Raw content of Bio::Symbol::Alphabet
<![CDATA[# $Id: Alphabet.pm,v 1.6 2002/10/22 07:45:21 lapp Exp $
#
# BioPerl module for Bio::Symbol::Alphabet
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Symbol::Alphabet - DESCRIPTION of Object
=head1 SYNOPSIS
{
my $alphabet = new Bio::Symbols::Alphabet(-symbols => [ @s ],
-subalphabets => [ @alphas ] );
my @symbols = $alphabet->symbols;
my @subalphas = $alphabet->alphabets;
if( $alphabet->contains($symbol) ) {
# do something
}
}
=head1 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.
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 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/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Symbol::Alphabet;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Symbol::AlphabetI;
@ISA = qw(Bio::Root::Root Bio::Symbol::AlphabetI );
=head2 new
Title : new
Usage : my $obj = new Bio::Symbol::Alphabet();
Function: Builds a new Bio::Symbol::Alphabet object
Returns : Bio::Symbol::Alphabet
Args : -symbols => Array ref of Bio::Symbol::SymbolI objects
-subalphas=> Array ref of Bio::Symbol::AlphabetI objects
representing sub alphabets
=cut
sub new {
my($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;
}
=head2 AlphabetI Interface methods
=cut
=head2 symbols
Title : symbols
Usage : my @symbols = $alphabet->symbols();
Function: Get/Set Symbol list for an alphabet
List of symbols, which make up this alphabet.
Returns : Array of Bio::Symbol::SymbolI objects
Args : (optionalalphabets) Array of Bio::Symbol::SymbolI objects
=cut
sub symbols {
my ($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'}};
}
=head2 alphabets
Title : alphabets
Usage : my @alphabets = $alphabet->alphabets();
Function: Get/Set Sub Alphabet list for an alphabet
Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
Returns : Array of Bio::Symbol::AlphabetI objects
Args : (optional) Array of Bio::Symbol::AlphabetI objects
=cut
sub alphabets {
my ($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'}};
}
=head2 contains
Title : contains
Usage : if($alphabet->contains($symbol)) { }
Function: Tests of Symbol is contained in this alphabet
Returns : Boolean
Args : Bio::Symbol::SymbolI
=cut
sub contains{
my ($self,$testsymbol) = @_;
foreach my $symbol ( $self->symbols ) {
return 1 if( $symbol->equals($testsymbol) );
}
return 0;
}
1;
]]>