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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Alphabet.t,v 1.3 2001/12/13 23:10:08 jason Exp $
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 90;
}
use Bio::Symbol::Alphabet;
use Bio::Symbol::Symbol;
use Bio::Symbol::DNAAlphabet;
use Bio::Symbol::ProteinAlphabet;
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 $T = new Bio::Symbol::Symbol(-token => 'T' );
my $rna = new Bio::Symbol::Alphabet( -symbols => [ $A, $U, $G, $T ] );
ok($rna);
my @symbols = $rna->symbols;
ok(scalar @symbols, 4);
ok($rna->contains($A));
ok($rna->contains($T));
ok($rna->contains($U));
ok($rna->contains($G));
my $dna = new Bio::Symbol::DNAAlphabet();
ok($dna->isa('Bio::Symbol::AlphabetI'));
my $count = 0;
my @dnasymbols = sort qw( A B C D G H K M N R S T U V W X Y );
foreach my $s ( sort { $a->name cmp $b->name } $dna->symbols ) {
ok($s->name, $dnasymbols[$count]);
ok($s->token, $dnasymbols[$count++]);
}
my $prot = new Bio::Symbol::ProteinAlphabet();
ok($prot->isa('Bio::Symbol::AlphabetI'));
my @protsymbols = sort qw( * A B C D E F G H I K L M N P Q R S T V W X Y Z);
my %h = (
'Ala' => 'A', 'Asx' => 'B',
'Cys' => 'C', 'Asp' => 'D',
'Glu' => 'E', 'Phe' => 'F',
'Gly' => 'G', 'His' => 'H',
'Ile' => 'I', 'Lys' => 'K',
'Leu' => 'L', 'Met' => 'M',
'Asn' => 'N', 'Pro' => 'P',
'Gln' => 'Q', 'Arg' => 'R',
'Ser' => 'S', 'Thr' => 'T',
'Val' => 'V', 'Trp' => 'W',
'Tyr' => 'Y', 'Ter' => '*',
'Xaa' => 'X', 'Glx' => 'Z'
);
my @protnms = sort { $h{$a} cmp $h{$b} } keys %h;
$count = 0;
foreach my $s ( sort { $a->token cmp $b->token } $prot->symbols ) {
ok($s->name, $protnms[$count]);
ok($s->token, $protsymbols[$count++]);
}
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