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.\" ========================================================================
.\"
.IX Title "Bio::PrimerDesigner::Result 3pm"
.TH Bio::PrimerDesigner::Result 3pm "2020-11-16" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::PrimerDesigner::Result \- a class for handling primer 
design or validation results
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::PrimerDesigner;
\& 
\&  #  
\&  # primer3  
\&  #  
\&  my $primer3_obj = Bio::PrimerDesigner\->new( program => \*(Aqprimer3 );  
\&  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 => \*(Aqprimer3 );
\&  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;   
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 3
\& 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.
.Ve
.SH "METHODS"
.IX Header "METHODS"
.SS "keys"
.IX Subsection "keys"
.Vb 3
\& 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
.Ve
.PP
\&\fBPrimer3 keys\fR
.IP "\(bu" 4
left        \*(-- left primer sequence
.IP "\(bu" 4
right       \*(-- right primer sequence
.IP "\(bu" 4
hyb_oligo   \*(-- internal oligo sequence
.IP "\(bu" 4
startleft   \*(-- left primer 5' sequence coordinate
.IP "\(bu" 4
startright  \*(-- right primer 5' sequence coordinate
.IP "\(bu" 4
tmleft      \*(-- left primer tm
.IP "\(bu" 4
tmright     \*(-- right primer tm
.IP "\(bu" 4
qual        \*(-- primer pair penalty (Q value)
.IP "\(bu" 4
lqual       \*(-- left primer penalty
.IP "\(bu" 4
rqual       \*(-- right primer penalty
.IP "\(bu" 4
leftgc      \*(-- left primer % gc
.IP "\(bu" 4
rightgc     \*(-- right primer % gc
.IP "\(bu" 4
lselfany    \*(-- left primer self-complementarity (any)
.IP "\(bu" 4
lselfend    \*(-- left primer self-complementarity (end)
.IP "\(bu" 4
rselfany    \*(-- right primer self-complementarity (any)
.IP "\(bu" 4
rselfend    \*(-- right primer self-complementarity (end)
.IP "\(bu" 4
pairanycomp \*(-- primer pair complementarity (any)
.IP "\(bu" 4
pairendcomp \*(-- primer pair complementarity (end)
.IP "\(bu" 4
lendstab    \*(-- left primer end stability
.IP "\(bu" 4
rendstab    \*(-- right primer end stability
.IP "\(bu" 4
amplicon    \*(-- amplified \s-1PCR\s0 product
.PP
\&\fBOther keys\fR
.IP "\(bu" 4
products    \*(-- number of \s-1PCR\s0 products
.IP "\(bu" 4
size        \*(-- product size
.IP "\(bu" 4
start       \*(-- product start coordinate
.IP "\(bu" 4
stop        \*(-- product stop coordinate
.IP "\(bu" 4
end         \*(-- synonymous with stop
.IP "\(bu" 4
strand      \*(-- strand of product relative to the ref. sequence (isPCR, ipcress)
.IP "\(bu" 4
amplicon    \*(-- returns the \s-1PCR\s0 product (isPCR only)
.SH "AUTHOR"
.IX Header "AUTHOR"
Copyright (c) 2003\-2009 Sheldon McKay <mckays@cshl.edu>,
Ken Youens-Clark <kclark@cpan.org>.
.SH "LICENSE"
.IX Header "LICENSE"
This program is free software; you can redistribute it and/or modify
it under the terms of the \s-1GNU\s0 General Public License as published by
the Free Software Foundation; version 3 or any later version.
.PP
This program is distributed in the hope that it will be useful, but
\&\s-1WITHOUT ANY WARRANTY\s0; without even the implied warranty of
\&\s-1MERCHANTABILITY\s0 or \s-1FITNESS FOR A PARTICULAR PURPOSE.\s0  See the \s-1GNU\s0
General Public License for more details.
.PP
You should have received a copy of the \s-1GNU\s0 General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, \s-1MA 02110\-1301
USA.\s0
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::PrimerDesigner.