Hey Guys. This is so frustrating. I added some code as suggested: 
push( @next_cell_arr, $protein_matrix[$row][$col+1] );# - note: 'right
+' cell is first element of array
        push( @next_cell_arr, $protein_matrix[$row+1][$col+1] );# - no
+te: 'diagonal' cell is second element of array
        push( @next_cell_arr, $protein_matrix[$row+1][$col] );# - note
+: 'bottom' cell is third element of array
    
        # - debug
        $arr_len = scalar @next_cell_arr;
        for( $var = 0; $var < $arr_len; $var++ ){
            print $next_cell_arr[$var];
            print "\n";
        }
        print "\n\n";
        #exit;
        # - debug
        
        # - if all values are equal, then the sequence gets a match of
+ suffers a mismatch (diagonal move), and not a gap penalty.  This als
+o saves me from having to compute the max of the three cells
        my $val1 = $next_cell_arr[0] || die "val1 is undefined!!\n"; 
        my $val2 = $next_cell_arr[1] || die "val2 is undefined!!\n";
        my $val3 = $next_cell_arr[2] || die "val3 is undefined!!\n";

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When I run my code, $val1 is indeed not being defined, but the debug loop, right above, $next_cell_arr[0] is displaying the correct value. This makes absolutely no sense to me. Something so incredibly simple is not working here. EDIT: By the way, I always use the -w flag, but adding 'use warnings' might be easier

In reply to Re: Understanding variable scope in perl by BioBoy
in thread Understanding variable scope in perl by BioBoy

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