Bio::PrimerDesigner::Result(3pm)			User Contributed Perl Documentation			  Bio::PrimerDesigner::Result(3pm)

NAME

       Bio::PrimerDesigner::Result - a class for handling primer design or validation results

SYNOPSIS

	 use Bio::PrimerDesigner;

	 #
	 # primer3
	 #
	 my $primer3_obj = Bio::PrimerDesigner->new( program => 'primer3 );
	 my $result = $primer3_obj->design( %hash_of_options );
	 my $left_primer = $result->left;
	 my @left_primers = $result->left(1..$num_primers);

	 #
	 # e-PCR -- first make a hash of options from primer3 results
	 # then run e-PCR
	 #
	 my $epcr_obj = Bio::PrimerDesigner->new( program => 'primer3 );
	 my $epcr_result = $epcr_obj->design( %hash_of_options );
	 my $num_products = $epcr_result->products;

	 #
	 # one product
	 #
	 my $first_prod_size = $epcr_result->size;
	 my $first_prod_start = $epcr_result->start;
	 my $first_prod_stop = $epcr_result->start;

	 #
	 # more than one product
	 #
	 my @pcr_product_sizes = ();
	 for (1..$num_products) {
	     push @pcr_product_sizes, $epcr_result->size;
	 }

DESCRIPTION

	Bio::PrimerDesigner::Result will autogenerate result access methods
	for for Native Boulder IO keys and Bio::PrimerDesigner keys for
	primer3, e-PCR, isPcr and ipcress.

METHODS

   keys
	This handles result method calls made via the
	Bio::PrimerDesigner::Result object.  Returns either a scalar or list
	depending on the on the arguments:

	 ------------------+------------------------
	  Args passed	   |  Returns
	 ------------------+------------------------
	  none		      scalar value for set 1
	  numeric n	      scalar value for set n
	  numeric list 1..n   list with n elements

	The aliased output methods (below) return a string when called in a
	scalar context and a list when called in a list context.  The native
	primer3 (Boulder IO) keys can also be used.  There are also e-PCR,
	isPcr and ipcress specific methods

       Primer3 keys

       o   left        -- left primer sequence

       o   right       -- right primer sequence

       o   hyb_oligo   -- internal oligo sequence

       o   startleft   -- left primer 5' sequence coordinate

       o   startright  -- right primer 5' sequence coordinate

       o   tmleft      -- left primer tm

       o   tmright     -- right primer tm

       o   qual        -- primer pair penalty (Q value)

       o   lqual       -- left primer penalty

       o   rqual       -- right primer penalty

       o   leftgc      -- left primer % gc

       o   rightgc     -- right primer % gc

       o   lselfany    -- left primer self-complementarity (any)

       o   lselfend    -- left primer self-complementarity (end)

       o   rselfany    -- right primer self-complementarity (any)

       o   rselfend    -- right primer self-complementarity (end)

       o   pairanycomp -- primer pair complementarity (any)

       o   pairendcomp -- primer pair complementarity (end)

       o   lendstab    -- left primer end stability

       o   rendstab    -- right primer end stability

       o   amplicon    -- amplified PCR product

       Other keys

       o   products    -- number of PCR products

       o   size        -- product size

       o   start       -- product start coordinate

       o   stop        -- product stop coordinate

       o   end	       -- synonymous with stop

       o   strand      -- strand of product relative to the ref. sequence (isPCR, ipcress)

       o   amplicon    -- returns the PCR product (isPCR only)

AUTHOR

       Copyright (c) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.

LICENSE

       This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
       the Free Software Foundation; version 3 or any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation,
       Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

SEE ALSO

       Bio::PrimerDesigner.

perl v5.10.0							    2009-08-04					  Bio::PrimerDesigner::Result(3pm)