Bio::Symbol AlphabetI
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Symbol::AlphabetI - A Symbol Alphabet
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Synopsis
    # get a Bio::Symbol::AlphabetI object somehow
    my @symbols = $alphabet->symbols;
    my @subalphas = $alphabet->alphabets;
    if( $alphabet->contains($symbol) ) {
	# do something
    }
Description
Alphabet contains set of symbols, which can be concatenated to form
symbol lists. Sequence string, for example, is stringified
representation of the symbol list (tokens of symbols).
This module was implemented for the purposes of meeting the
BSANE/BioCORBA spec 0.3 only.
Methods
symbolsDescriptionCode
alphabetsDescriptionCode
containsDescriptionCode
Methods description
symbolscode    nextTop
 Title   : symbols
 Usage   : my @symbols = $alphabet->symbols();
 Function: Get/Set Symbol list for an alphabet
           List of symbols, which make up this alphabet.
 Returns : Array of Bio::Symbol::SymbolI objects
 Args    : (optional) Array of Bio::Symbol::SymbolI objects
alphabetscodeprevnextTop
 Title   : alphabets
 Usage   : my @alphabets = $alphabet->alphabets();
 Function: Get/Set Sub Alphabet list for an alphabet 
           Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
 Returns : Array of Bio::Symbol::AlphabetI objects
 Args    : (optional) Array of Bio::Symbol::AlphabetI objects
containscodeprevnextTop
 Title   : contains
 Usage   : if($alphabet->contains($symbol)) { }
 Function: Tests of Symbol is contained in this alphabet
 Returns : Boolean
 Args    : Bio::Symbol::SymbolI
Methods code
symbolsdescriptionprevnextTop
sub symbols {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
alphabetsdescriptionprevnextTop
sub alphabets {
    my ($self,@args) = @_;
    $self->throw_not_implemented();
}
containsdescriptionprevnextTop
sub contains {
   my ($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/wiki/Mailing_lists  - 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 the
web:
  http://bugzilla.open-bio.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
AlphabetI Interface methodsTop