Apologies for the confusion, and thanks for the suggestions. I'll attempt to clarify.

>I'm not sure I understand exactly what you mean
>by "convert subroutines into modules".

>the variable @nreg which has a scope wider
>than just the subroutine (e.g., a global variable).

Originally, I had two subroutines, "addregion" and "isitin". The former is as I posted, and the latter looked like this: 
sub isitin 
{
    my ($hit,$what) = @_;
    my $within = 0;
    my $k;
    for ($k=0; $k<@nreg; $k++)
    {
        if ($what >= $nreg[$k][0] and $what <= $nreg[$k][1])
        {
            $within = 1;
        }
    }
    return $within;
}

[download]
...so that I could get a "1" back if a given base was within any of the regions defined with nreg. As this was all within one script, it was easy to use @nreg globally and re-set it at the top of a "while while (my $seq = $filein->next_seq()) " loop.
However, I'd like to re-use the code by creating an object for each sequence, that would contain the sequence id and the @nreg array. The hard bit is working out how to set up that object - hence all manner of bless errors as I attempt to comprehend the complexities of OO (not easy for an old shell script writer ;-).

BTW the code above is lifted directly from the original subroutines - hopefully I can keep the changes minimal and add some extra methods. It came about to solve this problem.

Essentially, I looped through each sequence, called "addregion" on each feature, then "isitin" on related features later in the loop. @nreg was re-set for the next genome. I can't find any code in the bioperl that I'm using that does this job, hence the attempt to write my own object for it.

In reply to Re: Re: Array of arrays used within object by knirirr
in thread Array of arrays used within object by knirirr

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.