Whilst attempting to convert some subroutines into module, I've run into difficulty with one particular feature. @nreg in the code below is used to store the start and end locations of features in a nucleotide sequence, so that another method may be used to determine whether a given base is within any of the defined regions. 
sub addregion 
{
    my ($start,$end) = @_;
    if ($start > $end)
    {
        ($start,$end) = ($end,$start);
    }
    my $done = 0;
    my $k;
    my $tempcoding = 0;

    for ($k=0;$k<@nreg;$k++)
    {
        # calculate sum of bases
        $tempcoding += $nreg[$k][1] - $nreg[$k][0] + 1;

        # new region starts after old region ends
        next if ($nreg[$k][1] < $start);

        # new region ends before old region starts
        if ($end < $nreg[$k][0])
        {
            splice(@nreg,$k,0,[$start,$end]);
            $done = 1;
            last;
        }

        # regions overlap
        $nreg[$k][0] = $start < $nreg[$k][0] ? $start : $nreg[$k][0];
        $nreg[$k][1] = $end > $nreg[$k][1] ? $end : $nreg[$k][1];
        $done = 1;

        # Combine two regions if the new section has brough about an o
+verlap
        while ($k < $#nreg and $nreg[$k][1] > $nreg[$k+1][0])
        {
            $nreg[$k][1] = $nreg[$k+1][1];
            splice(@nreg,$k+1,1);
        }
        last;
    }
    unless ($done)
    {
        push @nreg,[$start,$end];
    }
}

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Several (hundreds, even) sequences may be read, and it's apparently necessary to define a new object relating @nreg to the name of each sequence, as I find that the values for all sequences are pushed into the same array. Can anyone suggest a suitable way to set up a "new" method to relate a different @nreg to a particular sequence name, please? I've tried various permutations, which either use the same array every time or refuse to bless it (e.g. "Attempt to bless into a reference at..." messages appear). Thanks for any suggestions!

In reply to Array of arrays used within object by knirirr

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