/usr/share/perl5/Bio/Symbol/ProteinAlphabet.pm is in libbio-perl-perl 1.6.924-3.
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# BioPerl module for Bio::Symbol::ProteinAlphabet
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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::ProteinAlphabet - A ready made Protein alphabet
=head1 SYNOPSIS
use Bio::Symbol::ProteinAlphabet;
my $alpha = Bio::Symbol::ProteinAlphabet->new();
foreach my $symbol ( $alpha->symbols ) {
print "symbol is $symbol\n";
}
=head1 DESCRIPTION
This object builds an Alphabet with Protein symbols.
=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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=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::ProteinAlphabet;
use strict;
use Bio::Symbol::Symbol;
use Bio::Tools::IUPAC;
use Bio::SeqUtils;
use base qw(Bio::Symbol::Alphabet);
=head2 new
Title : new
Usage : my $obj = Bio::Symbol::ProteinAlphabet->new();
Function: Builds a new Bio::Symbol::ProteinAlphabet object
Returns : Bio::Symbol::ProteinAlphabet
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my %aa = Bio::SeqUtils->valid_aa(2);
my %codes = Bio::Tools::IUPAC->iupac_iup();
my %symbols;
my @left;
foreach my $let ( keys %codes ) {
if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
$symbols{$let} = Bio::Symbol::Symbol->new(-name => $aa{$let},
-token => $let);
}
foreach my $l ( @left ) {
my @subsym;
foreach my $sym ( @{$codes{$l}} ) {
push @subsym, $symbols{$sym};
}
my $alpha = Bio::Symbol::Alphabet->new(-symbols => \@subsym);
$symbols{$l} = Bio::Symbol::Symbol->new(-name => $aa{$l},
-token => $l,
-matches => $alpha,
-symbols => \@subsym);
}
$self->symbols(values %symbols);
return $self;
}
1;
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