebase_collection = $rebase->read();

         # Or create an empty collection and set the enzymes later. See
         # 'CUSTOM COLLECTIONS' below for more information.
         my $empty_collection =
           Bio::Restriction::EnzymeCollection->new( -empty => 1 );

         # Get an array of Bio::Restriction::Enzyme objects from the collection.
         my @enzymes = $default_collection->each_enzyme();

         # Get a Bio::Restriction::Enzyme object for a particular enzyme by name.
         my $enz = $default_collection->get_enzyme( 'EcoRI' );

         # Get a Bio::Restriction::EnzymeCollection object containing the enzymes
         # that have the equivalent of 6-bp recognition sequences.
         my $six_cutters = $default_collection->cutters( 6 );

         # Get a Bio::Restriction::EnzymeCollection object containing the enzymes
         # that are rare cutters.
         my $rare_cutters = $default_collection->cutters( -start => 6, -end => 8 );

         # Get a Bio::Restriction::EnzymeCollection object that contains enzymes
         # that generate blunt ends:
         my $blunt_cutters = $default_collection->blunt_enzymes();

         # See 'CUSTOM COLLECTIONS' below for an example of creating a
         # Bio::Restriction::EnzymeCollection object with a specified subset of
         # enzymes using methods provided by the Bio::RestrictionEnzyme class.

DESCRIPTION

       Bio::Restriction::EnzymeCollection represents a collection of restriction enzymes.

       If you create a new collection directly rather than from a REBASE file using
       Bio::Restriction::IO, it will be populated by a default set of enzymes with site and cut
       information only.

       Use Bio::Restriction::Analysis to figure out which enzymes are available and where they
       cut your sequence.

CUSTOM COLLECTIONS

       Note that the underlying Bio::Restriction::Enzyme objects have a rich variety of methods
       that allow more complicated selections than the methods that are defined by
       Bio::Restriction::EnzymeCollection.

       For example, the way to create a custom collection of Type II enzymes is as follows:

         my $complete_collection =
             Bio::Restriction::EnzymeCollection->new();
         my $type_ii_collection  =
             Bio::Restriction::EnzymeCollection->new( -empty => 1 );
         $type_ii_collection->enzymes(
             grep { $_->type() eq 'II' } $complete_collection->each_enzyme() );

SEE ALSO

       Bio::Restriction::IO - read in enzymes from REBASE files

       Bio::Restriction::Analysis - figure out what enzymes cut a sequence

       Bio::Restriction::Enzyme - define a single restriction enzyme

FEEDBACK

   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.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR

       Rob Edwards, redwards@utmem.edu

CONTRIBUTORS

       Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

COPYRIGHT

       Copyright (c) 2003 Rob Edwards.

       Some of this work is Copyright (c) 1997-2002 Steve A. Chervitz. All Rights Reserved.

       This module is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.

APPENDIX

       Methods beginning with a leading underscore are considered private and are intended for
       internal use by this module. They are not considered part of the public interface and are
       described here for documentation purposes only.

   new
        Title     : new
        Function  : Initializes the Restriction::EnzymeCollection object
        Returns   : The Restriction::EnzymeCollection object
        Arguments : optional named parameter -empty

       Set parameter -empty to true if you do NOT want the collection be populated by the default
       set of prototype type II enzymes.

       Alternatively, pass an array of enzymes to -enzymes parameter.

   Manipulate the enzymes within the collection
   enzymes
        Title     : enzyme
        Function  : add/get method for enzymes and enzyme collections
        Returns   : object itself
        Arguments : array of Bio::Restriction::Enzyme and
                    Bio::Restriction::EnzymeCollection objects

   each_enzyme
        Title     : each_enzyme
        Function  : get an array of enzymes
        Returns   : array of Bio::Restriction::Enzyme objects
        Arguments : -

   get_enzyme
        Title     : get_enzyme
        Function  : Gets a Bio::Restriction::Enzyme object for the enzyme name
        Returns   : A Bio::Restriction::Enzyme object or undef
        Arguments : An enzyme name that is in the collection

   available_list
        Title     : available_list
        Function  : Gets a list of all the enzymes that we know about
        Returns   : A reference to an array with all the enzyme names
                    that we have defined or 0 if none are defined
        Arguments : Nothing
        Comments  : Note, I maintain this for backwards compatibility,
                    but I don't like the name as it is very ambiguous

   longest_cutter
        Title     : longest_cutter
        Function  : Gets the enzyme with the longest recognition site
        Returns   : A Bio::Restriction::Enzyme object
        Arguments : Nothing
        Comments  : Note, this is used by Bio::Restriction::Analysis
                    to figure out what to do with circular sequences

   Filter enzymes
   blunt_enzymes
         Title     : blunt_enzymes
         Function  : Gets a list of all the enzymes that are blunt cutters
         Returns   : A reference to an array with all the enzyme names that
                     are blunt cutters or 0 if none are defined
         Arguments : Nothing
         Comments  :

       This is an example of the kind of filtering better done by the scripts using the rich
       collection of methods in Bio::Restriction::Enzyme.

   cutters
         Title     : cutters
         Function  : Gets a list of all the enzymes that recognize a
                     certain size, e.g. 6-cutters
         Usage     : $cutters = $collection->cutters(6);
         Returns   : A reference to an array with all the enzyme names
                     that are x cutters or 0 if none are defined
         Arguments : A positive number for the size of cutters to return
                     OR
                     A range: (-start => 6, -end => 8,
                               -inclusive => 1, -exclusive = 0 )

       The default for a range is 'inclusive'