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.\" ========================================================================
.\"
.IX Title "LLNL::LAVA::PrimerSet::LAMP 3"
.TH LLNL::LAVA::PrimerSet::LAMP 3 "2011-06-27" "perl v5.8.8" "User Contributed Perl Documentation"
.SH "NAME"
LLNL::LAVA::PrimerSet::LAMP \- Three LLNL::LAVA::PrimerSetInfo::PCRPair objects
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\&  # Instantiation
\&  $lampSignature = LLNL::LAVA::PrimerSet::LAMP->new(
\&    {
\&      # Strand orientation gets pretty weird here, so we're going to require
\&      # that all PCRPair-Infos have plus strand forward primers and minus
\&      # strand reverse primers.
\&      "inner_info" => $innerInfo,
\&      "middle_info" => $middleInfo,
\&      "outer_info" => $outerInfo,
\&    });
.Ve
.PP
.Vb 3
\&  $innerInfo = $lampSignature->getInnerInfo();
\&  $middleInfo = $lampSignature->getMiddleInfo();
\&  $outerInfo = $lampSignature->getOuterInfo();
.Ve
.PP
.Vb 6
\&  # But since we're going to be strict about how our internal pairs are, we can
\&  # also do cool things like:
\&  $outerForward = $lampSignature->getF3();
\&  $outerReverse = $lampSignature->getB3();
\&  $fip = $lampSignature->getBIP();
\&  $bip = $lampSignature->getFIP();
.Ve
.PP
.Vb 2
\&  # Helper for debugging and status printout
\&  $locationSummary = $lampSignature->getLocationSummary();
.Ve
.PP
.Vb 3
\&  # Get/set pair for the BIP and FIP linker
\&  $linker = $lampSignature->linker();
\&  $lampSignature->linker($newLinker);
.Ve
.PP
.Vb 5
\&  # PrimerSet inherited functions
\&  $location = $pair->getStartLocation();
\&  $location = $pair->getEndLocation();
\&  $length = $pair->getLength();
\&  $rangeString = $pair->getRangeAsString(); # String in the form of "start-end"
.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::LAMP is the object model of a pair of oligos from opposite strands that
can be used as \s-1PCR\s0 primers.
.SH "APPENDIX"
.IX Header "APPENDIX"
The following documentation describes the functions in this package
.Sh "new"
.IX Subsection "new"
.Vb 15
\& Usage     : $sigComponent = LLNL::LAVA::PrimerSet::LAMP->new(
\&               {
\&                 # We're requiring that all PCRPair-Infos have plus strand 
\&                 # forward primers and minus strand reverse primers.
\&                 "inner_info" => $innerInfo,
\&                 "middle_info" => $middleInfo,
\&                 "outer_info" => $outerInfo,
\&               });
\& Function  : Creates a new LLNL::LAVA::PrimerSet::LAMP 
\& Arguments : Hash ref - Parameters for initialization including:
\&               inner_info - LLNL::LAVA::PrimerSetInfo::PCRPair
\&               middle_info - LLNL::LAVA::PrimerSetInfo::PCRPair
\&               outer_info - LLNL::LAVA::PrimerSetInfo::PCRPair
\& Example   : See Usage
\& Returns   : A new LLNL::LAVA::PrimerSet::LAMP
.Ve
.Sh "getInnerInfo"
.IX Subsection "getInnerInfo"
.Vb 5
\& Usage     : $pcrPairInfo = $lampSignature->getInnerInfo();
\& Function  : Get a reference to this signature's inner pair's info
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : LLNL::LAVA::PrimerSetInfo::PCRPair - inner pair's info
.Ve
.Sh "getMiddleInfo"
.IX Subsection "getMiddleInfo"
.Vb 5
\& Usage     : $pcrPairInfo = $lampSignature->getMiddleInfo();
\& Function  : Get a reference to this signature's middle pair's info
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : LLNL::LAVA::PrimerSetInfo::PCRPair - middle pair's info
.Ve
.Sh "getOuterInfo"
.IX Subsection "getOuterInfo"
.Vb 5
\& Usage     : $pcrPairInfo = $lampSignature->getOuterInfo();
\& Function  : Get a reference to this signature's outer pair's info
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : LLNL::LAVA::PrimerSetInfo::PCRPair - outer pair's info
.Ve
.Sh "getF3"
.IX Subsection "getF3"
.Vb 5
\& Usage     : $f3Sequence = $lampSignature->getF3();
\& Function  : Get the sequence for this signature's outer forward primer
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - outer forward primer's sequence
.Ve
.Sh "getB3"
.IX Subsection "getB3"
.Vb 5
\& Usage     : $b3Sequence = $lampSignature->getB3();
\& Function  : Get the sequence for this signature's outer reverse primer
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - outer reverse primer's sequence
.Ve
.Sh "getFIP"
.IX Subsection "getFIP"
.Vb 5
\& Usage     : $fipSequence = $lampSignature->getFIP();
\& Function  : Get the sequence for this signature's FIP oligo complex 
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - Complete FIP oligo sequence
.Ve
.Sh "getBIP"
.IX Subsection "getBIP"
.Vb 5
\& Usage     : $bipSequence = $lampSignature->getBIP();
\& Function  : Get the sequence for this signature's BIP oligo complex 
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - Complete BIP oligo sequence
.Ve
.Sh "getF2"
.IX Subsection "getF2"
.Vb 5
\& Usage     : $f2Sequence = $lampSignature->getF2();
\& Function  : Get the sequence for this signature's middle forward primer
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - middle forward primer's sequence
.Ve
.Sh "getB2"
.IX Subsection "getB2"
.Vb 5
\& Usage     : $b2Sequence = $lampSignature->getB2();
\& Function  : Get the sequence for this signature's middle reverse primer
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - middle reverse primer's sequence
.Ve
.Sh "getF1"
.IX Subsection "getF1"
.Vb 5
\& Usage     : $f1Sequence = $lampSignature->getF1();
\& Function  : Get the sequence for this signature's inner forward primer
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - inner forward primer's sequence
.Ve
.Sh "getB1"
.IX Subsection "getB1"
.Vb 5
\& Usage     : $b1Sequence = $lampSignature->getB1();
\& Function  : Get the sequence for this signature's inner reverse primer
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - inner reverse primer's sequence
.Ve
.Sh "linker"
.IX Subsection "linker"
.Vb 6
\& Usage     : $linker = $lampSignature->linker();
\&             $lampSignature->linker($newLinker);
\& Function  : Get/Set pair for the FIP and BIP linker
\& Arguments : (optional) String - new linker
\& Example   : See Usage
\& Returns   : String - the FIP and BIP linker to use
.Ve
.Sh "getRevcomp"
.IX Subsection "getRevcomp"
.Vb 6
\& Usage     : $reverseComplementSequence = $lampSignature->getRevcomp($sequence);
\& Function  : More general helper function (TODO: belongs somewhere else).  
\&             This revcomps the parameter sequence, and does nothing to this object
\& Arguments : String - Sequence to find the reverse complement of
\& Example   : See Usage
\& Returns   : String - The reverse-complemented sequence
.Ve
.Sh "getLocationSummary"
.IX Subsection "getLocationSummary"
.Vb 7
\& Usage     : $locationSummary = $lampSignature->getLocationSummary();
\& Function  : Get a string describing the primer locations for this signature -
\&             This is primarily for debugging
\&             Kinda relies on forward primers being plus strand and reverse being minus
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - locations and spans of each primer locus
.Ve
.Sh "getLoopLocationSummary"
.IX Subsection "getLoopLocationSummary"
.Vb 8
\& Usage     : $locationSummary = $lampSignature->getLoopLocationSummary();
\& Function  : Get a string describing the loop primer locations for this signature -
\&             This is primarily for debugging
\&             Kinda relies on left loop primers being on the minus strand, and right
\&               loop primers being on the plus strand
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - locations and spans of each primer locus
.Ve
.Sh "getPenaltySummary"
.IX Subsection "getPenaltySummary"
.Vb 6
\& Usage     : $penaltySummary = $lampSignature->getPenaltySummary();
\& Function  : Get a string describing the primer penalties for this signature -
\&             This is primarily for debugging
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - penalties of each primer and pair
.Ve
.Sh "getTMSummary"
.IX Subsection "getTMSummary"
.Vb 7
\& Usage     : $tmSummary = $lampSignature->getTMSummary();
\& Function  : Get a string describing the primer tms for this signature -
\&             This is primarily for debugging
\&             Relies on primerInfo's having a "melting_temperature" tag
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : String - penalties of each primer and pair
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Clinton Torres (clinton.torres@llnl.gov)
.SH "SEE ALSO"
.IX Header "SEE ALSO"