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.IX Title "Bio::Phenotype::OMIM::OMIMentryAllelicVariant 3pm"
.TH Bio::Phenotype::OMIM::OMIMentryAllelicVariant 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Phenotype::OMIM::OMIMentryAllelicVariant \- Representation of a allelic
variant of the OMIM database
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
\&
\&  $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant\->new( \-number               => ".0001",
\&                                                            \-title                => "ALCOHOL INTOLERANCE",
\&                                                            \-symbol               => "ALDH2*2",
\&                                                            \-description          => "The ALDH2*2\-encoded ...",
\&                                                            \-aa_ori               => "GLU",
\&                                                            \-aa_mut               => "LYS",
\&                                                            \-position             => 487,
\&                                                            \-additional_mutations => "IVS4DS, G\-A, +1" );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This class models the allelic variant of the \s-1OMIM\s0 database.
This class is intended to be used together with a \s-1OMIM\s0 entry class.
.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 one
of 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"
.IX Header "AUTHOR"
Christian M. Zmasek
.PP
Email: czmasek\-at\-burnham.org  or  cmzmasek@yahoo.com
.PP
\&\s-1WWW:\s0   http://monochrome\-effect.net/
.PP
Address:
.PP
.Vb 3
\&  Genomics Institute of the Novartis Research Foundation
\&  10675 John Jay Hopkins Drive
\&  San Diego, CA 92121
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods.
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant\->new( \-number               => ".0001",
\&                                                                     \-title                => "ALCOHOL INTOLERANCE",
\&                                                                     \-symbol               => "ALDH2*2",
\&                                                                     \-description          => "The ALDH2*2\-encoded ...",
\&                                                                     \-aa_ori               => "GLU",
\&                                                                     \-aa_mut               => "LYS",
\&                                                                     \-position             => 487,
\&                                                                     \-additional_mutations => "IVS4DS, G\-A, +1" );                      
\& Function: Creates a new OMIMentryAllelicVariant object.
\& Returns : A new OMIMentryAllelicVariant object.
\& Args    : \-number               => the OMIM allelic variant number
\&           \-title                => the title
\&           \-symbol               => a symbol
\&           \-description          => a description
\&           \-aa_ori               => the original amino acid
\&           \-aa_mut               => the mutated amino acid
\&           \-position             => the position of the mutation
\&           \-additional_mutations => free form description of additional mutations
.Ve
.SS "init"
.IX Subsection "init"
.Vb 5
\& Title   : init()
\& Usage   : $av\->init();   
\& Function: Initializes this OMIMentryAllelicVariant to all "".
\& Returns : 
\& Args    :
.Ve
.SS "number"
.IX Subsection "number"
.Vb 8
\& Title   : number
\& Usage   : $av\->number( ".0001" );
\&           or
\&           print $av\->number();
\& Function: Set/get for the OMIM allelic variant number of this
\&           OMIMentryAllelicVariant.
\& Returns : The OMIM allelic variant number.
\& Args    : The OMIM allelic variant number (optional).
.Ve
.SS "title"
.IX Subsection "title"
.Vb 7
\& Title   : title
\& Usage   : $av\->title( "ALCOHOL INTOLERANCE" );
\&           or
\&           print $av\->title();
\& Function: Set/get for the title of this OMIMentryAllelicVariant.
\& Returns : The title.
\& Args    : The title (optional).
.Ve
.SS "symbol"
.IX Subsection "symbol"
.Vb 7
\& Title   : symbol
\& Usage   : $av\->symbol( "ALDH2*2" );
\&           or
\&           print $av\->symbol();
\& Function: Set/get for the symbol of this OMIMentryAllelicVariant.
\& Returns : A symbol.
\& Args    : A symbol (optional).
.Ve
.SS "description"
.IX Subsection "description"
.Vb 7
\& Title   : description
\& Usage   : $av\->description( "The ALDH2*2\-encoded protein has a change ..." );
\&           or
\&           print $av\->description();
\& Function: Set/get for the description of this OMIMentryAllelicVariant.
\& Returns : A description.
\& Args    : A description (optional).
.Ve
.SS "aa_ori"
.IX Subsection "aa_ori"
.Vb 7
\& Title   : aa_ori
\& Usage   : $av\->aa_ori( "GLU" );
\&           or
\&           print $av\->aa_ori();
\& Function: Set/get for the original amino acid(s).
\& Returns : The original amino acid(s).
\& Args    : The original amino acid(s) (optional).
.Ve
.SS "aa_mut"
.IX Subsection "aa_mut"
.Vb 7
\& Title   : aa_mut
\& Usage   : $av\->aa_mut( "LYS" );
\&           or
\&           print $av\->aa_mut();
\& Function: Set/get for the mutated amino acid(s).
\& Returns : The mutated amino acid(s).
\& Args    : The mutated amino acid(s) (optional).
.Ve
.SS "position"
.IX Subsection "position"
.Vb 7
\& Title   : position
\& Usage   : $av\->position( 487 );
\&           or
\&           print $av\->position();
\& Function: Set/get for the position of the mutation.
\& Returns : The position of the mutation.
\& Args    : The position of the mutation (optional).
.Ve
.SS "additional_mutations"
.IX Subsection "additional_mutations"
.Vb 7
\& Title   : additional_mutations
\& Usage   : $av\->additional_mutations( "1\-BP DEL, 911T" );
\&           or
\&           print $av\->additional_mutations();
\& Function: Set/get for free form description of (additional) mutation(s).
\& Returns : description of (additional) mutation(s).
\& Args    : description of (additional) mutation(s) (optional).
.Ve
.SS "to_string"
.IX Subsection "to_string"
.Vb 5
\& Title   : to_string()
\& Usage   : print $av\->to_string();
\& Function: To string method for OMIMentryAllelicVariant objects.
\& Returns : A string representations of this OMIMentryAllelicVariant.
\& Args    :
.Ve