-sam

Perhaps it hasn't propagated over to all mirrors (although I didn't think the web interface is mirrored???).

Is this URL not working for you?

http://search.cpan.org/~rvosa/Bio-Phylo-0.05/

That would be odd... it works for me...

Update: by the way, thanks for writing and making available your e-book on creating CPAN modules. Very useful!

Yup, when I hit that URL I see a "Not Found" screen. Maybe there's some dynamic load-balancing happening behind the scenes that's sending us to different sites.

And thanks!

-sam

I am working on big object trees (see my scratch pad for an overview if you're curious) and thought I'd comment on a problem you seem to have with memory leaks (according to your CPAN docs).

You consider inside out objects? Those seem cool, but ... new.

I don't store references in objects -- the objects store short Id strings. A central "objOwner" object hands out the objects from the Ids. It looks like this:

  my($superObj) = $o->GetObject($o->GetSupId());
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I did it like that because I thought it would be easier to test, less error prone and would make it easier to save/restore parts of the object tree (also easier to stub for rpc).

That it helps the GC algorithm I put under "easier to test".

This should be clear? Ask otherwise. (I hope to upload to CPAN in a few weeks. Writes examples and UI now... :-( )

Hey, thanks!

I've been experimenting with something that might be what you're saying: the node class would have a number of arrays (e.g. @parent, @next_sister, @previous_sister, @first_daughter, @last_daughter). The objects are blessed references to scalars holding integers.

Getters and setters would dereference and assign the respective arrays based on the object's integer value:

sub set_parent {
    my ( $self, $parent ) = ( $_[0], $_[1] );
    $parent[$$self] = $parent;
    return $self;
}

sub get_parent {
    my $self = $_[0];    
    return $parent[$$self];
}
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When you construct the node, a new, unique integer is generated by the InsideOutFactory, and when the node's DESTROY is called, the integer value is returned back to the InsideOutFactory, to push it into a pool for reuse. The instance data consists of elements of the class arrays. Kinda like this: inside-out objects using arrays?

(Mind you, the memory leak problem so far hasn't been noticeable in day-to-day usage, but it does show up when I check with Devel::Cycle.)

Sounds like the biggest diff is that I use 'son' or 'sub' instead of 'daughter' -- shorter. :-)

I have a method that gives a short unique ID-string. Easier to read (a number might be confused with other data). You probably get a little more speed of using arrays and ints.

I only store sup and an array with subs in obj and use methods to find brothers. Fewer possible bugs to keep obj updated when deleting/adding/serializing/etc.

I have Links between objects in different parts of the tree (you don't need that, I'd guess). Would have been better to make objects out of Links but I have a small subapi to e.g. add link, del link and find links to/from obj.

In total, this was little code and never gave me any problem. If I should redo it I'd probably let the IDs be invisible in the api, just to be cleaner.