.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40)
.\"
.\" Standard preamble:
.\" ========================================================================
.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.  \*(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-
.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" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::Variation::Allele 3pm"
.TH Bio::Variation::Allele 3pm "2021-12-02" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Variation::Allele \- Sequence object with allele\-specific attributes
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\&  $allele1 = Bio::Variation::Allele\->new ( \-seq => \*(AqA\*(Aq,
\&                                           \-id  => \*(AqAC00001.1\*(Aq,
\&                                           \-alphabet => \*(Aqdna\*(Aq,
\&                                           \-is_reference => 1
\&                                         );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
List of alleles describe known sequence alternatives in a variable region.
Alleles are contained in Bio::Variation::VariantI complying objects.
See Bio::Variation::VariantI for details.
.PP
Bio::Varation::Alleles are PrimarySeqI complying objects which can
contain database cross references as specified in
Bio::DBLinkContainerI interface, too.
.PP
A lot of the complexity with dealing with Allele objects are caused by
null alleles; Allele objects that have zero length sequence string.
.PP
In addition describing the allele by its sequence , it possible to
give describe repeat structure within the sequence. This done using
methods repeat_unit (e.g. 'ca') and repeat_count (e.g. 7).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the 
Bioperl mailing lists  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "is_reference"
.IX Subsection "is_reference"
.Vb 7
\& Title   : is_reference
\& Usage   : $obj\->is_reference()
\& Function: sets and returns boolean values. 
\&           Unset values return false.
\& Example : $obj\->is_reference()
\& Returns : boolean
\& Args    : optional true of false value
.Ve
.SS "add_DBLink"
.IX Subsection "add_DBLink"
.Vb 6
\& Title   : add_DBLink
\& Usage   : $self\->add_DBLink($ref)
\& Function: adds a link object
\& Example :
\& Returns : 
\& Args    :
.Ve
.SS "each_DBLink"
.IX Subsection "each_DBLink"
.Vb 6
\& Title   : each_DBLink
\& Usage   : foreach $ref ( $self\->each_DBlink() )
\& Function: gets an array of DBlink of objects
\& Example :
\& Returns : 
\& Args    :
.Ve
.SS "repeat_unit"
.IX Subsection "repeat_unit"
.Vb 3
\& Title   : repeat_unit
\& Usage   : $obj\->repeat_unit(\*(Aqca\*(Aq);
\& Function: 
\&
\&            Sets and returns the sequence of the repeat_unit the
\&            allele is composed of.
\&
\& Example : 
\& Returns : string
\& Args    : string
.Ve
.SS "repeat_count"
.IX Subsection "repeat_count"
.Vb 3
\& Title   : repeat_count
\& Usage   : $obj\->repeat_count();
\& Function: 
\&
\&            Sets and returns the number of repeat units in the allele.
\&
\& Example : 
\& Returns : string
\& Args    : string
.Ve
.SS "count"
.IX Subsection "count"
.Vb 3
\& Title   : count
\& Usage   : $obj\->count();
\& Function: 
\&
\&            Sets and returns the number of times this allele was observed.
\&
\& Example : 
\& Returns : string
\& Args    : string
.Ve
.SS "frequency"
.IX Subsection "frequency"
.Vb 3
\& Title   : frequency
\& Usage   : $obj\->frequency();
\& Function: 
\&
\&            Sets and returns the frequency of the allele in the observed
\&            population.
\&
\& Example : 
\& Returns : string
\& Args    : string
.Ve