Package 1:

package Bio::DB::Das::Chado;
use strict;
use Bio::Root::Root;
use vars qw(@ISA);
@ISA     = qw(Bio::Root::Root);

sub new {
  my $class = shift;
  my $self  = $class->SUPER::new(@_);

# do some work here to extract a DBI $hashref

  my $cvterm_id;  # this scalar is going to be a hashref
  while (my $hashref = $sth->fetchrow_hashref) {
    $$cvterm_id{$$hashref{termname}} = $$hashref{cvterm_id};
  }

  return bless {dbh  => $dbh,
                cvterm_id => $cvterm_id}, ref $self ||$self;
}

sub segment {
  my $self = shift;
  my ($name,$start,$end,$class,$version) =
      $self->_rearrange([qw(NAME
                            START
                            END
                            CLASS
                            VERSION)],@_);
  # _rearrange is in Bio::Root::Root; I'm allowed to use it
  # lets the Segment class handle all the lifting.
  return $self->Bio::DB::Das::Chado::Segment->new($name,$self,$start,$
+end);
}

1;
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package Bio::DB::Das::Chado::Segment;
use strict;
use Bio::Root::Root;
use vars '@ISA';
@ISA = qw(Bio::Root::Root);

sub new {
  my $self  = shift;

  my ($name,$dbadaptor,$start,$end) = @_;
  #$dbadaptor is 'Bio::DB::Das::Chado'
  # now do all kinds of work validating and obtaining info

  my $cvterm_id = $dbadaptor->{cvterm_id};
  # so $cvterm_id should be a reference to the same 
  # hash referenced in the first package, right?

  return bless {dbadaptor     => $dbadaptor,
                start         => $start,
                end           => $end,
                length        => $length,
                srcfeature_id => $srcfeature_id,
                cvterm_id     => $cvterm_id,
                name          => $name }, ref $self ||$self;
}

sub features {
  my $self = shift;

# do lots more stuff, mostly to build a sql query

  my %termhash = %{$self->{cvterm_id}};
  # shouldn't this be a reference to the hash ref in this
  #package's constructor, that in turn is a ref to the 
  # hash ref in the first package?

  my @keys = grep(/\sgene/i , keys %termhash );
  # this fails because %termhash isn't a hash.

  return;
}
1;
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