.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "Bio::PrimerDesigner::ispcr 3pm"
.TH Bio::PrimerDesigner::ispcr 3pm "2020-11-16" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::PrimerDesigner::ispcr \- A class for accessing the isPcr (in\-silico PCR)  binary
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::PrimerDesigner::ispcr;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A low-level interface to the isPcr program.  Uses supplied \s-1PCR\s0 primers,
\&\s-1DNA\s0 sequence and stringency parameters to predict both expected 
and unexpected \s-1PCR\s0 products.
.SH "METHODS"
.IX Header "METHODS"
.SS "run"
.IX Subsection "run"
Sets up the isPcr request for a single primer combination and returns
an Bio::PrimerDesigner::Result object
.PP
If the permute flag is true, all three possible primer combinations
will be tested (ie: forward + reverse, forward + forward, reverse + reverse)
.SS "request"
.IX Subsection "request"
Assembles the config file and command-line arguments and sends
the request to the local binary or remote server.
.SS "verify"
.IX Subsection "verify"
Check to make that the isPCR binary is installed and functioning
properly.  Since ispcr returns nothing if no \s-1PCR\s0 product is found
in the sequence, we have to be able to distinguish between a valid,
undefined output from a functioning ispcr and an undefined output
for some other reason.  verify uses sham ispcr data that is known
to produce a \s-1PCR\s0 product.
.SS "binary_name"
.IX Subsection "binary_name"
Defines the binary's name on the system.
.SS "list_aliases"
.IX Subsection "list_aliases"
There are no aliases to list for ispcr.
.SS "list_params"
.IX Subsection "list_params"
Returns a list of ispcr configuration options.  Required ispcr input is
a sequence string or file and the left and right primers.  Default values
will be used for the remaining options if none are supplied.
.SH "AUTHOR"
.IX Header "AUTHOR"
Copyright (C) 2003\-2009 Sheldon McKay <mckays@cshl.edu<gt>,
                     Ken Y. 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::primer3.