How do I change this to “idiomatic” Perl?

Question

I am beginning to delve deeper into Perl, but am having trouble writing \"Perl-ly\" code instead of writing C in Perl. How can I change the following code to use more Perl idiom

Answer 1

I have some other comments as well, but here is the first observation:

my $num_of_rows = length($self->{seq1}) + 1;
my $num_of_columns = length($self->{seq2}) + 1;

So $self->{seq1} and $self->{seq2} are strings and you keep accessing individual elements using substr. I would prefer to store them as arrays of characters:

$self->{seq1} = [ split //, $seq1 ];

Here is how I would have written it:

sub create_matrix {
    my $self = shift;

    my $matrix      = $self->{score_matrix};
    my $path_matrix = $self->{path_matrix};

    my $rows = @{ $self->{seq1} };
    my $cols = @{ $self->{seq2} };

    for my $row (0 .. $rows) {
        $matrix->[$row]->[0] =  $row * $self->{gap_cost};
        $path_matrix->[$row]->[0] = 1;
    }

    my $gap_cost = $self->{gap_cost};

    $matrix->[0] = [ map { $_ * $gap_cost } 0 .. $cols ];
    $path_matrix->[0] = [ (-1) x ($cols + 1) ];

    $path_matrix->[0]->[0] = 2;

    for my $row (1 .. $rows) {
        for my $col (1 .. $cols) {
            my $gap1 = $matrix->[$row - 1]->[$col] + $gap_cost;
            my $gap2 = $matrix->[$row]->[$col - 1] + $gap_cost;
            my $match_mismatch =
                $matrix->[$row - 1]->[$col - 1] +
                $self->get_match_score(
                    $self->{seq1}->[$row - 1],
                    $self->{seq2}->[$col - 1]
                );

            my $max = $matrix->[$row]->[$col] =
                max($gap1, $gap2, $match_mismatch);

            $path_matrix->[$row]->[$col] = $max == $gap1
                    ? -1
                    : $max == $gap2
                    ? 1
                    : 0;
            }
        }
    }