When you want to extend an existing class, you have two options: inheritance and aggregation. If you go the inheritance route your new method would look something like this:

use base qw(Net::FTP);   #5.8

#or for 5.10 and up
#use parent qw(Net::FTP);

sub new {
  my ($pkg, $server, $user, $timeout, @args) = @_;

  # some special class specific stuff

  # ... is params for super class structure
  my $self = $pkg->SUPER::new(...); 
  $self->server($server);
  $self->user($user);
  $self->timeout($timeout);
  $self->initialize();

  # some special class specific stuff

  # if SUPER::new is well behaved, $self will be a member
  # of the $pkg class even though it was built by the
  # the super class.
  return $self;
}
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If you go the aggregation route you might do something like this:

sub new {
   my ($pkg, $server, $user, $timeout, @args) = @_;

  # some special class specific stuff

  # ... is params for super class structure
  my $ftp = Net::FTP->new(...);
  $ftp->server($server);
  $ftp->user($user);
  $ftp->timeout($timeout);
  $ftp->initialize();

  my $self = { ftpHandle => $ftp };
  return bless($self, $pkg);
}
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If you want your own class to be implemented using a hash, you would go with the aggregation approach since Net::FTP doesn't return a hash. If you want to return the same kind of implementation as Net::FTP, then you would follow the inheritance pattern. You might find the sections on inheritance and aggregation in perltoot worth a read.

Best, beth