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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Symbol/Symbol.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,232 @@
+# $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 <[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::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.
+
+  [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::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;