Bio::Restriction::Enzyme MultiSite
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Summary
Bio::Restriction::Enzyme::MultiSite - A single restriction endonuclease
Package variables
No package variables defined.
Included modules
Data::Dumper
Inherit
Bio::Restriction::Enzyme
Synopsis
  # set up a single restriction enzyme. This contains lots of
# information about the enzyme that is generally parsed from a
# rebase file and can then be read back
use Bio::Restriction::Enzyme;
Description
This module is used for restriction enzymes that recogonize more than
one site. There are some enzymes that recognize sites that cannot be
represented by the ambiguous genetic code. For example, M.PhiBssHII
recognizes the sites: ACGCGT,CCGCGG,RGCGCY,RCCGGY, and GCGCGC
Each site gets its own object that Bio::Restriction::Enzyme will
refer to. Each also correlates with the other sites using the
method others which stores references to other objects
with alternative sites.
In this schema each object within an EnzymeCollection can be checked
for matching a sequence.
Methods
newDescriptionCode
othersDescriptionCode
purge_othersDescriptionCode
Methods description
newcode    nextTop
 Title     : new
Function
Function : Initializes the enzyme object
Returns : The Restriction::Enzyme::MultiSite object
Argument :
otherscodeprevnextTop
 Title     : others
Usage : $re->others(@others);
Function : Gets/Sets the a list of other sites that this enzyme recoginizes
Arguments : An array containing the other Bio::Restriction::Enzyme::MultiSite
objects.
Returns : An array containing the other Bio::Restriction::Enzyme::MultiSite
objects.
purge_otherscodeprevnextTop
 Title     : purge_others
Usage : $re->purge_references();
Function : Purges the set of references for this enzyme
Arguments :
Returns :
Methods code
newdescriptionprevnextTop
sub new {
    my($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($others) =
            $self->_rearrange([qw(
                                  OTHERS
                                 )], @args);

    $others && $self->others($others);
    return $self;
}
othersdescriptionprevnextTop
sub others {
    my $self = shift;
    push @{$self->{_others}}, @_ if @_;
    return unless $self->{_others};
    return @{$self->{'_others'}};
}
purge_othersdescriptionprevnextTop
sub purge_others {
    my ($self) = shift;
    $self->{_others} = [];

}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Rob Edwards, redwards@utmem.edu
COPYRIGHTTop
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.
SEE ALSOTop
Bio::Restriction::Enzyme, Bio::Restriction::Analysis,
Bio::Restriction::EnzymeCollection
APPENDIXTop
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.