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.\" ========================================================================
.\"
.IX Title "Bio::Symbol::Symbol 3pm"
.TH Bio::Symbol::Symbol 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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.SH "NAME"
Bio::Symbol::Symbol \- A biological symbol
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&    use Bio::Symbol::Symbol;
\&    my $thymine = Bio::Symbol::Symbol\->new(\-name => \*(AqThy\*(Aq,
\&                                          \-token=> \*(AqT\*(Aq);
\&    my $a = Bio::Symbol::Symbol\->new(\-token => \*(AqA\*(Aq );
\&    my $u = Bio::Symbol::Symbol\->new(\-token => \*(AqU\*(Aq );
\&    my $g = Bio::Symbol::Symbol\->new(\-token => \*(AqG\*(Aq );
\&
\&    my $M = Bio::Symbol::Symbol\->new(\-name  => \*(AqMet\*(Aq,
\&                                    \-token => \*(AqM\*(Aq,
\&                                    \-symbols => [ $a, $u, $g ]);
\&
\&    my ($name,$token) = ($a\->name, $a\->token);
\&    my @symbols       = $a\->symbols;
\&    my $matches       = $a\->matches;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Symbol represents a single token in the sequence. Symbol can have
multiple synonyms or matches within the same Alphabet, which
makes possible to represent ambiguity codes and gaps.
.PP
Symbols can be also composed from ordered list other symbols. For
example, codons can be represented by single Symbol using a
compound Alphabet made from three \s-1DNA\s0 Alphabets.
.PP
This module was implemented for the purposes of meeting the
BSANE/BioCORBA spec 0.3 only.
.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 list.  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
of 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 \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason@bioperl.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 "new"
.IX Subsection "new"
.Vb 9
\& Title   : new
\& Usage   : my $obj = Bio::Symbol::Symbol\->new();
\& Function: Builds a new Bio::Symbol::Symbol object 
\& Returns : Bio::Symbol::Symbol
\& Args    : \-name    => descriptive name (string) [e.g. Met]
\&           \-token   => Shorthand token (string)  [e.g. M]
\&           \-symbols => Symbols that make up this symbol (array) [e.g. AUG]
\&           \-matches => Alphabet in the event symbol is an ambiguity
\&                       code.
.Ve
.SS "name"
.IX Subsection "name"
.Vb 5
\& Title   : name
\& Usage   : my $name = $symbol\->name();
\& Function: Get/Set Descriptive name for Symbol
\& Returns : string
\& Args    : (optional) string
.Ve
.SS "token"
.IX Subsection "token"
.Vb 6
\& Title   : token
\& Usage   : my $token = $self\->token();
\& Function: Get/Set token for this symbol
\& Example : Letter A,C,G,or T for a DNA alphabet Symbol
\& Returns : string
\& Args    : (optional) string
.Ve
.SS "symbols"
.IX Subsection "symbols"
.Vb 6
\& Title   : symbols
\& Usage   : my @symbols = $self\->symbols();
\& Function: Get/Set Symbols this Symbol is composed from
\& Example : Ambiguity symbols are made up > 1 base symbol
\& Returns : Array of Bio::Symbol::SymbolI objects
\& Args    : (optional) Array of Bio::Symbol::SymbolI objects
.Ve
.SS "matches"
.IX Subsection "matches"
.Vb 8
\& Title   : matches
\& Usage   : my $matchalphabet = $symbol\->matches();
\& Function: Get/Set (Sub) alphabet of symbols matched by this symbol
\&           including the symbol itself (i.e. if symbol is DNA
\&           ambiguity code W then the matches contains symbols for W
\&           and T)
\& Returns : Bio::Symbol::AlphabetI
\& Args    : (optional) Bio::Symbol::AlphabetI
.Ve
.SS "equals"
.IX Subsection "equals"
.Vb 5
\& Title   : equals
\& Usage   : if( $symbol\->equals($symbol2) ) { }
\& Function: Tests if a symbol is equal to another 
\& Returns : Boolean
\& Args    : Bio::Symbol::SymbolI
.Ve