Raw content of Bio::Symbol::Symbol
<![CDATA[# $Id: Symbol.pm,v 1.6 2002/10/22 07:45:21 lapp Exp $
#
# BioPerl module for Bio::Symbol::Symbol
#
# 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::Symbol - A biological symbol
=head1 SYNOPSIS
use Bio::Symbol::Symbol;
my $thymine = new Bio::Symbol::Symbol(-name => 'Thy',
-token=> 'T');
my $a = new Bio::Symbol::Symbol(-token => 'A' );
my $u = new Bio::Symbol::Symbol(-token => 'U' );
my $g = new Bio::Symbol::Symbol(-token => 'G' );
my $M = new Bio::Symbol::Symbol(-name => 'Met',
-token => 'M',
-symbols => [ $a, $u, $g ]);
my ($name,$token) = ($a->name, $a->token);
my @symbols = $a->symbols;
my $matches = $a->matches;
=head1 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.
=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::Symbol;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Symbol::SymbolI;
use Bio::Symbol::Alphabet;
use Bio::Root::Root;
@ISA = qw( Bio::Root::Root Bio::Symbol::SymbolI );
=head2 new
Title : new
Usage : my $obj = new Bio::Symbol::Symbol();
Function: Builds a new Bio::Symbol::Symbol object
Returns : Bio::Symbol::Symbol
Args : -name => descriptive name (string) [e.g. Met]
-token => Shorthand token (string) [e.g. M]
-symbols => Symbols that make up this symbol (array) [e.g. AUG]
-matches => Alphabet in the event symbol is an ambiguity
code.
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_symbols'} = [];
my ($name, $token, $symbols,
$matches) = $self->_rearrange([qw(NAME TOKEN SYMBOLS
MATCHES)],
@args);
$token && $self->token($token);
$name && $self->name($name);
$symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols);
$matches && $self->matches($matches);
return $self;
}
=head2 name
Title : name
Usage : my $name = $symbol->name();
Function: Get/Set Descriptive name for Symbol
Returns : string
Args : (optional) string
=cut
sub name {
my ($self,$value) = @_;
if( $value ) {
$self->{'_name'} = $value;
}
return $self->{'_name'} || '';
}
=head2 token
Title : token
Usage : my $token = $self->token();
Function: Get/Set token for this symbol
Example : Letter A,C,G,or T for a DNA alphabet Symbol
Returns : string
Args : (optional) string
=cut
sub token{
my ($self,$value) = @_;
if( $value ) {
$self->{'_token'} = $value;
}
return $self->{'_token'} || '';
}
=head2 symbols
Title : symbols
Usage : my @symbols = $self->symbols();
Function: Get/Set Symbols this Symbol is composed from
Example : Ambiguity symbols are made up > 1 base symbol
Returns : Array of Bio::Symbol::SymbolI objects
Args : (optional) Array of Bio::Symbol::SymbolI objects
=cut
sub symbols{
my ($self,@args) = @_;
if( @args ) {
$self->{'_symbols'} = [@args];
}
return @{$self->{'_symbols'}};
}
=head2 matches
Title : matches
Usage : my $matchalphabet = $symbol->matches();
Function: Get/Set (Sub) alphabet of symbols matched by this symbol
including the symbol itself (i.e. if symbol is DNA
ambiguity code W then the matches contains symbols for W
and T)
Returns : Bio::Symbol::AlphabetI
Args : (optional) Bio::Symbol::AlphabetI
=cut
sub matches{
my ($self,$matches) = @_;
if( $matches ) {
if( ! $matches->isa('Bio::Symbol::AlphabetI') ) {
$self->warn("Must pass in a Bio::Symbol::AlphabetI object to matches function");
# stick with previous value
} else {
$self->{'_matches'} = $matches;
}
}
return $self->{'_matches'};
}
=head2 equals
Title : equals
Usage : if( $symbol->equals($symbol2) ) { }
Function: Tests if a symbol is equal to another
Returns : Boolean
Args : Bio::Symbol::SymbolI
=cut
sub equals{
my ($self,$symbol2) = @_;
# Let's just test based on Tokens for now
# Doesn't handle DNA vs PROTEIN accidential comparisons
return $self->token eq $symbol2->token;
}
1;
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