I don't know what you've tried, but those errors are from the undeclared variables cited. If you have just copied the erroneous code, you must have missed the earlier part where they were declared.
Update: Try replacing all instances of $self with $calc. Then change this line:
my $encp =$self->encp_r($seq,[$minTotal,[$A,$T,$C,$G]]);
my $encp =$calc->encp_r($seq);
All I did was remove the optional args from the encp_r method.
Update 2: I just saw this reference (http://biorxiv.org/content/early/2015/11/03/019265) on today's Perl Weekly which looks like something of interest to Perl Bio folks like supriyoch_2008.