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.\" ========================================================================
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.IX Title "LLNL::LAVA::PrimerAnalyzer 3"
.TH LLNL::LAVA::PrimerAnalyzer 3 "2011-06-27" "perl v5.8.8" "User Contributed Perl Documentation"
.SH "NAME"
LLNL::LAVA::PrimerAnalyzer \- Abstract base class that defines the interface
different PrimerAnalyzers must implement
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
do not use PrimerAnalyzer directly, use a concrete sub\-class.
.PP
.Vb 2
\&  # Get the analysis results for an oligo.
\&  $primerInfo = $analyzer->analyze($oligo);
.Ve
.PP
.Vb 8
\&  # Set parameter values.  Causes an error if a value is set for
\&  # a parameter name that doesn't already exist.  This means any parameters
\&  # for this PrimerAnalyzer need to be declared during instantiation.
\&  $analyzer->setParameters(
\&    {
\&      "parameter_name" => $value,
\&      ...
\&    });
.Ve
.PP
.Vb 3
\&  # Retrive a parameter value.  Causes an error if the value for an unknown
\&  # parameter is requested.
\&  $value = $analyzer->getParameterValue("parameter_name");
.Ve
.PP
.Vb 4
\&  # Tag use
\&  $analyzer->setTag("useful_tag_name", $value);
\&  $exists = $analyzer->getTagExists("useful_tag_name");
\&  $value = $analyzer->getTag("useful_tag_name");
.Ve
.SH "EXAMPLES"
.IX Header "EXAMPLES"
See synopsis.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
PrimerAnalyzer is an abstract base class which defines the interface for
concrete PrimerAnalyzer implementations (such as PCRPrimer).
.SH "APPENDIX"
.IX Header "APPENDIX"
The following documentation describes the functions in this package
.Sh "new"
.IX Subsection "new"
.Vb 6
\& Usage     : $analyzer = LLNL::LAVA::PrimerAnalyzer->new();
\& Function  : Creates a new LLNL::LAVA::PrimerAnalyzer, only sub-classes 
\&             should use this
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : A new LLNL::LAVA::PrimerAnalyzer
.Ve
.Sh "analyze"
.IX Subsection "analyze"
.Vb 6
\& Usage     : Do not use this directly 
\& Function  : Sub-class implementation must return a LLNL::LAVA::PrimerInfo
\& Arguments : L<LLNL::LAVA::Oligo> - subclass should accept an individual 
\&                                    oligo to analyze as a primer
\& Example   : See Usage
\& Returns   : L<LLNL::LAVA::PrimerInfo> - the result of analyzing the primer
.Ve
.Sh "setParameters"
.IX Subsection "setParameters"
.Vb 7
\& Usage     : $analyzer->setParameters({param_name => $param_value...});
\& Function  : Sets the analyzer parameters for analysis.  Will cause an error
\&             if a parameter is used that this module doesn't have a default 
\&             value for.
\& Arguments : Hash ref of name->value pairs
\& Example   : See Usage
\& Returns   : <n/a>
.Ve
.Sh "getParameterValue"
.IX Subsection "getParameterValue"
.Vb 7
\& Usage     : $paramValue = $analyzer->getParameterValue("parameter_name");
\& Function  : Returns the value of a named PrimerAnalyzer parameter.
\&             Will cause an error (using the Options module) if a parameter 
\&             name is requested that there is no value for.
\& Arguments : String - parameter name to get the value of
\& Example   : See Usage
\& Returns   : String - value of the named parameter
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Clinton Torres (clinton.torres@llnl.gov)
.SH "SEE ALSO"
.IX Header "SEE ALSO"