diff variant_effect_predictor/Bio/Symbol/Alphabet.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Symbol/Alphabet.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,191 @@
+# $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 <[e-mail]>
+#
+# 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.
+
+  [e-mail]              - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+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;