Raw content of Bio::Symbol::Symbol # $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;