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package AlignDB::Codon;
use Moose;
use Carp;

use AlignDB::IntSpan;
use List::MoreUtils::PP;
use YAML::Syck;

our $VERSION = '1.1.1';

# codon tables
has 'table_id' => ( is => 'ro', isa => 'Int', default => sub {1}, );
has 'table_name'    => ( is => 'ro', isa => 'Str', );
has 'table_content' => ( is => 'ro', isa => 'Str', );
has 'table_starts'  => ( is => 'ro', isa => 'Str', );

# codons
has 'codons'    => ( is => 'ro', isa => 'ArrayRef', );
has 'codon_idx' => ( is => 'ro', isa => 'HashRef', );
has 'codon2aa'  => ( is => 'ro', isa => 'HashRef', );

# lookup hash for the number of synonymous changes per codon
has 'syn_sites' => ( is => 'ro', isa => 'HashRef', );

# lookup hash of all pairwise combinations of codons differing by 1
#    1 = synonymous, 0 = non-synonymous, -1 = stop
has 'syn_changes' => ( is => 'ro', isa => 'HashRef', );

# One <=> Three
has 'one2three' => ( is => 'ro', isa => 'HashRef', );
has 'three2one' => ( is => 'ro', isa => 'HashRef', );

sub BUILD {
    my $self = shift;

    $self->_make_codons;
    $self->change_codon_table( $self->{table_id} );
    $self->_load_aa_code;

    return;
}

sub _make_codons {
    my $self = shift;

    # makes all codon combinations
    my @nucs = qw(T C A G);
    my @codons;
    for my $i (@nucs) {
        for my $j (@nucs) {
            for my $k (@nucs) {
                push @codons, "$i$j$k";
            }
        }
    }
    $self->{codons} = \@codons;

    my %codon_idx;
    for my $i ( 0 .. $#codons ) {
        $codon_idx{ $codons[$i] } = $i;
    }
    $self->{codon_idx} = \%codon_idx;

    return;
}

sub change_codon_table {
    my $self = shift;
    my $id   = shift;

    my @NAMES = (    #id
        'Strict',                      # 0, special option for ATG-only start
        'Standard',                    # 1
        'Vertebrate Mitochondrial',    # 2
        'Yeast Mitochondrial',         # 3
        'Mold, Protozoan, and Coelenterate Mitochondrial and Mycoplasma/Spiroplasma',    # 4
        'Invertebrate Mitochondrial',                                                    # 5
        'Ciliate, Dasycladacean and Hexamita Nuclear',                                   # 6
        '', '',
        'Echinoderm and Flatworm Mitochondrial',                                         # 9
        'Euplotid Nuclear',                                                              # 10
        'Bacterial, Archaeal and Plant Plastid',                                         # 11
        'Alternative Yeast Nuclear',                                                     # 12
        'Ascidian Mitochondrial',                                                        # 13
        'Alternative Flatworm Mitochondrial',                                            # 14
        'Blepharisma Nuclear',                                                           # 15
        'Chlorophycean Mitochondrial',                                                   # 16
        '', '', '', '',
        'Trematode Mitochondrial',                                                       # 21
        'Scenedesmus obliquus Mitochondrial',                                            # 22
        'Thraustochytrium Mitochondrial',                                                # 23