Bio::Symbol SymbolI
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Summary
Bio::Symbol::SymbolI - Interface for a Symbol
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Inherit
Bio::Root::RootI
Synopsis
    # get a Bio::Symbol::SymbolI object somehow

    my ($name,$token) = ($symbol->name, $symbol->token);
    my @symbols       = $symbol->symbols;
    my $matches       = $symbol->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.
Methods
equalsDescriptionCode
matchesDescriptionCode
nameDescriptionCode
symbolsDescriptionCode
tokenDescriptionCode
Methods description
equalscode    nextTop
 Title   : equals
 Usage   : if( $symbol->equals($symbol2) ) { }
 Function: Tests if a symbol is equal to another 
 Returns : Boolean
 Args    : Bio::Symbol::SymbolI
matchescodeprevnextTop
 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
namecodeprevnextTop
 Title   : name
 Usage   : my $name = $symbol->name();
 Function: Get/Set Descriptive name for Symbol
 Returns : string
 Args    : (optional) string
symbolscodeprevnextTop
 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
tokencodeprevnextTop
 Title   : token
 Usage   : my $token = $self->token();
 Function: Get/Set token for this symbol
 Example : Letter A,C,G,or T for a DNA alphabet Symbol
 Returns : string
 Args    : (optional) string
Methods code
equalsdescriptionprevnextTop
sub equals {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

1;
}
matchesdescriptionprevnextTop
sub matches {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
namedescriptionprevnextTop
sub name {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
symbolsdescriptionprevnextTop
sub symbols {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
tokendescriptionprevnextTop
sub token {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/MailList.shtml  - About the mailing lists
Reporting BugsTop
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/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Symbol::SymbolI interface methodsTop