Matrix Declaration / Data Structure Syntax Question

oxirane has asked for the wisdom of the Perl Monks concerning the following question:

I was exploring some of the dynamic alignment programs for protein and DNA used by biologists and came across a data construct that I didn't understand...could someone explain the square bracket/square bracket/curly bracket reference construct and comment on it being a good/bad way to go about dynamic matrix declaration

@matrix;
$matrix[0][0]{score}   = 0;
$matrix[0][0]{pointer} = "none";
for($j = 1; $j <= length($seq1); $j++) {
     $matrix[0][$j]{score}   = 0;
     $matrix[0][$j]{pointer} = "none";
}
for ($i = 1; $i <= length($seq2); $i++) {
     $matrix[$i][0]{score}   = 0;
     $matrix[$i][0]{pointer} = "none";
[download]

Comment on Matrix Declaration / Data Structure Syntax Question Download Code

Replies are listed 'Best First'.
Re: Matrix Declaration / Data Structure Syntax Question by kcott (Archbishop) on Mar 10, 2013 at 00:49 UTC
G'day oxirane, Welcome to the monastery. When presented with a complex data structure, you may find Data::Dumper to be a useful tool. Here's a simplified version of your matrix: `$ perl -Mstrict -Mwarnings -e ' use Data::Dumper; my @matrix; for my $i (0 .. 1) { for my $j (0 .. 1) { $matrix[$i][$j]{row} = $i; $matrix[$i][$j]{col} = $j; } } print Dumper \@matrix; ' $VAR1 = [ [ { 'col' => 0, 'row' => 0 }, { 'col' => 1, 'row' => 0 } ], [ { 'col' => 0, 'row' => 1 }, { 'col' => 1, 'row' => 1 } ] ];` [download] -- Ken	[reply] [d/l]
Re: Matrix Declaration / Data Structure Syntax Question by bioinformatics (Friar) on Mar 09, 2013 at 17:32 UTC
It's an array of arrays (two dimensional array) with `matrix[i][j]` pointing to a hash with defined keys (score and pointer). Arrays of arrays (denoted AoA) and hashes of hashes (HoH) are pretty useful and I use them constantly. I'd say it was a good way to keep everything in one data structure while maintaining speed and readability of the code. Bioinformatics	[reply] [d/l]
Re: Matrix Declaration / Data Structure Syntax Question by AnomalousMonk (Archbishop) on Mar 09, 2013 at 18:51 UTC
See also Perl Data Structures Cookbook (`perldoc perldsc`) and Manipulating Arrays of Arrays in Perl (`perldoc perllol`).	[reply] [d/l] [select]
Re: Matrix Declaration / Data Structure Syntax Question by CountZero (Bishop) on Mar 10, 2013 at 12:11 UTC
It is neither good nor bad. It is simply the way Perl uses multi-dimensional variables. CountZero A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James My blog: Imperial Deltronics	[reply]
Re: Matrix Declaration / Data Structure Syntax Question by Anonymous Monk on Mar 09, 2013 at 15:54 UTC
Do you know the types of variables in perl? In other words, have you read perlintro/perldata/ Modern Perl ch 3? { 'hashes', 'are', 'curly', 'ones' } [ 'arrays', 'are', 'square' ] ( 'lists are round' )	[reply]