Bio::Symbol Alphabet
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Summary
Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet
Package variables
No package variables defined.
Inherit
Bio::Root::Root Bio::Symbol::AlphabetI
Synopsis
  {
my $alphabet = Bio::Symbols::Alphabet->new(-symbols => [ @s ],
-subalphabets => [ @alphas ] );
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
newDescriptionCode
symbolsDescriptionCode
alphabetsDescriptionCode
containsDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Symbol::Alphabet->new();
Function: Builds a new Bio::Symbol::Alphabet object
Returns : Bio::Symbol::Alphabet
Args : -symbols => Array ref of Bio::Symbol::SymbolI objects
-subalphas=> Array ref of Bio::Symbol::AlphabetI objects
representing sub alphabets
symbolscodeprevnextTop
 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 : (optionalalphabets) 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($symbol)) { }
Function: Tests of Symbol is contained in this alphabet
Returns : Boolean
Args : Bio::Symbol::SymbolI
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    $self->{'_symbols'} = [];
    $self->{'_alphabets'} = [];
    my ($symbols, $subalphas) = $self->_rearrange([qw(SYMBOLS SUBALPHAS)],
						  @args);

    defined $symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols);
    defined $subalphas && ref($subalphas) =~ /array/i && $self->alphabets(@$subalphas);
    return $self;
}
symbolsdescriptionprevnextTop
sub symbols {
    my ($self,@args) = @_;
    if( @args ) { 
	$self->{'_symbols'} = [];
	foreach my $symbol ( @args ) {
	    if( ! defined $symbol || ! ref($symbol) || 
		! $symbol->isa('Bio::Symbol::SymbolI') ) {
		$self->warn("Did not provide a proper Bio::Symbol::SymbolI to method 'symbols' (got $symbol)");
	    } else { 
		push @{$self->{'_symbols'}}, $symbol;
	    }
	}
    }
    return @{$self->{'_symbols'}};
}
alphabetsdescriptionprevnextTop
sub alphabets {
    my ($self,@args) = @_;
   if( @args ) { 
       $self->{'_alphabets'} = [];
       foreach my $alpha ( @args ) {
	   if( ! $alpha->isa('Bio::Symbol::AlphabetI') ) {
	       $self->warn("Did not provide a proper Bio::Symbol::AlphabetI to method 'alphabets' (got $alpha)");
	   } else { 
	       push @{$self->{'_alphabets'}}, $alpha;
	   }
       }
   }
    return @{$self->{'_alphabets'}};
}
containsdescriptionprevnextTop
sub contains {
   my ($self,$testsymbol) = @_;
   foreach my $symbol ( $self->symbols ) {
       return 1 if( $symbol->equals($testsymbol) );
   }
   return 0;
}

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