foreach $key ( $ac->get_all_annotation_keys() ) {

[download]
if $ac is not a valid object of the right type, that code would throw an error: note that you are not indexing a hash here, you're calling an object method. see perltoot for more information on the perl OO system.

If you want to know what data is stored in a perl variable or object, an easy way to see that is to use the standard Data::Dumper module: 

use Data::Dumper;

# ...

print '$ac: ',Dumper($ac);
foreach $key ( $ac->get_all_annotation_keys() ) 
   print '$key: ',Dumper($key);
}

[download]

That should probably give you some indication of what these objects contain. Note that object can store data in such a way that Data::Dumper doesn't know how to get at it, but it's a start anyway.

"What should it profit a man, if he should win a flame war, yet lose his cool?"

In reply to Re^3: Bioperl + perl modules by Joost
in thread Bioperl + perl modules by Anonymous Monk

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.