.\" Automatically generated by Pod::Man v1.37, Pod::Parser v1.32
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sh \" Subsection heading
.br
.if t .Sp
.ne 5
.PP
\fB\\$1\fR
.PP
..
.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.  | will give a
.\" real vertical bar.  \*(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-|\(bv\*(Tr
.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" ''
'br\}
.\"
.\" If the F register is turned on, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.if \nF \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    nr % 0
.    rr F
.\}
.\"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.hy 0
.if n .na
.\"
.\" 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 "LLNL::LAVA::Oligo 3"
.TH LLNL::LAVA::Oligo 3 "2011-06-27" "perl v5.8.8" "User Contributed Perl Documentation"
.SH "NAME"
LLNL::LAVA::Oligo \- Individual oligo sequence representation
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use LLNL::LAVA::Oligo;
.Ve
.PP
.Vb 8
\&  # Instantiation
\&  $oligo = LLNL::LAVA::Oligo->new(
\&    {
\&      "sequence" => $sequence,
\&      "strand" => $strand, # becomes a tag, not a member, so retrieve the 
\&                           # value with $oligo->getTag("strand");
\&      "location" => $location, # 5' location, should be 0-indexed
\&    });
.Ve
.PP
.Vb 2
\&  # Can also instantiate with results from Bio::Tools::Run::Primer3
\&  $oligo = LLNL::LAVA::Oligo->newFromPrimer3($result);
.Ve
.PP
.Vb 4
\&  # Get the current sequence
\&  $sequence = $oligo->sequence();
\&  # Set to new sequence
\&  $oligo->sequence($newSequence);
.Ve
.PP
.Vb 4
\&  # Get the current location
\&  $location = $oligo->location();
\&  # Set to new location
\&  $oligo->location($newLocation);
.Ve
.PP
.Vb 2
\&  # Get the length
\&  $length = $oligo->length();
.Ve
.PP
.Vb 3
\&  # This special mutator does NOT return a reverse complement Oligo, it 
\&  # transforms this oligo into the reverse complement of itself.
\&  $oligo->reverseComplement(); # ACTUALLY CHANGES THE OLIGO!
.Ve
.PP
.Vb 2
\&  # Awkwardly duplicate - should probably move to using Storable's dclone()
\&  $newOligo = $oligo->clone();
.Ve
.PP
.Vb 4
\&  # Tag use
\&  $oligo->setTag("primer3_tm", $primer3TM);
\&  $exists = $oligo->getTagExists("primer3_tm");
\&  $tm = $oligo->getTag("primer3_tm");
.Ve
.SH "EXAMPLES"
.IX Header "EXAMPLES"
See synopsis.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Oligo is the object model of a \s-1DNA\s0 oligo that is used as a 
component in a signature.
.SH "APPENDIX"
.IX Header "APPENDIX"
The following documentation describes the functions in this package
.Sh "new"
.IX Subsection "new"
.Vb 15
\& Usage     : $oligo = LLNL::LAVA::Oligo->new(
\&               {
\&                 "sequence" => $sequence,                # required
\&                 "strand" => $strand, #"plus" or "minus" # optional 
\&                     # default strand is "plus", but strand becomes a tag, not
\&                     # a member, so retrieve with $oligo->getTag("strand");
\&                 "location" => $location,                # optional (0 = default)
\&               });
\& Function  : Creates a new LLNL::LAVA::Oligo 
\& Arguments : Hash ref - Parameters for initialization include:
\&               sequence - sequence for the component 
\&               strand - "plus" or "minus" (stored as a tag!)
\&               location - 5-prime sequence index of this component
\& Example   : See Usage
\& Returns   : A new LLNL::LAVA::Oligo
.Ve
.Sh "newFromPrimer3"
.IX Subsection "newFromPrimer3"
.Vb 5
\& Usage     : $oligo = LLNL::LAVA::Oligo->newFromPrimer3($primer3Answer);
\& Function  : Factory function for creating a new LLNL::LAVA::Oligo 
\& Arguments : Hash ref - oligo returned from Bio::Tools::Run::Primer3
\& Example   : See Usage
\& Returns   : A new LLNL::LAVA::Oligo
.Ve
.Sh "sequence"
.IX Subsection "sequence"
.Vb 6
\& Usage     : $sequence = $oligo->sequence();
\&             $oligo->sequence($newSequence);
\& Function  : Get/Set pair for sequence
\& Arguments : (optional) String - new sequence for the oligo
\& Example   : See Usage
\& Returns   : String - sequence of the oligo
.Ve
.Sh "location"
.IX Subsection "location"
.Vb 6
\& Usage     : $location = $oligo->location();
\&             $oligo->location($newLocation);
\& Function  : Get/Set pair for location
\& Arguments : (optional) Integer - new location for the oligo
\& Example   : See Usage
\& Returns   : Integer - location of the oligo;
.Ve
.Sh "length"
.IX Subsection "length"
.Vb 5
\& Usage     : $length = $oligo->length();
\& Function  : Get the length of this oligo, calculated from the sequence content
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : Integer - length of the oligo
.Ve
.Sh "reverseComplement"
.IX Subsection "reverseComplement"
.Vb 7
\& Usage     : $oligo->reverseComplement();
\& Function  : This special mutator does NOT return a reverse complement of this
\&             Oligo, it transforms this oligo into the reverse complement
\&             of itself. 
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : <n/a>
.Ve
.Sh "clone"
.IX Subsection "clone"
.Vb 5
\& Usage     : $newOligo = $oligo->clone();
\& Function  : Duplicates an oligo, but DOES NOT perform a deep copy of tag values
\& Arguments : <n/a>
\& Example   : See Usage
\& Returns   : A new LLNL::LAVA::Oligo
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Clinton Torres (clinton.torres@llnl.gov)
.SH "SEE ALSO"
.IX Header "SEE ALSO"