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.IX Title "LLNL::LAVA::PrimerInfo 3"
.TH LLNL::LAVA::PrimerInfo 3 "2011-06-27" "perl v5.8.8" "User Contributed Perl Documentation"
.SH "NAME"
LLNL::LAVA::PrimerInfo \- The basic functionality of PrimerInfo, which represents
an analysis result of an Oligo within a specific context.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use LLNL::LAVA::PrimerInfo;
.Ve
.PP
.Vb 10
\&  # Instantiation.  Usually, this is performed by a PrimerAnalyzer so you 
\&  # won't need to instantiate your own.
\&  my $primerInfo = LLNL::LAVA::PrimerInfo->new(
\&    {
\&      "penalty" => $penalty,
\&      "sequence" => $sequence,
\&      "location" => $loaction,
\&      "length" => $length,
\&      "analyzed_primer" => $primer,
\&    });"
.Ve
.PP
.Vb 7
\&  # All non-tag functions are read-only because a PrimerInfo represents
\&  # an analysis result within a context, and I want to prevent accidents.
\&  $penatly = $primerInfo->getPenalty();
\&  $sequence = $primerInfo->getSequence();
\&  $location = $primerInfo->getLocation();
\&  $length = $primerInfo->getLength();
\&  $primer = $primerInfo->getAnalyzedPrimer();
.Ve
.PP
.Vb 4
\&  # Tag use
\&  $primerInfo->setTag("useful_tag_name", $value);
\&  $exists = $primerInfo->getTagExists("useful_tag_name");
\&  $value = $primerInfo->getTag("useful_tag_name");
.Ve
.SH "EXAMPLES"
.IX Header "EXAMPLES"
See synopsis.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
PrimerInfo is the vehicle for oligo analysis results.  In the simplest case,
this is just the oligo sequence and associated penalty, location, etc..  In more
complicated cases, sub-classes will help represent the position-specific decisions
and penalties of oligo analysis. 
.SH "APPENDIX"
.IX Header "APPENDIX"
The following documentation describes the functions in this package
.Sh "new"
.IX Subsection "new"
.Vb 17
\& Usage     : $primerInfo = LLNL::LAVA::PrimerInfo->new(
\&               {
\&                 "penalty" => $penalty,
\&                 "sequence" => $sequence,
\&                 "location" => $loaction,
\&                 "length" => $length,
\&                 "analyzed_primer" => $primer,
\&               });"
\& Function  : Creates a new LLNL::LAVA::PrimerInfo
\& Arguments : Hash ref containing:
\&               penalty - the oligo's penalty score from an analysis context
\&               sequence - the representative sequence of the oligo
\&               location - the oligo's location
\&               length - the oligo's length
\&               analyzed_primer - LLNL::LAVA::Oligo used to create this info
\& Example   : See Usage
\& Returns   : A new LLNL::LAVA::PrimerInfo
.Ve
.Sh "getPenalty"
.IX Subsection "getPenalty"
.Vb 6
\& Usage     : $penalty = $primerInfo->getPenalty();
\& Function  : Gets the penalty for this PrimerInfo, built from a specific
\&             analysis context.
\& Arguments : <n/a> 
\& Example   : See Usage
\& Returns   : Float - in the simplest case, this can be the Primer3 penalty
.Ve
.Sh "getSequence"
.IX Subsection "getSequence"
.Vb 5
\& Usage     : $sequence = $primerInfo->getSequence();
\& Function  : Gets the sequence for this PrimerInfo.
\& Arguments : <n/a> 
\& Example   : See Usage
\& Returns   : String - Primer sequence that this PrimerInfo represents
.Ve
.Sh "getLocation"
.IX Subsection "getLocation"
.Vb 5
\& Usage     : $location = $primerInfo->getLocation();
\& Function  : Gets the location for this PrimerInfo.
\& Arguments : <n/a> 
\& Example   : See Usage
\& Returns   : Integer - the 0-indexed location this PrimerInfo is located at
.Ve
.Sh "getLength"
.IX Subsection "getLength"
.Vb 5
\& Usage     : $length = $primerInfo->getLength();
\& Function  : Gets the length of the primer this PrimerInfo represents.
\& Arguments : <n/a> 
\& Example   : See Usage
\& Returns   : Integer - how long the primer is that this PrimerInfo represent.
.Ve
.Sh "getAnalyzedPrimer"
.IX Subsection "getAnalyzedPrimer"
.Vb 5
\& Usage     : $primer = $primerInfo->getAnalyzedPrimer();
\& Function  : Gets the primer that was analyzed to create this PrimerInfo
\& Arguments : <n/a> 
\& Example   : See Usage
\& Returns   : LLNL::LAVA::Oligo - primer that was analyzed for this PrimerInfo
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Clinton Torres (clinton.torres@llnl.gov)
.SH "SEE ALSO"
.IX Header "SEE ALSO"