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