Summary

Bio::Tools::Primer::Pair - two primers on left and right side

Package variables

Inherit

Bio::Root::Root

Synopsis

    use Bio::Tools::Primer::Pair;

    my $pair = Bio::Tools::Primer::Pair->new( -left => $leftp , -right => $rightp);

    # helper functions

    print "GC percentage different",$pf->gc_difference(),"\n";
    print "product length is ",$pf->product_length,"\n";

Description

Primer Pairs represents one primer in a primer pair. This object is mainly for
designing primers, and probably principly used in the primer design system

Methods

Methods description

None available.

Methods code

sub new {

    my ( $caller, @args) = @_;   
    my ($self) = $caller->SUPER::new(@args); 

    my ($left,$right) = $self->_rearrange([qw(LEFT RIGHT)],@args);

    if( !defined $left || !defined $right ) {
	$self->throw("Pair must be initialised with left and right primers");
    }

    $self->left($left);
    $self->right($right);

    # done - we hope
    return $self;

}

sub left {

    my $self = shift;
    my $left = shift;

    if( defined $left ) {
	if( !ref $left || !$left->isa("Bio::Tools::Primer::Feature") ) {
	    $self->throw("left primer must be a Bio::Tools::Primer::Feature, not $left");
	}
	$self->{'left'} = $left;
    }

    return $self->{'left'};

}

sub right {

    my $self = shift;
    my $right = shift;

    if( defined $right ) {
	if( !ref $right || !$right->isa("Bio::Tools::Primer::Feature") ) {
	    $self->throw("right primer must be a Bio::Tools::Primer::Feature, not $right");
	}
	$self->{'right'} = $right;
    }

    return $self->{'right'};

}

sub gc_difference {

    my $self = shift;

    return abs ( $self->left->gc_percent - $self->right->gc_percent );

}

sub product_length {

    my $self = shift;

    return $self->right->end - $self->left->start +1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

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

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Email birney-at-ebi.ac.uk

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _