Bio::Tools::Primer Pair
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::Primer::Pair - two primers on left and right side
Package variables
No package variables defined.
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
new
No description
Code
left
No description
Code
right
No description
Code
gc_difference
No description
Code
product_length
No description
Code
Methods description
None available.
Methods code
newdescriptionprevnextTop
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;
}
leftdescriptionprevnextTop
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'};
}
rightdescriptionprevnextTop
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'};
}
gc_differencedescriptionprevnextTop
sub gc_difference {
    my $self = shift;

    return abs ( $self->left->gc_percent - $self->right->gc_percent );
}
product_lengthdescriptionprevnextTop
sub product_length {
    my $self = shift;

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


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
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
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
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney-at-ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _