/ 
BioPerl-1.6.921
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Symbol::Symbol

NAME

Bio::Symbol::Symbol - A biological symbol

SYNOPSIS

    use Bio::Symbol::Symbol;
    my $thymine = Bio::Symbol::Symbol->new(-name => 'Thy',
					  -token=> 'T');
    my $a = Bio::Symbol::Symbol->new(-token => 'A' );
    my $u = Bio::Symbol::Symbol->new(-token => 'U' );
    my $g = Bio::Symbol::Symbol->new(-token => 'G' );

    my $M = Bio::Symbol::Symbol->new(-name  => 'Met',
				    -token => 'M',
				    -symbols => [ $a, $u, $g ]);

    my ($name,$token) = ($a->name, $a->token);
    my @symbols       = $a->symbols;
    my $matches       = $a->matches;

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.

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 DNA Alphabets.

This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only.

FEEDBACK

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

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:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

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.

name

Title   : name
Usage   : my $name = $symbol->name();
Function: Get/Set Descriptive name for Symbol
Returns : string
Args    : (optional) string

token

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

symbols

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

matches

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

equals

Title   : equals
Usage   : if( $symbol->equals($symbol2) ) { }
Function: Tests if a symbol is equal to another 
Returns : Boolean
Args    : Bio::Symbol::SymbolI