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

Instead of dereferencing your two-dimensional arrays like this:

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

do this:

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

Also, you're doing a lot of if/then/else statements to match against particular subsequences: this could be better written as given statements (perl5.10's equivalent of C's switch). Read about it at perldoc perlsyn:

given ($matrix->[$row][$column])
{
    when ($seq1_gap)       { $path_matrix->[$row][$column] = -1; }
    when ($match_mismatch) { $path_matrix->[$row][$column] = 0; }
    when ($seq2_gap)       { $path_matrix->[$row][$column] = 1; }
}