diff variant_effect_predictor/Bio/Symbol/SymbolI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Symbol/SymbolI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,168 @@
+# $Id: SymbolI.pm,v 1.6 2002/10/22 07:45:21 lapp Exp $
+#
+# BioPerl module for Bio::Symbol::SymbolI
+#
+# 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::SymbolI - Interface for a Symbol
+
+=head1 SYNOPSIS
+
+    # get a Bio::Symbol::SymbolI object somehow
+
+    my ($name,$token) = ($symbol->name, $symbol->token);
+    my @symbols       = $symbol->symbols;
+    my $matches       = $symbol->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]
+
+=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::SymbolI;
+use strict;
+use Bio::Root::RootI;
+use vars qw(@ISA);
+@ISA = qw(Bio::Root::RootI);
+
+=head2 Bio::Symbol::SymbolI interface methods
+
+=cut
+
+=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,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=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,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 symbols
+
+ Title   : symbols
+ Usage   : my @symbols = $self->symbols();
+ Function: Get/Set Symbols this Symbol is composed from
+ Example : A codon is composed of 3 DNA symbols
+ Returns : Array of Bio::Symbol::SymbolI objects
+ Args    : (optional) Array of Bio::Symbol::SymbolI objects
+
+
+=cut
+
+sub symbols{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=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,@args) = @_;
+   $self->throw_not_implemented();   
+}
+
+=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,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+1;