No, really, this is not a database design issue. It's about how to design my objects to model the relationships: 
One-to-many:
taxon ---> node
      ---> node
      ---> sequence
      ---> sequence

One-to-one:
node ---> taxon

One-to-one:
sequence ---> taxon

[download]
Such that I can do: 
my @nodes = $taxon->get_nodes;
my @sequences = $taxon->get_sequences;
my $taxon = $node->get_taxon;
$taxon = $sequence->get_taxon;

[download]
...with an underlying architecture where the relationships automatically are bi-directional in an elegant way. For example: 
$node->set_taxon( $taxon );

[download]
...might mean that the $node now holds a reference to $taxon, but the $taxon now also has to hold a reference to $node. So should I then do: 
sub set_taxon {
    my ( $node, $taxon ) = @_;
    $node->{'_taxon'} = $taxon;
    # check if taxon already knows about me
    for my $known ( $taxon->get_nodes ) {
        return $node if $known == $node;
    }
    $taxon->add_node( $node );
    return $node;
}

[download]
...but then the $taxon->add_node( $node ) sub would likewise need to check if $node already knows about $taxon, and if not make the link in the other direction - without recursing add infinitum. All in all, that's not elegant.

So my question was: should the link making be managed by a third object (some sort of manager), to which the set_whatever, add_whatever, get_whatever method calls are re-routed. Or should I do something else entirely?

My question is not addressed by database designs, raw sql code, or object-relational mappers. Thank you for your input, though. I'm looking for suggestions for design patterns to deal with bi-directional relationships between objects. I understand that the suggestion for MVC has something to do with the issue (but the term MVC is so polluted at this point it's not unambiguously obvious how to apply it - perhaps the 'C' is the link manager?), so greatshots I think got what I was talking about, and so did graff.

I apologize to all others if I've phrased things so poorly that I made you write about databases.

In reply to Re^2: One to many, many to one relationships by rvosa
in thread One to many, many to one relationships by rvosa

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.