Bio::Symbol AlphabetI
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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();
}

# Other methods from BSANE - not sure if we will implement here or only in
# BioCORBA implementation
# Resolve symbols from the token string.
# SymbolList to_symbol(in string tokens) raises ( IllegalSymbolException) ;
# Convinience method, which returns gap symbol that do not
# match with any other symbols in the alphabet.
# Symbol get_gap_symbol() raises ( DoesNotExist) ;
# Returns a ambiguity symbol, which represent list of
# symbols. All symbols in a list must be members of
# this alphabet otherwise IllegalSymbolException is
# thrown.
# Symbol get_ambiguity( in SymbolList symbols) raises( IllegalSymbolException);
# Returns a Symbol, which represents ordered list of symbols
# given as a parameter. Each symbol in the list must be member of
# different sub-alphabet in the order defined by the alphabets
# attribute. For example, codons can be represented by a compound
# Alphabet of three DNA Alphabets, in which case the get_symbol(
# SymbolList[ a,g,t]) method of the Alphabet returns Symbol for
# the codon agt.<p>
# IllegalSymbolException is raised if members of symbols
# are not Symbols over the alphabet defined by
# get_alphabets()-method
# Symbol get_symbol(in SymbolList symbols) raises(IllegalSymbolException) ;
1;
}
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
Support Top
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 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:
  https://redmine.open-bio.org/projects/bioperl/
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