Bio::Symbol::SymbolI - Interface for a Symbol # get a Bio::Symbol::SymbolI object somehow my ($name,$token) = ($symbol->name, $symbol->token); my @symbols = $symbol->symbols; my $matches = $symbol->matches; 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.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Bio::Symbol::SymbolI interface methods

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 : A codon is composed of 3 DNA symbols 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