Bio::Symbol::Symbol(3)User Contributed Perl DocumentatioBio::Symbol::Symbol(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::Symbol::Symbol(3)
