#-*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: CodonTable.t,v 1.20 2006/08/16 21:07:01 cjfields Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use lib './';
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( $@ ) {
        use lib 't';
    }
    use Test;
    plan tests => 51;
}
use Bio::Tools::CodonTable;
use vars qw($DEBUG);
ok(1);
# create a table object by giving an ID
$DEBUG = 0;
my $myCodonTable = Bio::Tools::CodonTable -> new ( -id => 16);
ok defined $myCodonTable;
ok $myCodonTable->isa('Bio::Tools::CodonTable');
# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
ok $myCodonTable->id(), 1;
# change codon table
$myCodonTable->id(10);
ok $myCodonTable->id, 10;
ok $myCodonTable->name(), 'Euplotid Nuclear';
# enumerate tables as object method
my $table = $myCodonTable->tables();
ok (keys %{$table} >= 17); # currently 17 known tables
ok $table->{11}, q{"Bacterial"};
# enumerate tables as class method
$table = Bio::Tools::CodonTable->tables;
ok (values %{$table} >= 17); # currently 17 known tables
ok $table->{23}, 'Thraustochytrium Mitochondrial';
# translate codons
$myCodonTable->id(1);
eval {
    $myCodonTable->translate();
};
ok ($@ =~ /EX/) ;
ok $myCodonTable->translate(''), '';
my @ii  = qw(ACT acu ATN gt ytr sar);
my @res = qw(T   T   X   V  L   Z  );
my $test = 1;
for my $i (0..$#ii) {
    if ($res[$i] ne $myCodonTable->translate($ii[$i]) ) {
        $test = 0; 
        print $ii[$i], ": |", $res[$i], "| ne |", $myCodonTable->translate($ii[$i]), "|\n" if( $DEBUG);
        last ;
    }
}
ok ($test);
ok $myCodonTable->translate('ag'), '';
ok $myCodonTable->translate('jj'), '';
ok $myCodonTable->translate('jjg'), 'X';
ok $myCodonTable->translate('gt'), 'V'; 
ok $myCodonTable->translate('g'), '';
# a more comprehensive test on ambiguous codes
my $seq = <<SEQ;
atgaaraayacmacracwackacyacsacvachacdacbacxagragyatmatwatyathcarcayc
cmccrccwcckccyccsccvcchccdccbccxcgmcgrcgwcgkcgycgscgvcghcgdcgbcgxctmctrct
wctkctyctsctvcthctdctbctxgargaygcmgcrgcwgckgcygcsgcvgchgcdgcbgcxggmggrggw
ggkggyggsggvgghggdggbggxgtmgtrgtwgtkgtygtsgtvgthgtdgtbgtxtartaytcmtcrtcwt
cktcytcstcvtchtcdtcbtcxtgyttrttytramgamggmgrracratrayytaytgytrsaasagsartaa;
SEQ
    $seq =~ s/\s+//g;
@ii = grep { length == 3 } split /(.{3})/, $seq; 
print join (' ', @ii), "\n" if( $DEBUG);
my $prot = <<PROT;
MKNTTTTTTTTTTTRSIIIIQHPPPPPPPPPPPRRRRRRRRRRRLLLLLLLLLLLEDAAAAAAAAAAAGGG
GGGGGGGGVVVVVVVVVVV*YSSSSSSSSSSSCLF*RRRBBBLLLZZZ*
PROT
    $prot =~ s/\s//;
@res = split //, $prot;
print join (' ', @res), "\n" if( $DEBUG );
$test = 1;
for my $i (0..$#ii) {
    if ($res[$i] ne $myCodonTable->translate($ii[$i]) ) {
        $test = 0; 
        print $ii[$i], ": |", $res[$i], "| ne |", 
          $myCodonTable->translate($ii[$i]),  "| @ $i\n" if( $DEBUG);
        last ;
    }
}
ok $test;
# reverse translate amino acids 
ok $myCodonTable->revtranslate('U'), 0;
ok $myCodonTable->revtranslate('O'), 0;
ok $myCodonTable->revtranslate('J'), 9;
ok $myCodonTable->revtranslate('I'), 3;
@ii = qw(A l ACN Thr sER ter Glx);
@res = (
        [qw(gct gcc gca gcg)],
        [qw(ggc gga ggg act acc aca acg)],
        [qw(tct tcc tca tcg agt agc)],
        [qw(act acc aca acg)],
        [qw(tct tcc tca tcg agt agc)],
        [qw(taa tag tga)],
        [qw(gaa gag caa cag)]
        );
$test = 1;
 TESTING: {
     for my $i (0..$#ii) {
         my @codonres = $myCodonTable->revtranslate($ii[$i]);
         for my $j (0..$#codonres) {
             if ($codonres[$j] ne $res[$i][$j]) {
                 $test = 0;
                 print $ii[$i], ': ', $codonres[$j], " ne ", 
                 $res[$i][$j], "\n" if( $DEBUG);
                 last TESTING;
             }
         }
     }
 }
ok $test;
#  boolean tests
$myCodonTable->id(1);
ok $myCodonTable->is_start_codon('ATG');  
ok $myCodonTable->is_start_codon('GGH'), 0;
ok $myCodonTable->is_start_codon('HTG');
ok $myCodonTable->is_start_codon('CCC'), 0;
ok $myCodonTable->is_ter_codon('UAG');
ok $myCodonTable->is_ter_codon('TaG');
ok $myCodonTable->is_ter_codon('TaR');
ok $myCodonTable->is_ter_codon('tRa');
ok $myCodonTable->is_ter_codon('ttA'), 0;
ok $myCodonTable->is_unknown_codon('jAG');
ok $myCodonTable->is_unknown_codon('jg');
ok $myCodonTable->is_unknown_codon('UAG'), 0;
ok $myCodonTable->translate_strict('ATG'), 'M';
#
# adding a custom codon table
#
my @custom_table =
    ( 'test1',
      'FFLLSSSSYY**CC*WLLLL**PPHHQQR*RRIIIMT*TT*NKKSSRRV*VVAA*ADDEE*GGG'
    );
ok my $custct = $myCodonTable->add_table(@custom_table);
ok $custct, 24;
ok $myCodonTable->translate('atgaaraayacmacracwacka'), 'MKNTTTT';
ok $myCodonTable->id($custct);
ok $myCodonTable->translate('atgaaraayacmacracwacka'), 'MKXXTTT';
# test doing this via Bio::PrimarySeq object
use Bio::PrimarySeq;
ok $seq = Bio::PrimarySeq->new(-seq=>'atgaaraayacmacracwacka', -alphabet=>'dna');
ok $seq->translate()->seq, 'MKNTTTT';
ok $seq->translate(undef, undef, undef, undef, undef, undef, $myCodonTable)->seq, 'MKXXTTT';
# test gapped translated
ok $seq = Bio::PrimarySeq->new(-seq      => 'atg---aar------aay',
                                           -alphabet => 'dna');
ok $seq->translate->seq, 'M-K--N';
ok $seq = Bio::PrimarySeq->new(-seq=>'ASDFGHKL');
ok $myCodonTable->reverse_translate_all($seq), 'GCBWSNGAYTTYGGVCAYAARYTN';
ok $seq = Bio::PrimarySeq->new(-seq=>'ASXFHKL');
ok $myCodonTable->reverse_translate_all($seq), 'GCBWSNNNNTTYCAYAARYTN';