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.IX Title "LLNL::LAVA::PrimerSet 3"
.TH LLNL::LAVA::PrimerSet 3 "2011-06-27" "perl v5.8.8" "User Contributed Perl Documentation"
.SH "NAME"
LLNL::LAVA::PrimerSet \- A pair of LLNL::LAVA::PrimerInfo objects
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 7
\&  # Instantiation
\&  $pair = LLNL::LAVA::PrimerSet->new(
\&    {
\&      "start_location" => $startLocation,
\&      "end_location" => $endLocation,
\&      "length" => $length,
\&    });
.Ve
.PP
.Vb 5
\&  # Member functions are named with "get" prefixes as an indicator that
\&  # they can't be used to modify the PCR pair, just to get info about it.
\&  $location = $pair->getStartLocation();
\&  $location = $pair->getEndLocation();
\&  $length = $pair->getLength();
.Ve
.PP
.Vb 4
\&  # String in the form of "start-end".  Depending on how you created the pair,
\&  # the end location might be a smaller number than the start location.  It's
\&  # possible to have this behavior, we just don't explicitly support it yet.
\&  $rangeString = $pair->getRangeAsString();
.Ve
.PP
.Vb 4
\&  # Tag use (inherited from TagHolder)
\&  $oligo->setTag("useful_statistic", $usefulStatistic);
\&  $exists = $oligo->getTagExists("useful_statistic");
\&  $tm = $oligo->getTag("useful_statistic");
.Ve
.SH "EXAMPLES"
.IX Header "EXAMPLES"
See synopsis.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
PrimerSet is the object model of a group of oligos.  Sub-classes implement
behavior specific to different types of oligo combinations such as PCRPairs.
.SH "APPENDIX"
.IX Header "APPENDIX"
The following documentation describes the functions in this package
.Sh "new"
.IX Subsection "new"
.Vb 13
\& Usage     : $sigComponent = LLNL::LAVA::PrimerSet->new(
\&               {
\&                 "start_location" => $startLocation,
\&                 "end_location" => $endLocation,
\&                 "length" => $length, # Redundant, but keeping for now.
\&               });
\& Function  : Creates a new LLNL::LAVA::PrimerSet 
\& Arguments : Hash ref - Parameters for initialization including:
\&               start_location - Integer start location for the entire set
\&               end_location - Integer end location for the entire set
\&               length - Integer length/span of the entire set
\& Example   : See Usage
\& Returns   : A new LLNL::LAVA::PrimerSet
.Ve
.Sh "getStartLocation"
.IX Subsection "getStartLocation"
.Vb 5
\& Usage     : $location = $pair->getStartLocation();
\& Function  : Get the 5' start location of the forward primer
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : Integer - start location of the pair
.Ve
.Sh "getEndLocation"
.IX Subsection "getEndLocation"
.Vb 6
\& Usage     : $location = $pair->getEndLocation();
\& Function  : Get the 5' start location of the reverse primer, which is the
\&             3' end location of the PCR pair!
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : Integer - end location of the pair
.Ve
.Sh "getLength"
.IX Subsection "getLength"
.Vb 5
\& Usage     : $length = $pair->getLength();
\& Function  : Get the lengh of this PCR pair, calculated from primer locations
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : Integer - length of the expected PCR amplicon
.Ve
.Sh "getRangeAsString"
.IX Subsection "getRangeAsString"
.Vb 6
\& Usage     : $rangeString = $pair->getRangeAsString();
\& Function  : Get a string in the form of "start-end" (e.g. "123-456"), where
\&             the two numbers depend on primer locations
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - representation of the range of the primer pair
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Clinton Torres (clinton.torres@llnl.gov)
.SH "SEE ALSO"
.IX Header "SEE ALSO"